Powered by Deep Web Technologies
Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


1

U-183: ISC BIND DNS Resource Records Handling Vulnerability  

Broader source: Energy.gov [DOE]

This problem was uncovered while testing with experimental DNS record types. It is possible to add records to BIND with null (zero length) rdata fields.

2

DsrR, a Novel IscA-like Protein Lacking Iron- and Fe-S-Binding...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

scaffolds. However, DsrR does not retain the Fe-S- or the iron-binding ability of these proteins, which is due to the lack of all three highly conserved cysteine residues of...

3

IMPERIAL INNOVATION STUDIES CENTRE (ISC) The Innovation Studies Centre (ISC) at Imperial College London is undertaking a  

E-Print Network [OSTI]

impact of innovative new approaches to this for the NHS and social care system. Director: Mr Oliver Wells#12;IMPERIAL INNOVATION STUDIES CENTRE (ISC) The Innovation Studies Centre (ISC) at Imperial of innovation processes and how scientific and engineering potential can be unlocked for future prosperity

Oakley, Jeremy

4

Interim storage cask (ISC), a concrete and steel dry storage cask  

SciTech Connect (OSTI)

General Atomics (GA) has designed and is currently fabricating the Interim Storage Cask (ISC) for Westinghouse Hanford Company (WHC). The ISC is a dry storage cask that will safely store a Core Component Container (CCC) with Fast Flux Test Facility (FFTF) spent fuel assemblies or fuel pin containers for a period of up to 50 years at the US Department of Energy (DOE) Hanford site. The cask may also be used to transfer the fuel to different areas within the Hanford site. The ISC is designed to stringent criteria from both 10CFR71 and 10CFR72 for safe storage and on-site transportation of FFTF spent fuel and fuel pin containers. The cask design uses a combination of steel and concrete materials to achieve a cost-effective means of storing spent fuel. The casks will be extensively tested before use to verify that the design and construction meet the design requirements.

Grenier, R.M.; Koploy, M.A. [General Atomics, San Diego, CA (United States)

1995-12-31T23:59:59.000Z

5

Integrated Support Center (ISC) Homepage | U.S. DOE Office of Science (SC)  

Broader source: All U.S. Department of Energy (DOE) Office Webpages

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May Jun Jul(Summary)morphinanInformation InInformation InExplosion Monitoring: InnovationISC Home Integrated Support Center (ISC)

6

WORKING DOCUMENT for ISC -DRAFT -October 11th "Nanosciences, Nanotechnologies, Materials and new  

E-Print Network [OSTI]

WORKING DOCUMENT for ISC - DRAFT - October 11th 2006 Theme 4 "Nanosciences, Nanotechnologies ------------------------------------------------------------------------------- Table of contents I Context 1 II Content of Calls 5 Nanosciences and Nanotechnologies 7 Materials 18 New "Nanosciences, Nanotechnologies, Materials and new Production Technologies ­ NMP" is to fund research

Meju, Max

7

LIST OF SUBJECT AREA -CODES ISCED -(01.0 Agricultural Sciences) 62 Agriculture, forestry and fishery  

E-Print Network [OSTI]

LIST OF SUBJECT AREA - CODES ISCED - (01.0 Agricultural Sciences) 62 Agriculture, forestry and fishery (01.1 Agriculture) 620 Agriculture, forestry and fishery (broad programmes) (01.2 Agricultural Economics) 629 Agriculture, forestry and fishery (others) (01.3 Food Science and Technology) 541 Food

8

T-662: ISC BIND Packet Processing Flaw Lets Remote Users Deny Service |  

Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankCombustion |Energy Usage »of Energy StrainClient update resolve multiple | Department| Department

9

V-172: ISC BIND RUNTIME_CHECK Error Lets Remote Users Deny Service Against  

Broader source: Energy.gov (indexed) [DOE]

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May Jun Jul(Summary) "ofEarly Career Scientists' Research Petroleum ReserveDepartmentScripting Attacks

10

U-039: ISC Update: BIND 9 Resolver crashes after logging an error in  

Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankCombustion |Energy Usage »of EnergyTheTwo New Energy Storage6 (07/03) OMB Control2:Department

11

ISC Conventional Reading Rooms | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear SecurityTensile Strain Switched5 Industrial CarbonArticlesHuman Resources Human Resources and Administration (HRA)ISC

12

DsrR, a Novel IscA-like Protein Lacking Iron- and Fe-S-Binding Functions,  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation Proposed Newcatalyst phasesDataTranslocationDiurnalCommittee Draftfor $1.14 PerInvolved in the

13

REVIEW OF FAST FLUX TEST FACILITY (FFTF) FUEL EXPERIMENTS FOR STORAGE IN INTERIM STORAGE CASKS (ISC)  

SciTech Connect (OSTI)

Appendix H, Section H.3.3.10.11 of the Final Safety Analysis Report (FSAR), provides the limits to be observed for fueled components authorized for storage in the Fast Flux Test Facility (FFTF) spent fuel storage system. Currently, the authorization basis allows standard driver fuel assemblies (DFA), as described in the FSAR Chapter 17, Section 17.5.3.1, to be stored provided decay power per assembly is {le} 250 watts, post-irradiation time is four years minimum, average assembly burn-up is 150,000 MWD/MTHM maximum and the pre-irradiation enrichment is 29.3% maximum (per H.3.3.10.11). In addition, driver evaluation (DE), core characterizer assemblies (CCA), and run-to-cladding-breach (RTCB) assemblies are included based on their similarities to a standard DFA. Ident-69 pin containers with fuel pins from these DFAs can also be stored. Section H.3.3.10.11 states that fuel types outside the specification criteria above will be addressed on a case-by-case basis. There are many different types of fuel and blanket experiments that were irradiated in the FFTF which now require offload to the spent fuel storage system. Two reviews were completed for a portion of these special type fuel components to determine if placement into the Core Component Container (CCC)/Interim Storage Cask (ISC) would require any special considerations or changes to the authorization basis. Project mission priorities coupled with availability of resources and analysts prevented these evaluations from being completed as a single effort. Areas of review have included radiological accident release consequences, radiological shielding adequacy, criticality safety, thermal limits, confinement, and stress. The results of these reviews are available in WHC-SD-FF-RPT-005, Rev. 0 and 1, ''Review of FFTF Fuel Experiments for Storage at ISA'', (Reference I), which subsequently allowed a large portion of these components to be included in the authorization basis (Table H.3.3-21). The report also identified additional components and actions in Section 3.0 and Table 3 that require further evaluation. The purpose of this report is to evaluate another portion of the remaining inventory (i.e., delayed neutron signal fuel, blanket assemblies, highly enriched assemblies, newly loaded Ident-69 pin containers, and returned fuel) to ensure it can be safely off loaded to the FFTF spent fuel storage system.

CHASTAIN, S.A.

2005-10-24T23:59:59.000Z

14

Towards an InTerdIscIplInary approach To nexT-GeneraTIon BIofuels EnvironmEntal, tEchno-Economic, and GovErnancE  

E-Print Network [OSTI]

Towards an InTerdIscIplInary approach To nexT-GeneraTIon BIofuels EnvironmEntal, t. 2010. The Ecological Impact of Biofuels. Pages 351-377 in D. J. Futuyma, H. B. Shafer, and D. Huffer, S., Roche, C.M., Blanch, H.W., and Clark, D.S. (2012). Escherichia coli for biofuel production

Iglesia, Enrique

15

ISC2005v2.ppt  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation ProposedUsingFun withconfinementEtching. | EMSLthe U.S.;2cSupercomputing: The Top Three

16

Melanin-binding radiopharmaceuticals  

SciTech Connect (OSTI)

The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed. (PSB)

Packer, S; Fairchild, R G; Watts, K P; Greenberg, D; Hannon, S J

1980-01-01T23:59:59.000Z

17

Cellulose binding domain proteins  

DOE Patents [OSTI]

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc (Davis, CA); Doi, Roy (Davis, CA)

1998-01-01T23:59:59.000Z

18

Cellulose binding domain proteins  

DOE Patents [OSTI]

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

Shoseyov, O.; Shpiegl, I.; Goldstein, M.; Doi, R.

1998-11-17T23:59:59.000Z

19

Quarkonium Binding and Entropic Force  

E-Print Network [OSTI]

A Q-Qbar bound state represents a balance between repulsive kinetic and attractive potential energy. In a hot quark-gluon plasma, the interaction potential experiences medium effects. Color screening modifies the attractive binding force between the quarks, while the increase of entropy with Q-Qbar separation gives rise to a growing repulsion. We study the role of these phenomena for in-medium Q-Qbar binding and dissociation. It is found that the relevant potential for Q-Qbar binding is the free energy F; with increasing Q-Qbar separation, further binding through the internal energy U is compensated by repulsive entropic effects.

Satz, Helmut

2015-01-01T23:59:59.000Z

20

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity  

E-Print Network [OSTI]

of Electrical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA 6Molecular nature of gene regulation. Unlike individual transcription factors, complexes of interacting factors bind cooperatively to genomic regions that contain a favorable configuration of binding sites (Johnson, 1995

Rohs, Remo

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

Synthetic heparin-binding growth factor analogs  

DOE Patents [OSTI]

The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain that binds a heparin-binding growth factor receptor, covalently bound to a hydrophobic linker, which is in turn covalently bound to a non-signaling peptide that includes a heparin-binding domain. The synthetic heparin-binding growth factor analogs are useful as soluble biologics or as surface coatings for medical devices.

Pena, Louis A.; Zamora, Paul; Lin, Xinhua; Glass, John D.

2007-01-23T23:59:59.000Z

22

Skyrmions with low binding energies  

E-Print Network [OSTI]

Nuclear binding energies are investigated in two variants of the Skyrme model: the first replaces the usual Skyrme term with a term that is sixth order in derivatives, and the second includes a potential that is quartic in the pion fields. Solitons in the first model are shown to deviate significantly from ans\\"atze previously assumed in the literature. The binding energies obtained in both models are lower than those obtained from the standard Skyrme model, and those obtained in the second model are close to the experimental values.

Gillard, Mike; Speight, Martin

2015-01-01T23:59:59.000Z

23

Cellulose binding domain fusion proteins  

DOE Patents [OSTI]

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

1998-01-01T23:59:59.000Z

24

Cellulose binding domain fusion proteins  

DOE Patents [OSTI]

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

Shoseyov, O.; Yosef, K.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

1998-02-17T23:59:59.000Z

25

Mutant ATP-binding RNA Aptamers Reveal the Structural Basis for Ligand Binding  

E-Print Network [OSTI]

Mutant ATP-binding RNA Aptamers Reveal the Structural Basis for Ligand Binding Thorsten Dieckmann1, Massachusetts General Hospital, Boston, MA 02114 USA The solution structure of the ATP-binding RNA aptamer has. The binding properties of ATP binder mutants and modi®ed ligand molecules are explored using NMR spectroscopy

Heller, Eric

26

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human  

E-Print Network [OSTI]

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across occupied by the insulator binding protein CTCF across the human genome. These nucleosomes are highly of CTCF function. Citation: Fu Y, Sinha M, Peterson CL, Weng Z (2008) The Insulator Binding Protein CTCF

Weng, Zhiping

27

3710 McClintock Avenue Induced Seismicity Consortium (ISC)  

E-Print Network [OSTI]

injection, fluid production and disposal wells, enhanced geothermal resource development, and EOR/CO2

Southern California, University of

28

Induced Seismicity Consortium (ISC) Fred Aminzadeh, PI, Petroleum Engineering Program  

E-Print Network [OSTI]

fracturing operations waste water injection and disposal wells, geothermal resource development, and EOR/CO2

Southern California, University of

29

ISC-Reducing Congestion through Smart Parking Management | Open Energy  

Open Energy Info (EERE)

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Office of InspectorConcentrating Solar Power BasicsGermany:Information IDS Climate ChangeInformation

30

Institute for Sustainable Communities (ISC) | Open Energy Information  

Open Energy Info (EERE)

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home5b9fcbce19 No revision hasInformation Earth's Heat JumpInc Place: Eden Prairie,InfieldInstalled Geothermal Capacity Jump

31

Synthetic heparin-binding factor analogs  

DOE Patents [OSTI]

The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain, and preferably two peptide chains branched from a dipeptide branch moiety composed of two trifunctional amino acid residues, which peptide chain or chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a linker, which may be a hydrophobic linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

Pena, Louis A. (Poquott, NY); Zamora, Paul O. (Gaithersburg, MD); Lin, Xinhua (Plainview, NY); Glass, John D. (Shoreham, NY)

2010-04-20T23:59:59.000Z

32

Evolutionary relationships of ATP-Binding Cassette (ABC) uptake porters  

E-Print Network [OSTI]

Evolutionary relationships of ATP-Binding Cassette (ABC)MH Jr: Membrane porters of ATP-binding cassette transportand exporters in the evolution of ATP-binding cassette (ABC)

Zheng, Wei Hao; Vstermark, ke; Shlykov, Maksim A; Reddy, Vamsee; Sun, Eric I; Saier, Milton H

2013-01-01T23:59:59.000Z

33

Atomic structure of nitrate-binding protein crucial for photosynthetic...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

structure of nitrate-binding protein crucial for photosynthetic productivity. Atomic structure of nitrate-binding protein crucial for photosynthetic productivity. Abstract:...

34

affinity binding studies: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

for Ligand Binding Affinity Prediction Chemistry Websites Summary: of the binding free energy between a ligand and a protein is an important component in the virtual...

35

Crystallographic controls on uranyl binding at the quartz/water...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

controls on uranyl binding at the quartzwater interface. Abstract: Molecular dynamics methods were used to simulate UO2(OH)20 binding to pairs of oxo sites on three...

36

Sequestering Uranium from Seawater: Binding Strength and Modes...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl Complexes with Glutarimidedioxime Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl...

37

Single-Molecule Dynamics Reveals Cooperative Binding-Folding...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition . Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition . Abstract: The...

38

Hardware device binding and mutual authentication  

DOE Patents [OSTI]

Detection and deterrence of device tampering and subversion by substitution may be achieved by including a cryptographic unit within a computing device for binding multiple hardware devices and mutually authenticating the devices. The cryptographic unit includes a physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generates a binding PUF value. The cryptographic unit uses the binding PUF value during an enrollment phase and subsequent authentication phases. During a subsequent authentication phase, the cryptographic unit uses the binding PUF values of the multiple hardware devices to generate a challenge to send to the other device, and to verify a challenge received from the other device to mutually authenticate the hardware devices.

Hamlet, Jason R; Pierson, Lyndon G

2014-03-04T23:59:59.000Z

39

RNA binding protein and binding site useful for expression of recombinant molecules  

DOE Patents [OSTI]

The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

Mayfield, Stephen P.

2006-10-17T23:59:59.000Z

40

RNA binding protein and binding site useful for expression of recombinant molecules  

DOE Patents [OSTI]

The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

Mayfield, Stephen (Cardiff, CA)

2000-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

Polypyrimidine Track-binding Protein Binding Downstream of Caspase-2 Alternative Exon 9 Represses Its Inclusion*  

E-Print Network [OSTI]

Polypyrimidine Track-binding Protein Binding Downstream of Caspase-2 Alternative Exon 9 Represses (In100) located in the intron downstream of alternative exon 9. The upstream portion of this element downstream from the decoy 3 acceptor site. This downstream domain harbors several polypyrimidine track

Wu, Jane Y.

42

between ORC binding and nucleosome turnover, suggesting that turnover facilitates ORC binding.  

E-Print Network [OSTI]

between ORC binding and nucleosome turnover, suggesting that turnover facilitates ORC binding little if any de- pendence on ORC abundance (Fig. 3, H to P). Our findings support the hypothesis- titative correspondence of ORC to CATCH-IT data than to other chromatin measurements implies that the ORC

Pauly, Daniel

43

Structural Basis for Metal Binding Specificity: the N-terminal Cadmium Binding Domain of the  

E-Print Network [OSTI]

In bacteria, P1-type ATPases are responsible for resistance to di- and monovalent toxic heavy metals by taking years and no common mechanism for resistance toward toxic heavy metals such as Cd(II), Zn(II), HgStructural Basis for Metal Binding Specificity: the N-terminal Cadmium Binding Domain of the P1

Scott, Robert A.

44

Predicting binding free energies in solution  

E-Print Network [OSTI]

Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I summarize some of the many factors that could easily contribute 1-3 kcal/mol errors at 298 K: three-body dispersion effects, molecular symmetry, anharmonicity, spurious imaginary frequencies, insufficient conformational sampling, wrong or changing ionization states, errors in the solvation free energy of ions, and explicit solvent (and ion) effects that are not well-represented by continuum models. While the paper is primarily a synthesis of previously published work there are two new results: the adaptation of Legendre transformed free energies to electronic structure theory and a use of water clusters that maximizes error cancellation in binding free energies computed using explicit solvent molecules. While I focus on binding free energies in aqueous solution the approach also a...

Jensen, Jan H

2015-01-01T23:59:59.000Z

45

Nucleic acids encoding a cellulose binding domain  

DOE Patents [OSTI]

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

1996-01-01T23:59:59.000Z

46

Nucleic acids encoding a cellulose binding domain  

DOE Patents [OSTI]

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 15 figs.

Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

1996-03-05T23:59:59.000Z

47

U-101: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding...  

Broader source: Energy.gov (indexed) [DOE]

101: Mozilla Firefox Thunderbird SeaMonkey XBL Binding Use-After-Free Vulnerability U-101: Mozilla Firefox Thunderbird SeaMonkey XBL Binding Use-After-Free Vulnerability...

48

acid binding proteins: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

The adipocyte fatty acid-binding protein aP2 regulates systemic glucose (more) Shum, Bennett Oh Vic 2007-01-01 2 Fatty acid-binding protein in bovine skeletal muscle Texas A&M...

49

acid dopac binds: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

The adipocyte fatty acid-binding protein aP2 regulates systemic glucose (more) Shum, Bennett Oh Vic 2007-01-01 2 Fatty acid-binding protein in bovine skeletal muscle Texas A&M...

50

Prediction of the binding affinities of peptides to class II MHC using a ...  

E-Print Network [OSTI]

We introduce a new model for predicting binding affinities of peptides to ... peptide residues so that the total binding energy is a sum of the binding energies of.

andrew

2010-01-18T23:59:59.000Z

51

Membrane porters of ATP-binding cassette transport systems are polyphyletic  

E-Print Network [OSTI]

in Membrane porters of ATP-binding cassette transportin Membrane porters of ATP-binding cassette transportin Membrane porters of ATP-binding cassette transport

Wang, Bin

2010-01-01T23:59:59.000Z

52

Tight Binding Hamiltonians and Quantum Turing Machines  

E-Print Network [OSTI]

This paper extends work done to date on quantum computation by associating potentials with different types of computation steps. Quantum Turing machine Hamiltonians, generalized to include potentials, correspond to sums over tight binding Hamiltonians each with a different potential distribution. Which distribution applies is determined by the initial state. An example, which enumerates the integers in succession as binary strings, is analyzed. It is seen that for some initial states the potential distributions have quasicrystalline properties and are similar to a substitution sequence.

Paul Benioff

1996-10-17T23:59:59.000Z

53

PATTERNS & PHENOTYPES ATP-Binding Cassette (ABC) Transporter  

E-Print Network [OSTI]

a PATTERNS & PHENOTYPES ATP-Binding Cassette (ABC) Transporter Expression and Localization in Sea Urchin Development Lauren E. Shipp and Amro Hamdoun* Background: ATP-binding cassette (ABC) transporters of polarized cells. Accepted 26 March 2012 INTRODUCTION ATP-binding cassette (ABC) trans- porters

54

Experimental study of exiton binding energy in semiconducting carbon nanotubes  

E-Print Network [OSTI]

Experimental study of exiton binding energy in semiconducting carbon nanotubes Nicolas Izard,1, 2 to the exciton binding energy of nanotubes. Electroabsorption is a powerfull technique which directly probe dimensional nanotube leads to strong electron-hole localiza- tion, with binding energy as high as 0.5 e

Maruyama, Shigeo

55

Dual chain synthetic heparin-binding growth factor analogs  

DOE Patents [OSTI]

The invention provides synthetic heparin-binding growth factor analogs having two peptide chains each branched from a branch moiety, such as trifunctional amino acid residues, the branch moieties separated by a first linker of from 3 to about 20 backbone atoms, which peptide chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a second linker, which may be a hydrophobic second linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

Zamora, Paul O. (Gaithersburg, MD); Pena, Louis A. (Poquott, NY); Lin, Xinhua (Plainview, NY)

2012-04-24T23:59:59.000Z

56

Dual chain synthetic heparin-binding growth factor analogs  

DOE Patents [OSTI]

The invention provides synthetic heparin-binding growth factor analogs having two peptide chains each branched from a branch moiety, such as trifunctional amino acid residues, the branch moieties separated by a first linker of from 3 to about 20 backbone atoms, which peptide chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a second linker, which may be a hydrophobic second linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

Zamora, Paul O. (Gaithersburg, MD); Pena, Louis A. (Poquott, NY); Lin, Xinhua (Plainview, NY)

2009-10-06T23:59:59.000Z

57

T-550: Apache Denial of Service Vulnerability | Department of...  

Broader source: Energy.gov (indexed) [DOE]

1.2.8 Multiple Vulnerabilities U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability T-616: PHP Stream Component Remote Denial of Service Vulnerability...

58

Tight Binding Hamiltonians and Quantum Turing Machines  

SciTech Connect (OSTI)

This paper extends work done to date on quantum computation by association of potentials with different types of steps. Quantum Turing machine Hamiltonians, generalized to include potentials, correspond to sums over tight binding Hamiltonians each with a different potential distribution. Which distribution applies is determined by the initial state. An example, which enumerates the integers in succession as binary strings, is analyzed. It is seen that for some initial states, the potential distributions have quasicrystalline properties and are similar to a substitution sequence. {copyright} {ital 1997} {ital The American Physical Society}

Benioff, P. [Physics Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)] [Physics Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

1997-01-01T23:59:59.000Z

59

Gene encoding herbicide safener binding protein  

DOE Patents [OSTI]

The cDNA encoding safener binding protein (SafBP), also referred to as SBP1, is set forth in FIG. 5 and SEQ ID No. 1. The deduced amino acid sequence is provided in FIG. 5 and SEQ ID No. 2. Methods of making and using SBP1 and SafBP to alter a plant's sensitivity to certain herbicides or a plant's responsiveness to certain safeners are also provided, as well as expression vectors, transgenic plants or other organisms transfected with said vectors and seeds from said plants.

Walton, Jonathan D. (East Lansing, MI); Scott-Craig, John S. (East Lansing, MI)

1999-01-01T23:59:59.000Z

60

A Rare Earth-DOTA-Binding Antibody: Probe Properties and Binding Affinity across the Lanthanide Series  

E-Print Network [OSTI]

of applications in chemistry, environmental science, and medicine because they can bind target molecules with high and Eu, and the nuclear properties of Lu and the group IIIB element Y. The chelating ligand DOTA (Figure of the lanthanide ion, the stability of the protein-ligand complex changes in a regular fashion. The effect

Fisher, Andrew J.

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


61

Hardware device to physical structure binding and authentication  

DOE Patents [OSTI]

Detection and deterrence of device tampering and subversion may be achieved by including a cryptographic fingerprint unit within a hardware device for authenticating a binding of the hardware device and a physical structure. The cryptographic fingerprint unit includes an internal physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generate an internal PUF value. Binding logic is coupled to receive the internal PUF value, as well as an external PUF value associated with the physical structure, and generates a binding PUF value, which represents the binding of the hardware device and the physical structure. The cryptographic fingerprint unit also includes a cryptographic unit that uses the binding PUF value to allow a challenger to authenticate the binding.

Hamlet, Jason R.; Stein, David J.; Bauer, Todd M.

2013-08-20T23:59:59.000Z

62

Binding Energy of d Transition Metals to Alkenes By Wave...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Energy of d Transition Metals to Alkenes By Wave Function Theory and Density Functional Theory. Binding Energy of d Transition Metals to Alkenes By Wave Function Theory...

63

antigen papillomavirus binding: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

specificity, the present set of studies undertook similar goals by Corradin; Jacques M. Chiller 1979-01-01 124 Human Erythrocytes Selectively Bind and Enrich Infectious HIV-1...

64

antigen binding repertoire: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

specificity, the present set of studies undertook similar goals by Corradin; Jacques M. Chiller 1979-01-01 127 Human Erythrocytes Selectively Bind and Enrich Infectious HIV-1...

65

antigen binds phosphatase: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

specificity, the present set of studies undertook similar goals by Corradin; Jacques M. Chiller 1979-01-01 139 Human Erythrocytes Selectively Bind and Enrich Infectious HIV-1...

66

Biophysical Studies of Protein Folding and Binding Stability.  

E-Print Network [OSTI]

?? Interactions between charged residues are known to have significant effects on protein folding stability and binding properties. The contributions of different types of non-covalent (more)

Batra, Jyotica

2009-01-01T23:59:59.000Z

67

acid binding protein: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Richardson, Charles C. 17 Acidic pH Changes Receptor Binding Specificity of Helicobacter pylori: a Binary Adhesion Model in which Surface Heat Shock (Stress) Proteins...

68

Crown Ethers in Graphene Bring Strong, Selective Binding | ornl...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Materials Characterization Crown Ethers in Graphene Bring Strong, Selective Binding November 14, 2014 Schematic showing a graphene sheet containing an array of ideal crown ethers....

69

Correlation between fundamental binding forces and clinical prognosis...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Atomic force microscopy was used to fish for binding reactions between a fibronectin-coated probe (i.e., substrate simulating an implant device) and each of 15...

70

Crown Ethers Flatten in Graphene for Strong, Specific Binding...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

SHARE Crown Ethers Flatten in Graphene for Strong, Specific Binding ORNL discovery holds potential for separations, sensors, batteries, biotech and more This sheet of graphene...

71

Method and apparatus for detecting chemical binding  

DOE Patents [OSTI]

The method for screening binding between a target binder and potential pharmaceutical chemicals involves sending a solution (preferably an aqueous solution) of the target binder through a conduit to a size exclusion filter, the target binder being too large to pass through the size exclusion filter, and then sending a solution of one or more potential pharmaceutical chemicals (preferably an aqueous solution) through the same conduit to the size exclusion filter after target binder has collected on the filter. The potential pharmaceutical chemicals are small enough to pass through the filter. Afterwards, x-rays are sent from an x-ray source to the size exclusion filter, and if the potential pharmaceutical chemicals form a complex with the target binder, the complex produces an x-ray fluorescence signal having an intensity that indicates that a complex has formed.

Warner, Benjamin P. (Los Alamos, NM); Havrilla, George J. (Los Alamos, NM); Miller, Thomasin C. (Los Alamos, NM); Wells, Cyndi A. (Los Alamos, NM)

2007-07-10T23:59:59.000Z

72

Neptunium Binding Kinetics with Arsenazo(III)  

SciTech Connect (OSTI)

This document has been prepared to meet FCR&D level 2 milestone M2FT-14IN0304021, Report on the results of actinide binding kinetics with aqueous phase complexants This work was carried out under the auspices of the Thermodynamics and Kinetics of Advanced Separations Systems FCR&D work package. The report details kinetics experiments that were performed to measure rates of aqueous phase complexation for pentavalent neptunium with the chromotropic dye Arsenazo III (AAIII). The studies performed were designed to determine how pH, ionic strength and AAIII concentration may affect the rate of the reaction. A brief comparison with hexavalent neptunium is also made. It was identified that as pH was increased the rate of reaction also increased, however increasing the ionic strength and concentration of AAIII had the opposite effect. Interestingly, the rate of reaction of Np(VI) with AAIII was found to be slower than that of the Np(V) reaction.

Leigh R. Martin; Aaron T. Johnson; Stephen P. Mezyk

2014-08-01T23:59:59.000Z

73

Triton binding energy with realistic precision  

E-Print Network [OSTI]

We compute the binding energy of triton with realistic statistical errors stemming from NN scattering data uncertainties and the deuteron and obtain $E_t=-7.638(15) \\, {\\rm MeV}$. Setting the numerical precision as $\\Delta E_t^{\\rm num} \\lesssim 1 \\, {\\rm keV}$ we obtain the statistical error $\\Delta E_t^{\\rm stat}= 15(1) \\, {\\rm keV}$ which is mainly determined by the channels involving relative S-waves. This figure reflects the uncertainty of the input NN data, more than two orders of magnitude larger than the experimental precision $\\Delta E_t^{\\rm exp}= 0.1 \\, {\\rm keV}$ and provides a bottleneck in the realistic precision that can be reached. This suggests an important reduction in the numerical precision and hence in the computational effort.

R. Navarro Perez; E. Garrido; J. E. Amaro; E. Ruiz Arriola

2014-07-29T23:59:59.000Z

74

Molecular Mechanisms of Calcium and Magnesium Binding to Parvalbumin  

E-Print Network [OSTI]

between the coordinating residues of the EF-hand calcium binding loop of parvalbumin and the overallMolecular Mechanisms of Calcium and Magnesium Binding to Parvalbumin M. Susan Cates, Miguel L at EF loop position 12 results in a dramatically less tightly bound monodentate Ca2 coordination

Phillips, George N. Jr.

75

Binding of Nucleobases with Single-Walled Carbon Nanotubes  

E-Print Network [OSTI]

We have calculated the binding energy of various nucleobases (guanine (G), adenine (A), thymine (T) and cytosine (C)) with (5,5) single-walled carbon nanotubes (SWNTs) using ab-initio Hartre-Fock method (HF) together with force field calculations. The gas phase binding energies follow the sequence G $>$ A $>$ T $>$ C. We show that main contribution to binding energy comes from van-der Wall (vdW) interaction between nanotube and nucleobases. We compare these results with the interaction of nucleobases with graphene. We show that the binding energy of bases with SWNTs is much lower than the graphene but the sequence remains same. When we include the effect of solvation energy (Poisson-Boltzman (PB) solver at HF level), the binding energy follow the sequence G $>$ T $>$ A $>$ C $>$, which explains the experiment\\cite{zheng} that oligonucleotides made of thymine bases are more effective in dispersing the SWNT in aqueous solution as compared to poly (A) and poly (C). We also demonstrate experimentally that there is differential binding affinity of nucleobases with the single-walled carbon nanotubes (SWNTs) by directly measuring the binding strength using isothermal titration (micro) calorimetry. The binding sequence of the nucleobases varies as thymine (T) $>$ adenine (A) $>$ cytosine (C), in agreement with our calculation.

Anindya Das; A. K. Sood; Prabal K. Maiti; Mili Das; R. Varadarajan; C. N. R. Rao

2007-09-19T23:59:59.000Z

76

news and views nucleotide binds to the polymerase and  

E-Print Network [OSTI]

news and views nucleotide binds to the polymerase and before it is incorporated into DNA. Recent structures of several structurally diverse DNA polymerases complexed to DNA and nucleotide substrates have shown that their active sites adopt a closed conforma- tion upon binding to the correct nucleotide12

Schedl, Paul

77

Unexpected Nondissociative Binding of N2O on Oxygen Vacancies...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Nondissociative Binding of N2O on Oxygen Vacancies on a Rutile TiO2(110)-11 . Unexpected Nondissociative Binding of N2O on Oxygen Vacancies on a Rutile TiO2(110)-11 ....

78

Hydrogen Bonding Penalty upon Ligand Binding Hongtao Zhao, Danzhi Huang*  

E-Print Network [OSTI]

Hydrogen Bonding Penalty upon Ligand Binding Hongtao Zhao, Danzhi Huang* Department of Biochemistry, University of Zurich, Zurich, Switzerland Abstract Ligand binding involves breakage of hydrogen bonds with water molecules and formation of new hydrogen bonds between protein and ligand. In this work, the change

Caflisch, Amedeo

79

Characterization of the ATP-Binding Domain of the Sarco(endo)plasmic Reticulum -ATPase: Probing Nucleotide Binding by Multidimensional NMR  

E-Print Network [OSTI]

Characterization of the ATP-Binding Domain of the Sarco(endo)plasmic Reticulum Ca2+ -ATPase cycle catalyzed by SERCA1a, we have studied the ATP-binding domain of SERCA1a in both nucleotide containing the nucleotide-binding domain of SERCA1a spanning residues Thr357-Leu600. ATP binding activity

Ikura, Mitsuhiko

80

Baryon Binding Energy in Sakai-Sugimoto Model  

E-Print Network [OSTI]

The binding energy of baryon has been studied in the dual $AdS_5\\times S^5$ string theory with a black hole interior. In this picture baryon is constructed of a $D_5$ brane vertex wrapping on $S^5$ and $N_c$ fundamental strings connected to it. Here, we calculate the baryon binding energy in Sakai-Sugimoto model with a $D_4/D_8/\\bar{D_8}$ in which the supersymmetry is completely broken. Also we check the $T$ dependence of the baryon binding energy. We believe that this model represents an accurate description of baryons due to the existence of Chern-Simones coupling with the gauge field on the brane. We obtain an analytical expression for the baryon binding energy . In that case we plot the baryon binding energy in terms of radial coordinate. Then by using the binding energy diagram, we determine the stability range for baryon configuration. And also the position and energy of the stable equilibrium point is obtained by the corresponding diagram. Also we plot the baryon binding energy in terms of temperature and estimate a critical temperature in which the baryon would be dissociated.

J. Sadeghi; M. R. Pahlavani; S. Heshmatian; R. Morad

2009-10-20T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


81

XAS and Pulsed EPR Studies of the Copper Binding Site in Riboflavin Binding Protein  

SciTech Connect (OSTI)

Riboflavin Binding Protein (RBP) binds copper in a 1:1 molar ratio, forming a distinct well-ordered type II site. The nature of this site has been examined using X-ray absorption and pulsed electron paramagnetic resonance (EPR) spectroscopies, revealing a four coordinate oxygen/nitrogen rich environment. On the basis of analysis of the Cambridge Structural Database, the average protein bound copper-ligand bond length of 1.96 Angstroms, obtained by extended x-ray absorption fine structure (EXAFS), is consistent with four coordinate Cu(I) and Cu(II) models that utilize mixed oxygen and nitrogen ligand distributions. These data suggest a CuO3N coordination state for copper bound to RBP. While pulsed EPR studies including hyperfine sublevel correlation spectroscopy and electron nuclear double resonance show clear spectroscopic evidence for a histidine bound to the copper, inclusion of a histidine in the EXAFS simulation did not lead to any significant improvement in the fit.

Smith,S.; Bencze, K.; Wasiukanis, K.; Benore-Parsons, T.; Stemmler, T.

2008-01-01T23:59:59.000Z

82

E-Print Network 3.0 - altered lectin-binding sites Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Fluorescent microscopy of lectin binding: Untreated exoskeleton... microscope with an Optronics cooled CCD camera) to determine if lectin binding had occurred. Statistical......

83

E-Print Network 3.0 - alix binding requirements Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

alix binding requirements Search Powered by Explorit Topic List Advanced Search Sample search results for: alix binding requirements Page: << < 1 2 3 4 5 > >> 1 3025Commentary...

84

Membrane Porters of ATP-Binding Cassette Transport Systems Are Polyphyletic  

E-Print Network [OSTI]

REVIEW Membrane Porters of ATP-Binding Cassette Transportat Springerlink.com Abstract The ATP-binding cassette (ABC)classi?ed according to the ATP hydrolyzing constituents,

Wang, Bin; Dukarevich, Maxim; Sun, Eric I.; Yen, Ming Ren; Saier, Milton H.

2009-01-01T23:59:59.000Z

85

E-Print Network 3.0 - affect stability binding Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

stability binding Search Powered by Explorit Topic List Advanced Search Sample search results for: affect stability binding Page: << < 1 2 3 4 5 > >> 1 Chemistry Department 2011...

86

E-Print Network 3.0 - active maltose-binding fusion Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

a Summary: . Keywords: Fusion protein; inclusion bodies; maltose-binding protein; protein folding; solubility; aggre... - gation Escherichia coli maltose-binding protein (MBP) is...

87

E-Print Network 3.0 - adhesive binding mechanism Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

binding mechanism Page: << < 1 2 3 4 5 > >> 1 IOWA STATE UNIVERSITY DEPARTMENT OF MECHANICAL ENGINEERING Summary: in metastatic cancers. Adhesion is initiated by the binding of...

88

Metal binding proteins, recombinant host cells and methods  

DOE Patents [OSTI]

The present disclosure provides artificial heavy metal binding proteins termed chelons by the inventors. These chelons bind cadmium and/or mercuric ions with relatively high affinity. Also disclosed are coding sequences, recombinant DNA molecules and recombinant host cells comprising those recombinant DNA molecules for expression of the chelon proteins. In the recombinant host cells or transgenic plants, the chelons can be used to bind heavy metals taken up from contaminated soil, groundwater or irrigation water and to concentrate and sequester those ions. Recombinant enteric bacteria can be used within the gastrointestinal tracts of animals or humans exposed to toxic metal ions such as mercury and/or cadmium, where the chelon recombinantly expressed in chosen in accordance with the ion to be rededicated. Alternatively, the chelons can be immobilized to solid supports to bind and concentrate heavy metals from a contaminated aqueous medium including biological fluids.

Summers, Anne O.; Caguiat, Jonathan J.

2004-06-15T23:59:59.000Z

89

Research paper Drug diffusion and binding in ionizable interpenetrating networks  

E-Print Network [OSTI]

Research paper Drug diffusion and binding in ionizable interpenetrating networks from poly) (PVA), poly(acrylic acid) (PAA), and their interpenetrating networks (IPNs) were prepared using by measuring their equilibrium polymer volume fraction, equilibrium swelling ratio, and mesh size. Drug

Peppas, Nicholas A.

90

Galactoside-Binding Site in LacY Xiaoxu Jiang,  

E-Print Network [OSTI]

for Asn272 either markedly decrease affinity for the substrate (i.e., high KD) or abolish binding movement of H+ in response to the electrochemical H+ gradient (H +, interior negative and/or alkaline), Lac

White, Stephen

91

Understanding regulation of mRNA by RNA binding proteins  

E-Print Network [OSTI]

Posttranscriptional regulation of mRNA by RNA-binding proteins plays key roles in regulating the transcriptome over the course of development, between tissues and in disease states. The specific interactions between mRNA ...

Robertson, Alexander De Jong

2014-01-01T23:59:59.000Z

92

acid inhibitor binding: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

of correctly predicted inter- face residues in actual interface residues Zhou, Yaoqi 162 Sm-like protein Hfq: Location of the ATP-binding site and the effect of ATP on HfqRNA...

93

angiotensin binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 55 Similarity Analysis of Protein Binding Sites: A Generalization of the...

94

antigen binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 69 Similarity Analysis of Protein Binding Sites: A Generalization of the...

95

alcohol binding sites: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 56 Similarity Analysis of Protein Binding Sites: A Generalization of the...

96

albumin binding sites: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 54 Similarity Analysis of Protein Binding Sites: A Generalization of the...

97

anesthetic binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 57 Similarity Analysis of Protein Binding Sites: A Generalization of the...

98

acid binding sites: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 82 Similarity Analysis of Protein Binding Sites: A Generalization of the...

99

aml-1 binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 55 Similarity Analysis of Protein Binding Sites: A Generalization of the...

100

affinity binding sites: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 112 Similarity Analysis of Protein Binding Sites: A Generalization of the...

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


101

antagonist binding sites: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 58 Similarity Analysis of Protein Binding Sites: A Generalization of the...

102

alcohol binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 56 Similarity Analysis of Protein Binding Sites: A Generalization of the...

103

antidepressant binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 55 Similarity Analysis of Protein Binding Sites: A Generalization of the...

104

antibody binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 75 Binding of HIV-1 gp41-Directed Neutralizing and Non-Neutralizing...

105

autoantibody binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 56 Similarity Analysis of Protein Binding Sites: A Generalization of the...

106

auxin binding protein: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 150 A High-Throughput Solid-Phase Microplate Protein-Binding Assay to...

107

acid binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 82 Similarity Analysis of Protein Binding Sites: A Generalization of the...

108

androgen binding sites: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 55 Similarity Analysis of Protein Binding Sites: A Generalization of the...

109

affinity binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 112 Similarity Analysis of Protein Binding Sites: A Generalization of the...

110

a1 binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 59 Similarity Analysis of Protein Binding Sites: A Generalization of the...

111

amp binding proteins: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 4 Volume 159, number 1,2 FEBS 0638 August 1983 Specific DNA binding of the...

112

agonist binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 62 Similarity Analysis of Protein Binding Sites: A Generalization of the...

113

allosteric binding sites: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 68 Similarity Analysis of Protein Binding Sites: A Generalization of the...

114

allosteric binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 68 Similarity Analysis of Protein Binding Sites: A Generalization of the...

115

activator inhibitor-1 binding: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 147 Stress modulation of visuomotor binding CiteSeer Summary: The primate...

116

DB-PABP: a database of polyanion-binding proteins  

E-Print Network [OSTI]

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many...

Fang, Jianwen; Dong, Yinghua; Slamat-Miller, Nazila; Middaugh, C. Russell

2007-10-04T23:59:59.000Z

117

N NMR Investigation of the Covalent Binding of Reduced TNT  

E-Print Network [OSTI]

, HRP also shifted the binding away from heterocyclic condensation product toward imine formation leaching of TNT and its toxic reductive degradation products into ground and surface waters is a major

118

Molecular Binding Energies from Partition Density Functional Theory  

SciTech Connect (OSTI)

Approximate molecular calculations via standard Kohn-Sham density functional theory are exactly reproduced by performing self-consistent calculations on isolated fragments via partition density functional theory [P. Elliott, K. Burke, M. H. Cohen, and A. Wasserman, Phys. Rev. A 82, 024501 (2010)]. We illustrate this with the binding curves of small diatomic molecules. We find that partition energies are in all cases qualitatively similar and numerically close to actual binding energies. We discuss qualitative features of the associated partition potentials.

Nafziger, J.; Wu, Q.; Wasserman, A.

2011-12-21T23:59:59.000Z

119

Fatty acid-binding protein in bovine skeletal muscle  

E-Print Network [OSTI]

FATTY ACID-BINDING PROTEIN IN BOVINE SKELETAL MUSCLE A Thesis by KIMBERLY KIRBY MOORE Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE... December 1989 Major Subject: Nutrition FATTY ACID-BINDING PROTEIN IN BOVINE SKELETAL MUSCLE A Thesis by KIMBERLY KIRBY MOORE Approved as to style and content by: Ste en B. Smith (Chair of Committee) Karen S. Kubena (Member) Gary C. Smith (Head...

Moore, Kimberly Kirby

2012-06-07T23:59:59.000Z

120

NEM modication prevents high-anity ATP binding to the rst nucleotide binding fold of the sulphonylurea receptor, SUR1  

E-Print Network [OSTI]

NEM modi¢cation prevents high-a¤nity ATP binding to the ¢rst nucleotide binding fold, UK Received 7 July 1999; received in revised form 11 August 1999 Abstract Pancreatic LL-cell ATP WWM 8-azido- [KK-32 P]ATP or 8-azido-[QQ-32 P]ATP was inhibited by NEM with Ki of 1.8 WWM and 2.4 WWM

Tucker, Stephen J.

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


121

1 Copyright 2012 by ASME Proceedings of the ASME/ISCE International Symposium on Flexible Automation  

E-Print Network [OSTI]

, USA ABSTRACT The popularity of forklifts that use fuel cells based on proton exchange membranes (PEMs designed for PEM forklifts tend to have lower material-handling costs, improved closeness ratings Automation ISFA12 June 18-20, 2012, St. Louis, MO, USA ISFA2012-7116 IMPACT OF USING PEM FORKLIFTS

Gosavi, Abhijit

122

Using ISC & GIS to predict sulfur deposition from coal-fired power plants  

E-Print Network [OSTI]

. '. 674 478 I 678 I 3877 3877 3578 I 0 0 0 0 a? 875 675 474 35544? + I 0 Il o 6 II . . ! d I I eaa aaa" I 657 ael I 668, . I dade 4dda I 685C 0 II 4- aa 8 65 55 68 aa le 65 85 86 aa 86 ?" 2' I 10 0' 0' 67...

Lopez, Jose Ignacio

1993-01-01T23:59:59.000Z

123

MANAGING TIGHT BINDING RECEPTORS FOR NEW SPEARATIONS TECHNOLOGIES  

SciTech Connect (OSTI)

Much of the earth's pollution involves compounds of the metallic elements, including actinides, strontium, cesium, technetium, and RCRA metals. Metal ions bind to molecules called ligands, which are the molecular tools that can manipulate the metal ions under most conditions. This DOE-EMSP sponsored program strives (1) to provide the foundations for using the most powerful ligands in transformational separations technologies and (2) to produce seminal examples of their applications to separations appropriate to the DOE EM mission. These ultra tight-binding ligands can capture metal ions in the most competitive of circumstances (from mineralized sites, lesser ligands, and even extremely dilute solutions), but they react so slowly that they are useless in traditional separations methodologies. Two attacks on this problem are underway. The first accommodates to the challenging molecular lethargy by developing a seminal slow separations methodology termed the soil poultice. The second designs ligands that are only tight-binding while wrapped around the targeted metal ion, but can be put in place by switch-binding and removed by switch-release. We envision a kind of molecular switching process to accelerate the union between metal ion and tight-binding ligand. Molecular switching processes are suggested for overcoming the slow natural equilibration rate with which ultra tight-binding ligands combine with metal ions. Ligands that bind relatively weakly combine with metal ions rapidly, so the trick is to convert a ligand from a weak, rapidly binding species to a powerful, slow releasing ligand--during the binding of the ligand to the metal ion. Such switch-binding ligands must react with themselves, and the reaction must take place under the influence of the metal ion. For example, our generation 1 ligands showed that a well-designed linear ligand with ends that readily combine, forms a cyclic molecule when it wraps around a metal ion. Our generation 2 ligands are even more interesting. They convert from rings to structures that wrap around a metal ion to form a cage. These ligands are called cryptands. Switch release is accomplished by photolytic cleavage of a bond to convert a cyclic ligand into a linear ligand or to break similar bonds in a cryptate. Our studies have demonstrated switch binding and switch release with cryptates of calcium. These remarkable cyclic ligands and cage-like ligands are indeed tight-binding and may, in principle, be incorporated in various separations methodologies, including the soil poultice. The soil poultice mimics the way in which microbes secrete extremely powerful ligands into the soil in order to harvest iron. The cellular membrane of the microbe recognizes the iron/ligand complex and admits it into the cell. The soil poultice uses molecularly imprinted polymers (MIPs) to play the role of the cellular membrane. Imprinting involves creation of the polymer in the presence of the metal/ligand complex. In principle, a well design ligand/MIP combination can be highly selective toward almost any targeted metal ion. The principles for that design are the focus of these investigations. An imprinting molecule can interact with the polymer through any, some, or all of the so-called supramolecular modes; e.g., hydrogen bonding, electrostatic charge, minor ligand bonding, Pi-Pi stacking, and hydrophobic and van der Waals interactions. Historically these modes of binding have given MIPs only small re-binding capacities and very limited selectivities. This program has shown that each mode of interaction can be made more powerful than previously suspected and that combinations of different supramolecular interaction modes can produce remarkable synergisms. The results of this systematic study provide a firm foundation for tailoring molecular imprinted polymers for reclamation of specific metal ion, including those important to the DOE EM mission.

DARYLE H BUSCH RICHARD S GIVENS

2004-12-10T23:59:59.000Z

124

ORIGINAL PAPER A bacterial ice-binding protein from the Vostok ice core  

E-Print Network [OSTI]

to produce a 54 kDa ice-binding protein (GenBank EU694412) that is similar to ice-binding proteins previously- vival at sub-zero temperatures by producing proteins that bind to and inhibit the growth of ice crystalsORIGINAL PAPER A bacterial ice-binding protein from the Vostok ice core James A. Raymond ? Brent C

Christner, Brent C.

125

Changes in misonidazole binding with hypoxic fraction in mouse tumors  

SciTech Connect (OSTI)

Binding of misonidazole (MISO) or a derivative to hypoxic cells in tumors has been proposed as a method for identifying tumors, and measuring their level of hypoxia. The author has recently shown that the hypoxic fraction of tumor cells can be altered over a wide range in vivo by acutely changing the hematocrit of the host animal by transfusion. The present study is aimed to investigate the changes in binding by /sup 14/C MISO that accompanied this procedure. Tumor bearing mice were injected with /sup 14/C MISO, irradiated with a single dose of X rays (20 Gy) and their tumor excised and bisected. One half of each tumor was used to determine cell survival in vitro, the other was used for /sup 14/C scintillation counting. As previously described, tumor cell survival was dramatically increased in acutely anemic mice and this was accompanied by an increase in /sup 14/C MISO binding to the tumors. The relationship between clonogenic cell survival and binding was found to be linear on a log-log plot for each of the tumor lines studied, but the slopes of the lines were different in different tumor lines and generally steeper than the value of 1.0 expected for a 1:1 correspondence between cells binding radioactivity and radiobiological resistance.

Hirst, D.G.; Hazlehurst, J.L.; Brown, J.M.

1985-07-01T23:59:59.000Z

126

Accurate nuclear radii and binding energies from a chiral interaction  

E-Print Network [OSTI]

The accurate reproduction of nuclear radii and binding energies is a long-standing challenge in nuclear theory. To address this problem two-nucleon and three-nucleon forces from chiral effective field theory are optimized simultaneously to low-energy nucleon-nucleon scattering data, as well as binding energies and radii of few-nucleon systems and selected isotopes of carbon and oxygen. Coupled-cluster calculations based on this interaction, named NNLOsat, yield accurate binding energies and radii of nuclei up to 40Ca, and are consistent with the empirical saturation point of symmetric nuclear matter. In addition, the low-lying collective 3- states in 16O and 40Ca are described accurately, while spectra for selected p- and sd-shell nuclei are in reasonable agreement with experiment.

Ekstrom, A; Wendt, K A; Hagen, G; Papenbrock, T; Carlsson, B D; Forssen, C; Hjorth-Jensen, M; Navratil, P; Nazarewicz, W

2015-01-01T23:59:59.000Z

127

Functional characterization of acyl-CoA binding protein (ACBP) and oxysterol binding protein-related proteins (ORPS) from Cryptosporidium parvum  

E-Print Network [OSTI]

maltose-binding protein fusion system and expressed as a recombinant protein for functional analysis. Acyl-CoA-binding assays clearly revealed that the preferred binding substrate for CpACBP1 is palmitoyl-CoA. RT-PCR, Western blotting and immunolabelling...

Zeng, Bin

2009-05-15T23:59:59.000Z

128

Methods of use of cellulose binding domain proteins  

DOE Patents [OSTI]

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

1997-09-23T23:59:59.000Z

129

Methods of use of cellulose binding domain proteins  

DOE Patents [OSTI]

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

1997-01-01T23:59:59.000Z

130

Methods of detection using a cellulose binding domain fusion product  

DOE Patents [OSTI]

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Shimshon, IL); Shpiegl, Itai (North Gallilea, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

1999-01-01T23:59:59.000Z

131

Similarity of Position Frequency Matrices for Transcription Factor Binding Sites  

E-Print Network [OSTI]

approximating the binding energy of the profiled transcription factor. Comparison tools for TFBS PFMs: Software is available to use over the web at http://rulai.cshl.edu/MatCompare Contact: dschones, sumazin to the average log likelihood ratio method and the Pearson correlation coef- ficient method on simulated data

132

A probabilistic approach to microRNA-target binding  

SciTech Connect (OSTI)

Highlights: {yields} A new probabilistic model is introduced for microRNA-target binding. {yields} The new model significantly outperforms RNAHybrid and miRTif. {yields} The experiments can unveil the effects of the type and directions of distinct base pairings. -- Abstract: Elucidation of microRNA activity is a crucial step in understanding gene regulation. One key problem in this effort is how to model the pairwise interactions of microRNAs with their targets. As this interaction is strongly mediated by their sequences, it is desired to set-up a probabilistic model to explain the binding preferences between a microRNA sequence and the sequence of a putative target. To this end, we introduce a new model of microRNA-target binding, which transforms an aligned duplex to a new sequence and defines the likelihood of this sequence using a Variable Length Markov Chain. It offers a complementary representation of microRNA-mRNA pairs for microRNA target prediction tools or other probabilistic frameworks of integrative gene regulation analysis. The performance of present model is evaluated by its ability to predict microRNA-target mRNA interaction given a mature microRNA sequence and a putative mRNA binding site. In regard to classification accuracy, it outperforms two recent methods based on thermodynamic stability and sequence complementarity. The experiments can also unveil the effects of base pairing types and non-seed region in duplex formation.

Ogul, Hasan, E-mail: hogul@baskent.edu.tr [Department of Computer Engineering, Baskent University, Baglica TR-06810, Ankara (Turkey)] [Department of Computer Engineering, Baskent University, Baglica TR-06810, Ankara (Turkey); Umu, Sinan U. [Department of Chemistry, Middle East Technical University, Cankaya TR-06800, Ankara (Turkey) [Department of Chemistry, Middle East Technical University, Cankaya TR-06800, Ankara (Turkey); Bioinformatics Program, Informatics Institute, Middle East Technical University, Cankaya TR-06800, Ankara (Turkey); Tuncel, Y. Yener [Bioinformatics Program, Informatics Institute, Middle East Technical University, Cankaya TR-06800, Ankara (Turkey)] [Bioinformatics Program, Informatics Institute, Middle East Technical University, Cankaya TR-06800, Ankara (Turkey); Akkaya, Mahinur S. [Department of Chemistry, Middle East Technical University, Cankaya TR-06800, Ankara (Turkey)] [Department of Chemistry, Middle East Technical University, Cankaya TR-06800, Ankara (Turkey)

2011-09-16T23:59:59.000Z

133

Supplemental Data Directed Evolution of ATP Binding Proteins  

E-Print Network [OSTI]

Supplemental Data Directed Evolution of ATP Binding Proteins from a Zinc Finger Domain Using m TG 3'). Denaturing Ni-NTA was performed on the ATP-column elution for round 2, and then FLAG with the resin, but instead passed directly over the immobilized ATP. The selection was performed at room

Heller, Eric

134

Methods of detection using a cellulose binding domain fusion product  

DOE Patents [OSTI]

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 34 figs.

Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

1999-01-05T23:59:59.000Z

135

Biomaterials 28 (2007) 49914999 Targeted binding of PLA microparticles with  

E-Print Network [OSTI]

Biomaterials 28 (2007) 4991­4999 Targeted binding of PLA microparticles with lipid comprised of poly(lactic acid) (PLA) with incorporated poly(ethylene glycol)-lipids (PEG-lipids). Particles/O/W) technique are poly(lactic acid) (PLA) [8,9] and poly(lactic-co-glycolic acid) (PLGA) [10­12], both of which

136

Molecular Cell High-Affinity Binding of Chp1 Chromodomain  

E-Print Network [OSTI]

Molecular Cell Article High-Affinity Binding of Chp1 Chromodomain to K9 Methylated Histone H3, Chp1, and siRNAs derived from centro- meric repeats. Recruitment of RITS to centromeres has been establishment. Our crystal structure of Chp1's chromodomain in complex with a trimethylated lysine 9 H3 peptide

Halazonetis, Thanos

137

Off-Shell NN Potential and Triton Binding Energy  

E-Print Network [OSTI]

The NONLOCAL Bonn-B potential predicts 8.0 MeV binding energy for the triton (in a charge-dependent 34-channel Faddeev calculation) which is about 0.4 MeV more than the predictions by LOCAL NN potentials. We pin down origin and size of the nonlocality in the Bonn potential, in analytic and numeric form. The nonlocality is due to the use of the correct off-shell Feynman amplitude of one-boson-exchange avoiding the commonly used on-shell approximations which yield the local potentials. We also illustrate how this off-shell behavior leads to more binding energy. We emphasize that the increased binding energy is not due to on-shell differences (differences in the fit of the NN data or phase shifts). In particular, the Bonn-B potential reproduces accurately the $\\epsilon_1$ mixing parameter up to 350 MeV as determined in the recent Nijmegen multi-energy NN phase-shift analysis. Adding the relativistic effect from the relativistic nucleon propagators in the Faddeev equations, brings the Bonn-B result up to 8.2 MeV triton binding. This leaves a difference of only 0.3 MeV to experiment, which may possibly be explained by refinements in the treatment of relativity and the inclusion of other nonlocalities (e.~g., quark-gluon exchange at short range). Thus, it is conceivable that a realistic NN potential which describes the NN data up to 300 MeV correctly may explain the triton binding energy without recourse to 3-N forces; relativity would play a major role for this result.

Y. Song; R. Machleidt

1994-03-31T23:59:59.000Z

138

E-Print Network 3.0 - atp-binding rna aptamer Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

aptamer Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding rna aptamer Page: << < 1 2 3 4 5 > >> 1 Mutant ATP-binding RNA Aptamers Reveal...

139

E-Print Network 3.0 - angiostatin binds atp Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

binds atp Search Powered by Explorit Topic List Advanced Search Sample search results for: angiostatin binds atp Page: << < 1 2 3 4 5 > >> 1 Molecular Biology of the Cell Vol. 16,...

140

E-Print Network 3.0 - arabidopsis atp-binding cassette Sample...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

atp-binding cassette Search Powered by Explorit Topic List Advanced Search Sample search results for: arabidopsis atp-binding cassette Page: << < 1 2 3 4 5 > >> 1 BioMed Central...

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


141

E-Print Network 3.0 - abcc9-encoded nucleotide binding Sample...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Biology and Medicine 2 Nucleotide binding and hydrolysis by GlcV Thermodynamics of the ATP hydrolysis cycle of GlcV, Summary: Nucleotide binding and hydrolysis by GlcV 43...

142

High-Affinity Binding and Direct Electron Transfer to Solid Metals...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Binding and Direct Electron Transfer to Solid Metals by the Shewanella oneidensis MR-1 Outer Membrane c-type High-Affinity Binding and Direct Electron Transfer to Solid Metals...

143

acid-binding protein genes: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

The adipocyte fatty acid-binding protein aP2 regulates systemic glucose (more) Shum, Bennett Oh Vic 2007-01-01 2 Fatty acid-binding protein in bovine skeletal muscle Texas A&M...

144

acid-binding protein ii: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

The adipocyte fatty acid-binding protein aP2 regulates systemic glucose (more) Shum, Bennett Oh Vic 2007-01-01 2 Fatty acid-binding protein in bovine skeletal muscle Texas A&M...

145

acid-binding immunoglobulin-like lectin-6: Topics by E-print...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

The adipocyte fatty acid-binding protein aP2 regulates systemic glucose (more) Shum, Bennett Oh Vic 2007-01-01 2 Fatty acid-binding protein in bovine skeletal muscle Texas A&M...

146

E-Print Network 3.0 - affinity brain membrane-binding Sample...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

brain membrane-binding Search Powered by Explorit Topic List Advanced Search Sample search results for: affinity brain membrane-binding Page: << < 1 2 3 4 5 > >> 1 Inositol...

147

DOI: 10.1002/cbic.200500285 Binding of Helix-Threading Peptides to E. coli  

E-Print Network [OSTI]

] To further explore and develop the capabilities of the HTP design for binding RNA selectively, we identified duplex grooves. To further explore and develop the capabili- ties of the HTP design for binding RNA

Beal, Peter A.

148

E-Print Network 3.0 - atp-binding cassette transporters Sample...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

transporters Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette transporters...

149

E-Print Network 3.0 - atp-binding cassette transporter Sample...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

transporter Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette transporter...

150

E-Print Network 3.0 - atp-binding cassette transport Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

transport Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette transport...

151

E-Print Network 3.0 - aptamers binding reversal Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

will be covered. Keywords Affinity binding Aptamer Aptasensor Biosensor Microfluidics ... - and nanoscale aptasensors, which are biosensors that exploit aptamers, or...

152

Uranium Exerts Acute Toxicity by Binding to Pyrroloquinoline Quinone Cofactor  

SciTech Connect (OSTI)

Uranium as an environmental contaminant has been shown to be toxic to eukaryotes and prokaryotes; however, no specific mechanisms of uranium toxicity have been proposed so far. Here a combination of in vivo, in vitro, and in silico studies are presented describing direct inhibition of pyrroloquinoline quinone (PQQ)-dependent growth and metabolism by uranyl cations. Electrospray-ionization mass spectroscopy, UV-vis optical spectroscopy, competitive Ca2+/uranyl binding studies, relevant crystal structures, and molecular modeling unequivocally indicate the preferred binding of uranyl simultaneously to the carboxyl oxygen, pyridine nitrogen, and quinone oxygen of the PQQ molecule. The observed toxicity patterns are consistent with the biotic ligand model of acute metal toxicity. In addition to the environmental implications, this work represents the first proposed molecular mechanism of uranium toxicity in bacteria, and has relevance for uranium toxicity in many living systems.

Michael R. VanEngelen; Robert I. Szilagyi; Robin Gerlach; Brady E. Lee; William A. Apel; Brent M. Peyton

2011-02-01T23:59:59.000Z

153

A new phenomenological formula for ground state binding energies  

E-Print Network [OSTI]

A phenomenological formula based on liquid drop model has been proposed for ground state binding energies of nuclei. The effect due to bunching of single particle levels has been incorporated through a term resembling the one-body Hamiltonian. The effect of n-p interaction has been included through a function of valence nucleons. A total of 50 parameters has been used in the present calculation. The r.m.s. deviation for the binding energy values for 2140 nuclei comes out to be 0.376 MeV, and that for 1091 alpha decay energies is 0.284 MeV. The correspondence with the conventional liquid drop model is discussed.

G. Gangopadhyay

2010-07-09T23:59:59.000Z

154

Nuclear binding, correlations and the origin of EMC effect  

E-Print Network [OSTI]

Recent data for the slope of the EMC-ratio in the intermediate $x$-region for {\\em light} nuclei, with $3 \\leq A \\leq 12$, have the potential to shed new light on the origin of the EMC effect. Here we study the role of nuclear binding using the scaling variable ${\\tilde y}$, best suited to take into account this effect, and the understanding of the average nucleon removal energies, $\\bar{E}$, provided by state-of-the-art calculations based on nuclear many body theory. We find an excellent correlation between the new EMC data at $x \\sim 0.5$ and $\\bar{E}$ for nuclei with $A$ from 3 to $\\infty$, indicating that in this $x$ region binding is an important ingredient to explain the EMC effect. The role played by nucleon-nucleon correlations in this context is also discussed.

Omar Benhar; Ingo SIck

2012-07-19T23:59:59.000Z

155

Nuclear binding, correlations and the origin of EMC effect  

E-Print Network [OSTI]

Recent data for the slope of the EMC-ratio in the intermediate $x$-region for {\\em light} nuclei, with $3 \\leq A \\leq 12$, have the potential to shed new light on the origin of the EMC effect. Here we study the role of nuclear binding using the scaling variable ${\\tilde y}$, best suited to take into account this effect, and the understanding of the average nucleon removal energies, $\\bar{E}$, provided by state-of-the-art calculations based on nuclear many body theory. We find an excellent correlation between the new EMC data at $x \\sim 0.5$ and $\\bar{E}$ for nuclei with $A$ from 3 to $\\infty$, indicating that in this $x$ region binding is an important ingredient to explain the EMC effect. The role played by nucleon-nucleon correlations in this context is also discussed.

Benhar, Omar

2012-01-01T23:59:59.000Z

156

Discovery and Characterization of a Cell-Permeable, Small-Molecule c-Abl Kinase Activator that Binds to the Myristoyl Binding Site  

SciTech Connect (OSTI)

c-Abl kinase activity is regulated by a unique mechanism involving the formation of an autoinhibited conformation in which the N-terminal myristoyl group binds intramolecularly to the myristoyl binding site on the kinase domain and induces the bending of the {alpha}I helix that creates a docking surface for the SH2 domain. Here, we report a small-molecule c-Abl activator, DPH, that displays potent enzymatic and cellular activity in stimulating c-Abl activation. Structural analyses indicate that DPH binds to the myristoyl binding site and prevents the formation of the bent conformation of the {alpha}I helix through steric hindrance, a mode of action distinct from the previously identified allosteric c-Abl inhibitor, GNF-2, that also binds to the myristoyl binding site. DPH represents the first cell-permeable, small-molecule tool compound for c-Abl activation.

Yang, Jingsong; Campobasso, Nino; Biju, Mangatt P.; Fisher, Kelly; Pan, Xiao-Qing; Cottom, Josh; Galbraith, Sarah; Ho, Thau; Zhang, Hong; Hong, Xuan; Ward, Paris; Hofmann, Glenn; Siegfried, Brett; Zappacosta, Francesca; Washio, Yoshiaki; Cao, Ping; Qu, Junya; Bertrand, Sophie; Wang, Da-Yuan; Head, Martha S.; Li, Hu; Moores, Sheri; Lai, Zhihong; Johanson, Kyung; Burton, George; Erickson-Miller, Connie; Simpson, Graham; Tummino, Peter; Copeland, Robert A.; Oliff, Allen (GSKPA)

2014-10-02T23:59:59.000Z

157

Accelerated Articles Direct Electrical Transduction of Antibody Binding  

E-Print Network [OSTI]

Using Electrochemical Impedance Li-Mei C. Yang, Juan E. Diaz, Theresa M. McIntire, Gregory A. Weiss-2025 Electrochemical impedance spectroscopy is used to detect the binding of a 148.2 kDa antibody to a "covalent virusM but noise compromised the reproducibility of the p-Ab measurement at frequencies below 40 Hz. A "signal-to-noise

Weiss, Gregory A.

158

ATM Networking in Linux Bindings occur at four distinct times  

E-Print Network [OSTI]

the following call: sock_register(pvc_proto_ops.family, &pvc_proto_ops); Family is PF_ATMPVC (as in PF_INET) pvc_len); : For ATM PVCs the structure is filled in as follows: static struct proto_ops pvc_proto_ops = { PF_ATMPVC, atm_create, pvc_dup, atm_release, pvc_bind, pvc_connect, : · The entry point addresses

Westall, James M.

159

ATM Networking in Linux Bindings occur at four distinct times  

E-Print Network [OSTI]

using the following call: sock_register(pvc_proto_ops.family, &pvc_proto_ops); Family is PF_ATMPVC (as in PF_INET) pvc_proto_ops is a table of entry point addresses: struct proto_ops { int family; int_ops pvc_proto_ops = { PF_ATMPVC, atm_create, pvc_dup, atm_release, pvc_bind, pvc_connect, : . The entry

Westall, James M.

160

High molecular weight polysaccharide that binds and inhibits virus  

DOE Patents [OSTI]

This invention provides a high molecular weight polysaccharide capable of binding to and inhibiting virus and related pharmaceutical formulations and methods on inhibiting viral infectivity and/or pathogenicity, as well as immunogenic compositions. The invention further methods of inhibiting the growth of cancer cells and of ameliorating a symptom of aging. Additionally, the invention provides methods of detecting and/or quantifying and/or isolating viruses.

Konowalchuk, Thomas W

2014-01-14T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


161

Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Danzhi Huang and Amedeo Caflisch*  

E-Print Network [OSTI]

Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Solvation Danzhi Huang of the absolute free energy of binding. A predictive accuracy of about 1.0 kcal/mol is obtained for 13 and 29 into proteins of known structure require fast and accurate methods for the evaluation of binding free energies.1

Caflisch, Amedeo

162

Theory of Free Energy and Entropy in Noncovalent Binding Huan-Xiang Zhou*,  

E-Print Network [OSTI]

Theory of Free Energy and Entropy in Noncovalent Binding Huan-Xiang Zhou*, and Michael K. Gilson, Rockville, Maryland 20850 Received December 23, 2008 Contents 1. Introduction 4092 2. Free Energy, Partition.4. Solvation and a Temperature-Dependent Energy Function 4096 3. Binding Free Energy and Binding Constant 4096

Weston, Ken

163

DNA binding shifts the redox potential of the transcription factor SoxR  

E-Print Network [OSTI]

DNA binding shifts the redox potential of the transcription factor SoxR Alon A. Gorodetsky , Lars E-modified electrodes are used to probe the effects of binding to DNA on the redox potential of SoxR, a transcription in the absence of DNA. Using Redmond red as a covalently bound redox reporter affixed above the SoxR binding site

Dietrich, Lars

164

Journal of Cellular Biochemistry 80:580588 (2001) Characterization of Nuclear Factors Binding to  

E-Print Network [OSTI]

). It was suggested that these elements might play a role in deter- mining the activity of the p53 promoter [Bienz that the binding proteins did not require divalent cation for DNA-binding activity. In addition, the binding. The mutations of the gene have been observed in over 50% of all human cancers [Hollstein et al., 1991; Levine et

Park, Jong-Sang

165

Molecular dissection of the roles of nucleotide binding and hydrolysis in dynein's AAA domains  

E-Print Network [OSTI]

Molecular dissection of the roles of nucleotide binding and hydrolysis in dynein's AAA domains (ATPase associated with various cellular activities) domains that are thought to bind nucleotide; the role of nucleotide binding and hydrolysis in each of these four AAA domains has constituted an important and unre

Vale, Ronald D.

166

Deciphering the Effect of Nemaline-Myopathy Nebulin Mutations on Desmin Binding  

E-Print Network [OSTI]

-disc of the muscle sarcomere. The Z-disk peripheral region binds desmin (Bang et al., 2002; Conover et al, 2009). The N-terminus of nebulin binds tropomodulin at the pointed end of the thin filament (McElhinny et al., 2001). Tropomodulin acts to bind and cap...

Jacobs, Krystyna M

2012-07-11T23:59:59.000Z

167

oligomeric and polymeric DNA Large electrostatic differences in the binding thermodynamics of a cationic peptide to  

E-Print Network [OSTI]

oligomeric and polymeric DNA Large electrostatic differences in the binding thermodynamics electrostatic differences in the binding thermodynamics of a cationic peptide to oligomeric and polymeric DNA binding to polymeric and oligomeric DNA are not equivalent because of long-range electrostatic effects

Lohman, Timothy M.

168

Binding of cobalt and iron to cavities in silicon  

SciTech Connect (OSTI)

The chemisorption binding of Co and Fe to cavity walls in Si was quantitatively characterized in the temperature range 973{endash}1273 K in order to evaluate the efficacy of cavities for impurity gettering. The cavities were formed by He ion implantation and annealing. Then, with the solution concentration of Co or Fe being held at the solid solubility through prior formation of excess metal-silicide phase, the equilibrium number of metal atoms bound to the cavities was measured. Using this information in conjunction with published solubilities, a binding free energy relative to interstitial solution was extracted. The binding free energies for cavity-wall chemisorption of Co and Fe were found to be less than those for precipitation of the respective silicide phases, a reversal of the ordering previously observed by us for Cu and Au. Nevertheless, model calculations indicate that the chemisorption mechanism is important together with silicide precipitation for cavity gettering of all four elements. The results of this work, taken with the known thermal stability and the anticipated device-side compatibility of cavities, suggest that these sinks will prove attractive for gettering.

Myers, S.M.; Petersen, G.A.; Seager, C.H. [Sandia National Laboratories, P.O. Box 5800, Albuquerque, New Mexico 87185-1056 (United States)] [Sandia National Laboratories, P.O. Box 5800, Albuquerque, New Mexico 87185-1056 (United States)

1996-10-01T23:59:59.000Z

169

Crystal Structure of the Chromodomain Helicase DNA-binding Protein 1 (Chd1) DNA-binding Domain in Complex with DNA  

SciTech Connect (OSTI)

Chromatin remodelers are ATP-dependent machines that dynamically alter the chromatin packaging of eukaryotic genomes by assembling, sliding, and displacing nucleosomes. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding domain that is required for efficient nucleosome sliding and believed to be essential for sensing the length of DNA flanking the nucleosome core. The structure of the Chd1 DNA-binding domain was recently shown to consist of a SANT and SLIDE domain, analogous to the DNA-binding domain of the ISWI family, yet the details of how Chd1 recognized DNA were not known. Here we present the crystal structure of the Saccharomyces cerevisiae Chd1 DNA-binding domain in complex with a DNA duplex. The bound DNA duplex is straight, consistent with the preference exhibited by the Chd1 DNA-binding domain for extranucleosomal DNA. Comparison of this structure with the recently solved ISW1a DNA-binding domain bound to DNA reveals that DNA lays across each protein at a distinct angle, yet contacts similar surfaces on the SANT and SLIDE domains. In contrast to the minor groove binding seen for Isw1 and predicted for Chd1, the SLIDE domain of the Chd1 DNA-binding domain contacts the DNA major groove. The majority of direct contacts with the phosphate backbone occur only on one DNA strand, suggesting that Chd1 may not strongly discriminate between major and minor grooves.

Sharma A.; Heroux A.; Jenkins K. R.; Bowman G. D.

2011-12-09T23:59:59.000Z

170

Mechanism of Ubiquinol Oxidation by the bc1 Complex: Different Domains of the Quinol Binding Pocket and Their Role in the Mechanism and Binding of Inhibitors  

E-Print Network [OSTI]

electron-transfer systems, occurring ubiquitously in respiratory and photosynthetic chains of mitochondriaMechanism of Ubiquinol Oxidation by the bc1 Complex: Different Domains of the Quinol Binding Pocket and Their Role in the Mechanism and Binding of Inhibitors Antony R. Crofts,*, Blanca Barquera, Robert B. Gennis

Crofts, Antony R.

171

Hydroxyapatite-binding peptides for bone growth and inhibition  

DOE Patents [OSTI]

Hydroxyapatite (HA)-binding peptides are selected using combinatorial phage library display. Pseudo-repetitive consensus amino acid sequences possessing periodic hydroxyl side chains in every two or three amino acid sequences are obtained. These sequences resemble the (Gly-Pro-Hyp).sub.x repeat of human type I collagen, a major component of extracellular matrices of natural bone. A consistent presence of basic amino acid residues is also observed. The peptides are synthesized by the solid-phase synthetic method and then used for template-driven HA-mineralization. Microscopy reveal that the peptides template the growth of polycrystalline HA crystals .about.40 nm in size.

Bertozzi, Carolyn R. (Berkeley, CA); Song, Jie (Shrewsbury, MA); Lee, Seung-Wuk (Walnut Creek, CA)

2011-09-20T23:59:59.000Z

172

DNA-Binding Mechanism in Prokaryotic Partition Complex Formation  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation Proposed Newcatalyst phases onOrganization FY Middle SchoolARM-TR-01468This4t cDNA-Binding

173

Relativistic Nuclear Energy Density Functionals: adjusting parameters to binding energies  

E-Print Network [OSTI]

We study a particular class of relativistic nuclear energy density functionals in which only nucleon degrees of freedom are explicitly used in the construction of effective interaction terms. Short-distance (high-momentum) correlations, as well as intermediate and long-range dynamics, are encoded in the medium (nucleon density) dependence of the strength functionals of an effective interaction Lagrangian. Guided by the density dependence of microscopic nucleon self-energies in nuclear matter, a phenomenological ansatz for the density-dependent coupling functionals is accurately determined in self-consistent mean-field calculations of binding energies of a large set of axially deformed nuclei. The relationship between the nuclear matter volume, surface and symmetry energies, and the corresponding predictions for nuclear masses is analyzed in detail. The resulting best-fit parametrization of the nuclear energy density functional is further tested in calculations of properties of spherical and deformed medium-heavy and heavy nuclei, including binding energies, charge radii, deformation parameters, neutron skin thickness, and excitation energies of giant multipole resonances.

T. Niksic; D. Vretenar; P. Ring

2008-09-08T23:59:59.000Z

174

Identification of protein binding sites in the promoter regions of a light-responsive gene family in a cyanobacterium  

E-Print Network [OSTI]

binding sites were characterized that display some interdependence for protein binding ability. One binding site was identified as the primary sequence required for protein binding to the second site. Mutations were introduced into the first binding...lment of the requirements for the degree of MASTER OF SCIENCE December 1991 Major Subject: Biology ZDIBlTZPZCATION OP PROTEIN BINDINQ SITES IN TEB PROMOTER REGIONS OP A LIGHT RESPONSIVE SBBB FAMILY IN A CYANOBACTBRZUM A Thesis by ULRICH WOLFGANG...

Mueller, Ulrich Wolfgang

1991-01-01T23:59:59.000Z

175

Investigation of the Copper Binding Site And the Role of Histidine As a Ligand in Riboflavin Binding Protein  

SciTech Connect (OSTI)

Riboflavin Binding Protein (RBP) binds copper in a 1:1 molar ratio, forming a distinct well-ordered type II site. The nature of this site has been examined using X-ray absorption and pulsed electron paramagnetic resonance (EPR) spectroscopies, revealing a four coordinate oxygen/nitrogen rich environment. On the basis of analysis of the Cambridge Structural Database, the average protein bound copper-ligand bond length of 1.96 {angstrom}, obtained by extended x-ray absorption fine structure (EXAFS), is consistent with four coordinate Cu(I) and Cu(II) models that utilize mixed oxygen and nitrogen ligand distributions. These data suggest a Cu-O{sub 3}N coordination state for copper bound to RBP. While pulsed EPR studies including hyperfine sublevel correlation spectroscopy and electron nuclear double resonance show clear spectroscopic evidence for a histidine bound to the copper, inclusion of a histidine in the EXAFS simulation did not lead to any significant improvement in the fit.

Smith, S.R.; Bencze, K.Z.; Russ, K.A.; Wasiukanis, K.; Benore-Parsons, M.; Stemmler, T.L.

2009-05-26T23:59:59.000Z

176

The effects of temperature on thyroid hormone binding to serum proteins in sea turtles  

E-Print Network [OSTI]

. S. , Texas AKN University Chair of Advisory Committee: Dr. Duncan S. HacKenzie The high affinity binding of thyroid hormones to plasma proteins is a critical step in their peripheral delivery. This study was undertaken to investigate whether... changes in temperature might alter thyroid hormone binding to plasma binding proteins in poikilotherms. The objectives were to determine if high affinity thyroid hormo plasma hi ding proteins e ist i the green (ghelo ia %dash, ioggerhead tata caretta...

Haynes, Shane Patrick

1990-01-01T23:59:59.000Z

177

E-Print Network 3.0 - atp binding cassette Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Search Powered by Explorit Topic List Advanced Search Sample search results for: atp binding cassette Page: << < 1 2 3 4 5 > >> 1 12-13( Humulus Lupulus,...

178

E-Print Network 3.0 - atomic binding energy Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

energy Search Powered by Explorit Topic List Advanced Search Sample search results for: atomic binding energy Page: << < 1 2 3 4 5 > >> 1 Extended Xray Absorption Fine Structure...

179

E-Print Network 3.0 - androgen binding protein Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

data showing that androgen binding increases AR protein stability (Kemppainen et al., 1992... and protein biosynthesis. Androgen levels in CRPC appear adequate to stimulate AR...

180

E-Print Network 3.0 - a-binding protein acbp6 Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Biology and Medicine 3 Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding Summary: kinetics using FRET with acyl-CoA binding protein. In protein folding,...

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


181

U-227: bind-dyndb-ldap DN Escaping Flaw Lets Remote Users Deny Service  

Broader source: Energy.gov [DOE]

A vulnerability has been reported in bind-dyndb-ldap, which can be exploited by malicious people to cause a DoS (Denial of Service).

182

E-Print Network 3.0 - adipocyte fatty acid-binding Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Biochemistry 221: 127132, 2001. 2001 Kluwer Academic Publishers. Printed in the Netherlands. Summary: acid, gene regulation Introduction Fatty acid-binding proteins (FABPs)...

183

Energy landscapes for protein folding, binding, and aggregation : simple funnels and beyond  

E-Print Network [OSTI]

coordinates capture protein folding on smooth landscapes.in the Prediction of Protein Folding Kinetics. Proc. Natl.Landscapes for Protein Folding, Binding, and Aggregation:

Cho, Samuel Sung-Il

2007-01-01T23:59:59.000Z

184

E-Print Network 3.0 - adiponectin retinol binding Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

(CRBP1) located... , the acyltransferase activity of LRAT requires exclusion of water and binding of retinol in LRAT's active site... , is facilitated by three...

185

Anthraquinone Photonuclease Structure Determines Its Mode of Binding to DNA and the Cleavage  

E-Print Network [OSTI]

Anthraquinone Photonuclease Structure Determines Its Mode of Binding to DNA and the Cleavage recently described a set of anthraquinone derivatives that act as photonucleases.6 Three classes

Williams, Loren

186

E-Print Network 3.0 - adenosine binding pocket Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

adenosine into a binding pocket similar... 17, 2000 ABSTRACT: ADARs are ... Source: Beal, Peter A. - Department of Chemistry, University of Utah Collection: Chemistry 10...

187

Quasielastic electron-deuteron scattering in the weak binding approximation  

SciTech Connect (OSTI)

We perform a global analysis of all available electron-deuteron quasielastic scattering data using Q^2-dependent smearing functions that describe inclusive inelastic e-d scattering within the weak binding approximation. We study the dependence of the cross sections on the deuteron wave function and the off-shell extrapolation of the elastic electron-nucleon cross section, which show particular sensitivity at x >> 1. The excellent overall agreement with data over a large range of Q^2 and x suggest a limited need for effects beyond the impulse approximation, with the exception of the very high-x or very low-Q^2 regions, where short-distance effects in the deuteron become more relevant.

Ethier, Jacob J. [William and Mary College, JLAB; Doshi, Nidhi P. [Carnegie Mellon University; Malace, Simona P. [JLAB; Melnitchouk, Wally [JLAB

2014-06-01T23:59:59.000Z

188

ATP binding to a multisubunit enzyme: statistical thermodynamics analysis  

E-Print Network [OSTI]

Due to inter-subunit communication, multisubunit enzymes usually hydrolyze ATP in a concerted fashion. However, so far the principle of this process remains poorly understood. In this study, from the viewpoint of statistical thermodynamics, a simple model is presented. In this model, we assume that the binding of ATP will change the potential of the corresponding enzyme subunit, and the degree of this change depends on the state of its adjacent subunits. The probability of enzyme in a given state satisfies the Boltzmann's distribution. Although it looks much simple, this model can fit the recent experimental data of chaperonin TRiC/CCT well. From this model, the dominant state of TRiC/CCT can be obtained. This study provided a new way to understand biophysical processes by statistical thermodynamics analysis.

Yunxin Zhang

2012-03-22T23:59:59.000Z

189

ATP binding to a multisubunit enzyme: statistical thermodynamics analysis  

E-Print Network [OSTI]

Due to inter-subunit communication, multisubunit enzymes usually hydrolyze ATP in a concerted fashion. However, so far the principle of this process remains poorly understood. In this study, from the viewpoint of statistical thermodynamics, a simple model is presented. In this model, we assume that the binding of ATP will change the potential of the corresponding enzyme subunit, and the degree of this change depends on the state of its adjacent subunits. The probability of enzyme in a given state satisfies the Boltzmann's distribution. Although it looks much simple, this model can fit the recent experimental data of chaperonin TRiC/CCT well. From this model, the dominant state of TRiC/CCT can be obtained. This study provided a new way to understand biophysical processes by statistical thermodynamics analysis.

Zhang, Yunxin

2012-01-01T23:59:59.000Z

190

On the nuclear interaction. Potential, binding energy and fusion reaction  

E-Print Network [OSTI]

The nuclear interaction is responsible for keeping neutrons and protons joined in an atomic nucleus. Phenomenological nuclear potentials, fitted to experimental data, allow one to know about the nuclear behaviour with more or less success where quantum mechanics is hard to be used. A nuclear potential is suggested and an expression for the potential energy of two nuclear entities, either nuclei or nucleons, is developed. In order to estimate parameters in this expression, some nucleon additions to nuclei are considered and a model is suggested as a guide of the addition process. Coulomb barrier and energy for the addition of a proton to each one of several nuclei are estimated by taking into account both the nuclear and electrostatic components of energy. Studies on the binding energies of several nuclei and on the fusion reaction of two nuclei are carried out.

I. Casinos

2008-05-22T23:59:59.000Z

191

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model  

SciTech Connect (OSTI)

Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an induced fit or conformational selection mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.

Knott, Michael [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom)] [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Best, Robert B., E-mail: robertbe@helix.nih.gov [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States)

2014-05-07T23:59:59.000Z

192

Binding and Translocation of Termination Factor Rho Studied at the Single-Molecule Level  

E-Print Network [OSTI]

Binding and Translocation of Termination Factor Rho Studied at the Single-Molecule Level Daniel J; force spectroscopy Rho termination factor is an essential hexameric helicase responsible for terminating to investigate RhoRNA binding in- teractions at the Rho utilization site of the tR1 terminator. Our results

Straight, Aaron

193

Geometric Binding Site Design for Surface-Tension Driven Self-Assembly  

E-Print Network [OSTI]

Geometric Binding Site Design for Surface-Tension Driven Self-Assembly Xiaorong Xiong, Sheng 98195-2500 Email: xrxiong@u.washington.edu Abstract-- Surface-tension driven self-assembly techniques-assembly, micro assembly, MEMS, hy- drophobic, hydrophilic, surface energy, surface tension force, binding site

194

Origin of the Variation of Exciton Binding Energy in Semiconductors Marc Dvorak,1  

E-Print Network [OSTI]

Origin of the Variation of Exciton Binding Energy in Semiconductors Marc Dvorak,1 Su-Huai Wei,2 Renewable Energy Laboratory, Golden, Colorado 80401, USA (Received 13 July 2012; revised manuscript received, and the exciton binding energy Eb in technologically important semiconductors varies from merely a few me

Wu, Zhigang

195

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces  

E-Print Network [OSTI]

, while identification of a hot spot by alanine scanning establishes the potential to generate substantial, termed "hot spots", that comprise the subset of residues that contribute the bulk of the binding free proposed as prime targets for drug binding.1,4 The established approach to the identification of such hot

Vajda, Sandor

196

Measuring molecular rupture forces between single actin filaments and actin-binding proteins  

E-Print Network [OSTI]

Measuring molecular rupture forces between single actin filaments and actin-binding proteins Jorge, and accepted by the Editorial Board April 24, 2008 (received for review June 29, 2007) Actin-binding proteins to model the mechanical properties of actin networks grown in vitro; however, there is a lack

Kamm, Roger D.

197

Host Range and Variability of Calcium Binding by Surface Loops in the Capsids of Canine and  

E-Print Network [OSTI]

Host Range and Variability of Calcium Binding by Surface Loops in the Capsids of Canine and Feline, consisting of residues 359 to 375 of the capsid protein. This loop binds a divalent calcium ion in FPV and in the presence or absence of Ca2 . The largest structural difference was found to occur in a ¯exible surface loop

Rossmann, Michael G.

198

ATP Hydrolysis and DNA Binding by the Escherichia coli RecF Protein*  

E-Print Network [OSTI]

ATP Hydrolysis and DNA Binding by the Escherichia coli RecF Protein* (Received for publication ATP hydrolytic activity. ATP hydrolysis leads to RecF dissociation from double-stranded (ds to DNA. A mutant RecF protein that can bind but cannot hydrolyze ATP (RecF K36R) does not readily

Cox, Michael M.

199

Structure and Evolutionary Analysis of a Non-biological ATP-binding Protein  

E-Print Network [OSTI]

Structure and Evolutionary Analysis of a Non-biological ATP-binding Protein Sheref S. Mansy1 sequence into a stably folded, high affinity ATP binding protein structure. While the evolutionarily and functional data was then used to interpret the significance of each amino acid mutation. The enhanced ATP

Heller, Eric

200

Exciton binding energies in carbon nanotubes from two-photon photoluminescence J. Maultzsch,1,  

E-Print Network [OSTI]

Exciton binding energies in carbon nanotubes from two-photon photoluminescence J. Maultzsch,1, * R; their energy splitting is the fingerprint of excitonic interactions in carbon nanotubes. By ab initio experiment and theory we find binding energies of 0.3­0.4 eV for nanotubes with diameters between 6.8 and 9

Nabben, Reinhard

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


201

ON THE THERMODYNAMICS AND KINETICS OF THE COOPERATIVE BINDING OF BACTERIOPHAGE T4-  

E-Print Network [OSTI]

ON THE THERMODYNAMICS AND KINETICS OF THE COOPERATIVE BINDING OF BACTERIOPHAGE T4- CODED GENE 32 of thermodynamic, and preliminary kinetic, studies on the molecular details and specificity of interaction of phage into the molecular origins of binding cooperativity is obtained by determining these thermodynamic parameters also

Kowalczykowski, Stephen C.

202

A Novel Dimerization Interface of Cyclic Nucleotide Binding Domain, which is  

E-Print Network [OSTI]

1 A Novel Dimerization Interface of Cyclic Nucleotide Binding Domain, which is Disrupted Modeling 18, 9 (2012) 4053-4060" DOI : 10.1007/s00894-012-1404-5 #12;2 ABSTRACT Cyclic nucleotide binding and eukaryota. CNBD activation by cyclic nucleotide monophosphate (cNMP) is studied well in case of several

Paris-Sud XI, Université de

203

Control of DNA minor groove width and Fis protein binding by the purine 2-amino group  

E-Print Network [OSTI]

Control of DNA minor groove width and Fis protein binding by the purine 2-amino group Stephen P within the center of the Fis­DNA complex narrows to about half the mean minor groove width of canonical B by the Fis protein, reduce binding affinities up to 2000-fold over A/T-rich sequences. We show here through

Rohs, Remo

204

Ultrastrong Optical Binding of Metallic Nanoparticles Vassili Demergis and Ernst-Ludwig Florin*  

E-Print Network [OSTI]

is limited by heating and radiation damage to the sample, such as with biological material.5,12,13 Focus hasUltrastrong Optical Binding of Metallic Nanoparticles Vassili Demergis and Ernst-Ludwig Florin the optical binding force, which has been assumed to be weak compared to the optical gradient and scattering

Texas at Austin. University of

205

DNA Profiling Using Solid-State Nanopores: Detection of DNA-Binding  

E-Print Network [OSTI]

for drug development, necessitating new in vitro methods for rapid and low-cost assessment of the binding nanopores fabricated in ultrathin silicon membranes. A measurable shift in the residual ion current through affinities toward a cyanine dye. Nucleic acid-binding fluorophores were used here to validate our nanopore

Meller, Amit

206

USING DNASE DIGESTION DATA TO ACCURATELY IDENTIFY TRANSCRIPTION FACTOR BINDING SITES  

E-Print Network [OSTI]

USING DNASE DIGESTION DATA TO ACCURATELY IDENTIFY TRANSCRIPTION FACTOR BINDING SITES KAIXUAN LUO1. But methods combining DNase digestion data with TF binding specificity information could potentially be used on the genomic digestion prod- ucts of deoxyribonuclease I (DNase I, which we will simply call DNase) might

Hartemink, Alexander

207

Chemical binding energies of point defects in palladium doped with hydrogen and d impurities  

E-Print Network [OSTI]

1001 Chemical binding energies of point defects in palladium doped with hydrogen and d impurities C calculate the chemical binding energy of a pair of hydrogen atoms in palladium within the infinite dilution] it is often assumed that the dominant contribution to the interaction energy between hydrogen atoms

Paris-Sud XI, Université de

208

Dynamics of intracellular Ca$^{2+}$ oscillations in the presence of multisite Ca$^{2+}$-binding proteins  

E-Print Network [OSTI]

We study the dynamics of intracellular calcium oscillations in the presence of proteins that bind calcium on multiple sites and that are generally believed to act as passive calcium buffers in cells. We find that multisite calcium-binding proteins set a sharp threshold for calcium oscillations. Even with high concentrations of calcium-binding proteins, internal noise, which shows up spontaneously in cells in the process of calcium wave formation, can lead to self-oscillations. This produces oscillatory behaviors strikingly similar to those observed in real cells. In addition, for given intracellular concentrations of both calcium and calcium-binding proteins the regularity of these oscillations changes and reaches a maximum as a function noise variance, and the overall system dynamics displays stochastic coherence. We conclude that calcium-binding proteins may have an important and active role in cellular communication.

Roberto Chignola; Alessio Del Fabbro; Edoardo Milotti

2009-09-10T23:59:59.000Z

209

Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding  

SciTech Connect (OSTI)

The bacterial enzyme organophosphorus hydrolase (OPH) exhibits both catalytic and substrate promiscuity. It hydrolyzes bonds in a variety of phosphotriester (P-O), phosphonothioate (P-S), phosphofluoridate (P-F) and phosphonocyanate (F-CN) compounds. However, its catalytic efficiency varies markedly for different substrates, limiting the broad-range application of OPH as catalyst in the bioremediation of pesticides and chemical war agents. In the present study, pK{sub a} calculations and multiple explicit-solvent molecular dynamics (MD) simulations were performed to characterize and contrast the structural dynamics of OPH bound to two substrates hydrolyzed with very distinct catalytic efficiencies: the nerve agent soman (O-pinacolyl-methyl-phosphonofluoridate) and the pesticide paraoxon (diethyl p-nitrophenyl phosphate). pK{sub a} calculations for the substrate-bound and unbound enzyme showed a significant pK{sub a} shift from standard values ({Delta}pK{sub a} = {+-} 3 units) for residues 254His and 275Arg. MD simulations of the doubly protonated 254His revealed a dynamic hydrogen bond network connecting the catalytic residue 301Asp via 254His to 232Asp, 233Asp, 275Arg and 235Asp, and is consistent with a previously postulated proton relay mechanism to ferry protons away from the active site with substrates that do not require activation of the leaving group. Hydrogen bonds between 301Asp and 254His were persistent in the OPH-paraoxon complex but not in the OPH-soman one, suggesting a potential role for such interaction in the more efficient hydrolysis of paraoxon over soman by OPH. These results are in line with previous mutational studies of residue 254His, which led to an increase of the catalytic efficiency of OPH over soman yet decreased its efficiency for paraoxon. In addition, comparative analysis of the molecular trajectories for OPH bound to soman and paraoxon suggests that binding of the latter facilitates the conformational transition of OPH from the open to the closed substate promoting a tighter binding of paraoxon.

Gomes, Diego Eb; Lins, Roberto D.; Pascutti, Pedro G.; Lei, Chenghong; Soares, Thereza A.

2011-12-31T23:59:59.000Z

210

Binding Energy and the Fundamental Plane of Globular Clusters  

E-Print Network [OSTI]

A physical description of the fundamental plane of Galactic globular clusters is developed which explains all empirical trends and correlations in a large number of cluster observables and provides a small but complete set of truly independent constraints on theories of cluster formation and evolution in the Milky Way. Within the theoretical framework of single-mass, isotropic King models, it is shown that (1) 39 regular (non--core-collapsed) globulars with measured core velocity dispersions share a common V-band mass-to-light ratio of 1.45 +/- 0.10, and (2) a complete sample of 109 regular globulars reveals a very strong correlation between cluster binding energy and total luminosity, regulated by Galactocentric position: E_b \\propto (L^{2.05} r_{\\rm gc}^{-0.4}). The observational scatter about either of these two constraints can be attributed fully to random measurement errors, making them the defining equations of a fundamental plane for globular clusters. A third, weaker correlation, between total luminosity and the King-model concentration parameter, c, is then related to the (non-random) distribution of globulars on the plane. The equations of the FP are used to derive expressions for any cluster observable in terms of only L, r_{\\rm gc}, and c. Results are obtained for generic King models and applied specifically to the globular cluster system of the Milky Way.

Dean E. McLaughlin

2000-02-03T23:59:59.000Z

211

Structural basis of substrate discrimination and integrin binding by autotaxin  

SciTech Connect (OSTI)

Autotaxin (ATX, also known as ectonucleotide pyrophosphatase/phosphodiesterase-2, ENPP2) is a secreted lysophospholipase D that generates the lipid mediator lysophosphatidic acid (LPA), a mitogen and chemoattractant for many cell types. ATX-LPA signaling is involved in various pathologies including tumor progression and inflammation. However, the molecular basis of substrate recognition and catalysis by ATX and the mechanism by which it interacts with target cells are unclear. Here, we present the crystal structure of ATX, alone and in complex with a small-molecule inhibitor. We have identified a hydrophobic lipid-binding pocket and mapped key residues for catalysis and selection between nucleotide and phospholipid substrates. We have shown that ATX interacts with cell-surface integrins through its N-terminal somatomedin B-like domains, using an atypical mechanism. Our results define determinants of substrate discrimination by the ENPP family, suggest how ATX promotes localized LPA signaling and suggest new approaches for targeting ATX with small-molecule therapeutic agents.

Hausmann, Jens; Kamtekar, Satwik; Christodoulou, Evangelos; Day, Jacqueline E.; Wu, Tao; Fulkerson, Zachary; Albers, Harald M.H.G.; van Meeteren, Laurens A.; Houben, Anna J.S.; van Zeijl, Leonie; Jansen, Silvia; Andries, Maria; Hall, Troii; Pegg, Lyle E.; Benson, Timothy E.; Kasiem, Mobien; Harlos, Karl; Vander Kooi, Craig W.; Smyth, Susan S.; Ovaa, Huib; Bollen, Mathieu; Morris, Andrew J.; Moolenaar, Wouter H.; Perrakis, Anastassis (Pfizer); (Leuven); (Oxford); (NCI-Netherlands); (Kentucky)

2013-09-25T23:59:59.000Z

212

Invisible surface defects in a tight-binding lattice  

E-Print Network [OSTI]

Surface Tamm states arise in one-dimensional lattices from some defects at the lattice edge and their energy generally falls in a gap of the crystal. The defects at the surface change rather generally the phase of propagative Bloch waves scattered off at the lattice edge, so that an observer, far from the surface, can detect the existence of edge defects from e.g. time-of-flight measurements as a delay or an advancement of a Bloch wave packet. Here we show that a special class of defects can sustain surface Tamm states which are invisible, in a sense that reflected waves acquire the same phase as in a fully homogeneous lattice with no surface state. Surface states have an energy embedded into the tight-binding lattice band and show a lower than exponential (algebraic) localization. Like most of bound states in the continuum of von Neumann - Wigner type, such states are fragile and decay into resonance surface states in presence of perturbations or lattice disorder. The impact of structural lattice imperfections and disorder on the invisibility of the defects is investigated by numerical simulations.

Stefano Longhi

2014-06-24T23:59:59.000Z

213

http://www.isc.tohoku.ac.jp/map.html 1 Dr. Jan Hrdlicka (Czech Technical University in Prague, Czech Republic)  

E-Print Network [OSTI]

(Czech Technical University in Prague, Czech Republic) · Renewable energy in Europe: Wind and solar a trend during last years and current problems with wind power installation in Northern Germany (impact current situation with the energy share for electricity generation in Europe and the present state

Murota, Kazuo

214

Dynamic Nuclear Polarization Study of Inhibitor Binding to the M2[subscript 1860] Proton Transporter from Influenza A  

E-Print Network [OSTI]

We demonstrate the use of dynamic nuclear polarization (DNP) to elucidate ligand binding to a membrane protein using dipolar recoupling magic angle spinning (MAS) NMR. In particular, we detect drug binding in the proton ...

Andreas, Loren B.

215

Effect of primer binding probability on amplified misprimed DNA by means of a computational study on the polymerase chain reaction  

E-Print Network [OSTI]

parameters are provided and the effects discussed. Finally, the conclusions are presented. It is noted that there was effect of the primer binding probability on the production of amplified DNA of interest in the presence of multiple binding sites...

Gopalakrishnan, Sanjay

1999-01-01T23:59:59.000Z

216

End-to-End Support for QoS-Aware Service Selection, Binding and Mediation in VRESCo  

E-Print Network [OSTI]

to them (see Figure 1b). Service Contract Service Registry Service Provider Service Consumer Bind/Execute PublishFind (a) SOA Model Service Contract Service Provider Service Consumer Bind/Execute (b) SOA Practice

Dustdar, Schahram

217

NMR studies of DNA oligomers and their interactions with minor groove binding ligands  

SciTech Connect (OSTI)

The cationic peptide ligands distamycin and netropsin bind noncovalently to the minor groove of DNA. The binding site, orientation, stoichiometry, and qualitative affinity of distamycin binding to several short DNA oligomers were investigated by NMR spectroscopy. The oligomers studied contain A,T-rich or I,C-rich binding sites, where I = 2-desaminodeoxyguanosine. I{center_dot}C base pairs are functional analogs of A{center_dot}T base pairs in the minor groove. The different behaviors exhibited by distamycin and netropsin binding to various DNA sequences suggested that these ligands are sensitive probes of DNA structure. For sites of five or more base pairs, distamycin can form 1:1 or 2:1 ligand:DNA complexes. Cooperativity in distamycin binding is low in sites such as AAAAA which has narrow minor grooves, and is higher in sites with wider minor grooves such as ATATAT. The distamycin binding and base pair opening lifetimes of I,C-containing DNA oligomers suggest that the I,C minor groove is structurally different from the A,T minor groove. Molecules which direct chemistry to a specific DNA sequence could be used as antiviral compounds, diagnostic probes, or molecular biology tools. The author studied two ligands in which reactive groups were tethered to a distamycin to increase the sequence specificity of the reactive agent.

Fagan, P.A. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry]|[Lawrence Berkeley National Lab., CA (United States). Structural Biology Div.

1996-05-01T23:59:59.000Z

218

Receptor binding characteristics of tritiated misoprostol free acid in enriched canine parietal cells  

SciTech Connect (OSTI)

Misoprostol (MISO) is a synthetic prostaglandin (PG) E/sub 1/ methyl ester with gastric antisecretory and mucosal protective properties. MISO is rapidly de-esterified to misoprostol free acid (MISO-FA) in enriched (65-80%) canine parietal cell preparations. Both forms appear to possess equivalent antisecretory potency and (/sup 3/H) MISO-FA is stable in these preparations. (/sup 3/H) MISO-FA binding was reversible and saturable with a maximal number of binding sites estimated at 8138 +/- 1893 per cell. The scatchard plot was linear, indicating a single, high affinity receptor population with a dissociation constant of 11 +/- 2.6 x 10/sup -9/ M. Unlabeled MISO-FA and MISO were equally potent inhibitors (IC/sub 50/, approx. 10/sup -8/M) of (/sup 3/H) MISO-FA binding. At 10/sup -5/ M, the dinor and tetranor ..beta..-oxidation metabolites of MISO were weak binding inhibitors. Strict stereospecific binding was shown by MISO stereoisomers, and the 11R, 16S isomer was most active. Both PGE/sub 1/ and 16,16 dimethyl PGE/sub 2/ were potent binding inhibitors, but PGF/sub 1/..cap alpha.. (10/sup -6/ M) and Hoe 892 (10/sup -5/ M), a stable PGI/sub 2/ analog, were weak inhibitors. Neither histamine or cimetidine competed for binding sites. These data indicate the presence of stereospecific E-type prostaglandin receptors in enriched canine parietal cell preparations.

Tsai, B.S.; Kessler, L.K.; Conway, R.G.; Schoenhard, G.; Stolzenbach, J.; Collins, P.; Kramer, S.; Butchko, G.M.; Bauer, R.F.

1986-03-01T23:59:59.000Z

219

Z .Biochimica et Biophysica Acta 1342 1997 164174 Calcium binding to recoverin: implications for secondary structure and  

E-Print Network [OSTI]

a calcium-binding loop com- 0167-4838r97r$17.00 q 1997 Elsevier Science B.V. All rights reserved. Z .PII SZ .Biochimica et Biophysica Acta 1342 1997 164­174 Calcium binding to recoverin: implications Received 15 May 1997; accepted 30 May 1997 Abstract Recoverin is an EF-hand calcium-binding protein

Palczewski, Krzysztof

220

A Novel, Modification-Dependent ATP-Binding Aptamer Selected from an RNA Library Incorporating a Cationic Functionality  

E-Print Network [OSTI]

A Novel, Modification-Dependent ATP-Binding Aptamer Selected from an RNA Library Incorporating this library yielded a novel receptor that binds ATP under physiological pH and salt conditions in a manner structure model for the ATP binding site were obtained by the analysis of functional sequences selected from

Heller, Eric

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


221

A Two-site Kinetic Mechanism for ATP Binding and Hydrolysis by E. coli Rep Helicase Dimer Bound to a  

E-Print Network [OSTI]

A Two-site Kinetic Mechanism for ATP Binding and Hydrolysis by E. coli Rep Helicase Dimer Bound that are coupled to ATP binding and hydrolysis. We have investi- gated the kinetic mechanism of ATP binding 17(?2) s?1 ; KM 3 mM), pre-steady-state studies provide evidence for a two-ATP site mechanism

Lohman, Timothy M.

222

Biochemistry 1994,33, 14565-14578 14565 Kinetic Mechanism of Adenine Nucleotide Binding to and Hydrolysis by the  

E-Print Network [OSTI]

Biochemistry 1994,33, 14565-14578 14565 Kinetic Mechanism of Adenine Nucleotide Binding nucleotides, we have investigated the kinetic mechanism of adenine nucleotide binding to the Rep monomer not significantly change the intrinsic tryptophan fluorescence, the binding of the fluorescent nucleotide analogue

Lohman, Timothy M.

223

Partial proteolytic digestion of the mammary prolactin receptor: Identification of smaller prolactin binding fragments  

SciTech Connect (OSTI)

Partial proteolytic digestion of the mammary prolactin (PRL) receptor was used to generate receptor fragments and analyze their immunoreactivity and PRL binding properties. Tryptic digestion of the PRL receptor produced two immunoreactive fragments (Mr approximately 30,000 and approximately 15,000) that reacted with a monoclonal anti-PRL receptor antibody and still specifically bound PRL, while the complete immunoreactive PRL binding unit (Mr approximately 42,000) disappeared. Neither chymotrypsin nor V8 protease were able to generate any immunoreactive receptor fragments. These receptor fragments may represent smaller PRL binding receptor form(s) of biological significance.

Dusanter-Fourt, I.; Kelly, P.A.; Djiane, J. (Institut National de la Recherche Agronomique, Jouy-en-Josas (France))

1990-01-01T23:59:59.000Z

224

GABA{sub A} receptor open-state conformation determines non-competitive antagonist binding  

SciTech Connect (OSTI)

The {gamma}-aminobutyric acid (GABA) type A receptor (GABA{sub A}R) is one of the most important targets for insecticide action. The human recombinant {beta}3 homomer is the best available model for this binding site and 4-n-[{sup 3}H]propyl-4'-ethynylbicycloorthobenzoate ([{sup 3}H]EBOB) is the preferred non-competitive antagonist (NCA) radioligand. The uniquely high sensitivity of the {beta}3 homomer relative to the much-less-active but structurally very-similar {beta}1 homomer provides an ideal comparison to elucidate structural and functional features important for NCA binding. The {beta}1 and {beta}3 subunits were compared using chimeragenesis and mutagenesis and various combinations with the {alpha}1 subunit and modulators. Chimera {beta}3/{beta}1 with the {beta}3 subunit extracellular domain and the {beta}1 subunit transmembrane helices retained the high [{sup 3}H]EBOB binding level of the {beta}3 homomer while chimera {beta}1/{beta}3 with the {beta}1 subunit extracellular domain and the {beta}3 subunit transmembrane helices had low binding activity similar to the {beta}1 homomer. GABA at 3 {mu}M stimulated heteromers {alpha}1{beta}1 and {alpha}1{beta}3 binding levels more than 2-fold by increasing the open probability of the channel. Addition of the {alpha}1 subunit rescued the inactive {beta}1/{beta}3 chimera close to wildtype {alpha}1{beta}1 activity. EBOB binding was significantly altered by mutations {beta}1S15'N and {beta}3N15'S compared with wildtype {beta}1 and {beta}3, respectively. However, the binding activity of {alpha}1{beta}1S15'N was insensitive to GABA and {alpha}1{beta}3N15'S was stimulated much less than wildtype {alpha}1{beta}3 by GABA. The inhibitory effect of etomidate on NCA binding was reduced more than 5-fold by the mutation {beta}3N15'S. Therefore, the NCA binding site is tightly regulated by the open-state conformation that largely determines GABA{sub A} receptor sensitivity. - Graphical Abstract: Display Omitted Research Highlights: > The {beta}1 and {beta}3 subunits were compared by chimeragenesis, mutagenesis and modulators. > Low {beta}1 NCA binding was rescued by replacing its transmembrane helices with those of {beta}3. > GABA at 3 {mu}M stimulated heteromers {alpha}1{beta}1 and {alpha}1{beta}3 binding levels more than 2-fold. > Mutation at 15' position in TM2 reduced GABA stimulation of NCA binding. > The open-state conformation largely determines GABAA receptor sensitivity to NCAs.

Chen Ligong [Environmental Chemistry and Toxicology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720 (United States); Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 (United States); Xue Ling [Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 (United States); Giacomini, Kathleen M. [Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 (United States); Casida, John E., E-mail: ectl@berkeley.edu [Environmental Chemistry and Toxicology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720 (United States)

2011-02-01T23:59:59.000Z

225

Method for detecting binding events using micro-X-ray fluorescence spectrometry  

DOE Patents [OSTI]

Method for detecting binding events using micro-X-ray fluorescence spectrometry. Receptors are exposed to at least one potential binder and arrayed on a substrate support. Each member of the array is exposed to X-ray radiation. The magnitude of a detectable X-ray fluorescence signal for at least one element can be used to determine whether a binding event between a binder and a receptor has occurred, and can provide information related to the extent of binding between the binder and receptor.

Warner, Benjamin P. (Los Alamos, NM); Havrilla, George J. (Los Alamos, NM); Mann, Grace (Hong Kong, HK)

2010-12-28T23:59:59.000Z

226

PEVK Domain of Titin: An Entropic Spring with Actin-Binding Properties  

E-Print Network [OSTI]

as an entropic spring with the properties of a random coil exhibiting mechanical conforma- tions of differentPEVK Domain of Titin: An Entropic Spring with Actin-Binding Properties Wolfgang A. Linke,*,1

Fernandez, Julio M.

227

Nuclear Magnetic Resonance based Characterization of the Protein Binding Pocket using Hyperpolarized Ligand  

E-Print Network [OSTI]

Polarization (DNP) combined with Nuclear Magnetic Resonance (NMR) has emerged as a new tool for studying interactions between different molecules. In this study, the DNP-NMR technique was employed for characterization of the protein binding pocket through...

Min, Hlaing

2014-08-04T23:59:59.000Z

228

E-Print Network 3.0 - atp-binding cassette subfamily Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette subfamily Page: << < 1 2 3 4 5 > >> 1 PharmGKB Submission Update: IV....

229

E-Print Network 3.0 - atp binding site Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

site Search Powered by Explorit Topic List Advanced Search Sample search results for: atp binding site Page: << < 1 2 3 4 5 > >> 1 ATP Utilization by Yeast Replication Factor C II....

230

E-Print Network 3.0 - atp-binding protein evolved Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

evolved Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding protein evolved Page: << < 1 2 3 4 5 > >> 1 Chemistry & Biology, Vol. 11,...

231

E-Print Network 3.0 - atp-binding cassette abc Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

abc Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette abc Page: << < 1 2 3 4 5 > >> 1 PharmGKB Submission Update: IV. PMT...

232

E-Print Network 3.0 - atp-binding cassette multidrug Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette multidrug Page: << < 1 2 3 4 5 > >> 1 LIST OF PUBLICATONS Sakamoto, K....

233

E-Print Network 3.0 - atp binding residues Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Search Powered by Explorit Topic List Advanced Search Sample search results for: atp binding residues Page: << < 1 2 3 4 5 > >> 1 Asymmetric deceleration of ClpB or Hsp104...

234

E-Print Network 3.0 - atp binding domain Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

domain Search Powered by Explorit Topic List Advanced Search Sample search results for: atp binding domain Page: << < 1 2 3 4 5 > >> 1 ATP Utilization by Yeast Replication Factor C...

235

E-Print Network 3.0 - atp-binding motifs play Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

play Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding motifs play Page: << < 1 2 3 4 5 > >> 1 Chemistry & Biology, Vol. 11, 865874,...

236

E-Print Network 3.0 - atp binding protein Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

protein Search Powered by Explorit Topic List Advanced Search Sample search results for: atp binding protein Page: << < 1 2 3 4 5 > >> 1 Biochemistry 1989, 28, 5871-5881 5871...

237

E-Print Network 3.0 - atp-binding cassette systems Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

systems Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette systems Page: << < 1 2 3 4 5 > >> 1 PharmGKB Submission Update: IV....

238

E-Print Network 3.0 - atp-binding site lesions Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

lesions Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding site lesions Page: << < 1 2 3 4 5 > >> 1 NEM modication prevents high-anity ATP...

239

Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex  

E-Print Network [OSTI]

DRM is a conserved transcription factor complex that includes E2F/DP and pRB family proteins and plays important roles in development and cancer. Here we describe new aspects of DRM binding and function revealed through ...

Tabuchi, Tomoko M.

240

E-Print Network 3.0 - at-rich sequence-binding protein-1 Sample...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

2003, Copyright 2003 by Cell Press ReviewEnigmatic Variations Summary: 6 and Cdt1 with ORC allows complex binds to asymmetric AT-rich sequences and the complex to load... for...

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


241

Control of HslUV protease function by nucleotide binding and hydrolysis  

E-Print Network [OSTI]

Many proteins act as molecular machines, using the power of nucleotide binding and hydrolysis to drive conformational changes in themselves and their target substrates. Like other AAA+ proteases, HslUV recognizes, unfolds, ...

Yakamavich, Joseph Andrew

2008-01-01T23:59:59.000Z

242

Stabilizing the cystic fibrosis transmembrane conductance regulator (CFTR) by nucleotide derivative binding to promote proper folding  

E-Print Network [OSTI]

Seventy percent of people who suffer from cystic fibrosis have a cystic fibrosis transmembrane conductance regulator gene on chromosome 7 that contains a three base-pair deletion of phenylalanine at position 508, in a nucleotide binding domain...

Smith, Ryan Craig

2013-02-22T23:59:59.000Z

243

Nucleotide Binding and Conformational Switching in the Hexameric Ring of a AAA+ Machine  

E-Print Network [OSTI]

ClpX, a AAA+ ring homohexamer, uses the energy of ATP binding and hydrolysis to power conformational changes that unfold and translocate target proteins into the ClpP peptidase for degradation. In multiple crystal structures, ...

Stinson, Benjamin Michael

244

Structures of Human Pumilio with Noncognate RNAs Reveal Molecular Mechanisms for Binding Promiscuity  

SciTech Connect (OSTI)

Pumilio is a founder member of the evolutionarily conserved Puf family of RNA-binding proteins that control a number of physiological processes in eukaryotes. A structure of human Pumilio (hPum) Puf domain bound to a Drosophila regulatory sequence showed that each Puf repeat recognizes a single nucleotide. Puf domains in general bind promiscuously to a large set of degenerate sequences, but the structural basis for this promiscuity has been unclear. Here, we describe the structures of hPum Puf domain complexed to two noncognate RNAs, CycBreverse and Puf5. In each complex, one of the nucleotides is ejected from the binding surface, in effect, acting as a 'spacer.' The complexes also reveal the plasticity of several Puf repeats, which recognize noncanonical nucleotides. Together, these complexes provide a molecular basis for recognition of degenerate binding sites, which significantly increases the number of mRNAs targeted for regulation by Puf proteins in vivo.

Gupta,Y.; Nair, D.; Wharton, R.; Aggarwal, A.

2008-01-01T23:59:59.000Z

245

E-Print Network 3.0 - assisted binding site Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Press 4994--5002 Nucleic Acids Research, 1997, Vol. 25, No. 24 Summary: analysis of Fis binding sites Paul N. Hengen 1 , Stacy L. Bartram 1,2,+ , Lisa E. Stewart 1 and Thomas...

246

A Rationally-designed Fluorescence Competitive Binding Assay for Continuous Glucose Monitoring Applications  

E-Print Network [OSTI]

on the protein, Concanavalin A. However, to date, this assay has continually shown problems with sensitivity, stability, and reversibility in free solution. This work uses rational design to generate a new version of the competitive binding assay that can...

Cummins, Brian Michael

2014-03-18T23:59:59.000Z

247

Structural and functional consequences of platinum anticancer drug binding to free and nucleosomal DNA  

E-Print Network [OSTI]

Cisplatin, carboplatin, and oxaliplatin are three FDA-approved members of the platinum anticancer drug family. These compounds induce apoptosis in tumor cells by binding to nuclear DNA, forming a variety of adducts, and ...

Todd, Ryan Christopher, 1981-

2010-01-01T23:59:59.000Z

248

Engineering and targeting glycan receptor binding of influenza A virus hemagglutinin  

E-Print Network [OSTI]

The critical first step in the host infection by influenza A virus is the binding of the viral surface glycoprotein hemagglutinin (HA) to the sialylated glycan receptors terminated by N-acetyineuraminic acid (Neu5Ac) ...

Jayaraman, Akila

2011-01-01T23:59:59.000Z

249

acyl-coa binding protein: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 131 A High-Throughput Solid-Phase Microplate Protein-Binding Assay to...

250

ap-2alpha binding site: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 53 Similarity Analysis of Protein Binding Sites: A Generalization of the...

251

acyl-coa binding proteins: Topics by E-print Network  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 131 A High-Throughput Solid-Phase Microplate Protein-Binding Assay to...

252

Analysis of variation at transcription factor binding sites in Drosophila and humans  

E-Print Network [OSTI]

Background: Advances in sequencing technology have boosted population genomics and made it possible to map the positions of transcription factor binding sites (TFBSs) with high precision. Here we investigate TFBS variability ...

Spivakov, Mikhail

253

2D IR spectroscopy and computational modeling : application to protein folding and binding  

E-Print Network [OSTI]

In this thesis, dynamics experiments are developed that can be used to study protein conformational changes such as folding and binding. Every functional motion of a protein is inextricably linked to conformational dynamics. ...

Ganim, Ziad

2010-01-01T23:59:59.000Z

254

Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations  

E-Print Network [OSTI]

Conformational Transitions upon Ligand Binding: Holo- Structure Prediction from Apo Conformations Daniel Seeliger, Bert L. de Groot* Computational Biomolecular Dynamics Group, Max design. Hence, if only an unbound (apo) structure is available distinct from the ligand

de Groot, Bert

255

Networks of Coupled Rotators: Relationship between Structures and Internal Dynamics in Metal-Binding Proteins.  

E-Print Network [OSTI]

-Binding Proteins. Applications to apo- and holo-Calbindin Anne Dhulesia, Daniel Abergel,* and Geoffrey Bodenhausen, France Received October 17, 2006; E-mail: daniel.abergel@ens.fr Abstract: This article presents

256

Lis1 Acts as a ``Clutch'' between the ATPase and Microtubule-Binding  

E-Print Network [OSTI]

and single-particle electron micro- scopy. We show that rather than binding to the main ATPase site within, even during cycles of ATP hydro- lysis that would canonically induce detachment. Thus, Lis1 operates

257

E-Print Network 3.0 - allele specific binding Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Infectieuses (GEMI), UMR CNRS-IRD 2724 UR 165 Collection: Biology and Medicine 9 J Forensic Sci, July 2004, Vol. 49, No. 4 Paper ID JFS2004032 Summary: to primer binding site...

258

Effects of dietary fiber and carcinogen on fatty acid binding protein expression in exfoliated colonocytes  

E-Print Network [OSTI]

EFFECTS OF DIETARY FIBER AND CARCINOGEN ON FATTY ACID BINDING PROTEIN EXPRESSION IN EXFOLIATED COLONOCYTES A Thesis by AMY EUNICE CLARK Submitted to the Office of Gmduate Studies of Texas A&M University in partial fulfillment...) Bryan H. Johnson (Head of Department) August 1997 Major Subject: Nutrition ABSTRACT Effects of Dietary Fiber and Carcinogen on Fatty Acid Binding Protein Expression in Exfoliated Colonocytes. (August 1997) Amy Eunice Clark, B. S. , Texas A...

Clark, Amy Eunice

1997-01-01T23:59:59.000Z

259

Studies on immunoglobulins and complement binding to the surface of Schistosoma mansoni  

E-Print Network [OSTI]

). Tavares et al. (32) demonstrated that mice treated with cobra venom factor (CVF) (inactivates C 3) increased significantly the worm burden of immune mice suggesting that an in vivo involvement of the complement system in the effector mechanisms occurs... of specific ant1-schistosome antibody. Fresh worms were not able to demonstrate specific anti- schistosome antibody binding, suggesting a protective role for adsorbed serum components. The binding of complement component C 3 in the surface pits...

Rasmussen, Kathleen Ruth

1983-01-01T23:59:59.000Z

260

Internal binding sites for MSH: Analyses in wild-type and variant Cloudman melanoma cells  

SciTech Connect (OSTI)

Cloudman S91 mouse melanoma cells express both external (plasma membrane) and internal binding sites for MSH. Using 125I-beta melanotropin (beta-MSH) as a probe, we report here an extensive series of studies on the biological relevance of these internal sites. Cells were swollen in a hypotonic buffer and lysed, and a particulate fraction was prepared by high-speed centrifugation. This fraction was incubated with 125I-beta-MSH with or without excess nonradioactive beta-MSH in the cold for 2 hours. The material was then layered onto a step-wise sucrose gradient and centrifuged; fractions were collected and counted in a gamma counter or assayed for various enzymatic activities. The following points were established: (1) Specific binding sites for MSH were observed sedimenting at an average density of 50% sucrose in amelanotic cells and at higher densities in melanotic cells. (2) These sites were similar in density to those observed when intact cells were labeled externally with 125I-beta-MSH and then warmed to promote internalization of the hormone. (3) Most of the internal binding sites were not as dense as fully melanized melanosomes. (4) In control experiments, the MSH binding sites were not found in cultured hepatoma cells. (5) Variant melanoma cells, which differed from the wild-type in their responses to MSH, had reduced expression of internal binding sites even though their ability to bind MSH to the outer cell surface appeared normal. (MSH-induced responses included changes in tyrosinase, dopa oxidase, and dopachrome conversion factor activities, melanization, proliferation, and morphology.) (6) Isobutylmethylxanthine, which enhanced cellular responsiveness to MSH, also enhanced expression of internal binding sites. The results indicate that expression of internal binding sites for MSH is an important criterion for cellular responsiveness to the hormone.

Orlow, S.J.; Hotchkiss, S.; Pawelek, J.M. (Yale Univ. School of Medicine, New Haven, CT (USA))

1990-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


261

Purification and expression of fatty acid binding proteins in chicken liver and intestine  

E-Print Network [OSTI]

PURIFICATION AND EXPRESSION OF FATTY ACID BINDING PROTEINS IN CHICKEN LIVER AND INTESTINE A Thesis by JULIA ELLEN SEWELL Submitted to the Graduate College of Texas A&M University in partial fulfillment of the requirements for the degree... of MASTER OF SCIENCE August 1988 Major subject: Nutrition PURIFICATION AND EXPRESSION OF FATTY ACID BINDING PROTEINS IN CHICKEN LIVER AND INTESTINE A Thesis by JULIA ELLEN SEWELL Approved as to style and content by: Pamela S. Hargi (Chair of Committ...

Sewell, Julia Ellen

1988-01-01T23:59:59.000Z

262

AK---------Adaptive Kernel estimates of home-range BLM-------Bureau of Land Management (USDI)  

E-Print Network [OSTI]

Conservation Areas IPs --------- Industrial Private (Timber Companies) ISC -------- Interagency Scientific

Standiford, Richard B.

263

Binding proteins for growth hormone and prolactin in rabbit kidney cytosol  

SciTech Connect (OSTI)

Two soluble, receptor-like binding proteins with apparent somatotrophic (growth hormone (GH)) and lactogenic (prolactin (PRL)) specificities, respectively, and that are present in rabbit kidney cytosol have now been examined in more detail using specific GH receptor and PRL receptor monoclonal antibodies (MAb). Gel chromatography of {sup 125}I-labeled human GH ({sup 125}I-hGH) kidney cytosol complexes in the absence of these MAbs revealed two specifically bound regions of radioactivity at molecular weights (MW) of {approximately}120,000 and {approximately}60,000, which are similar in size to complexes formed by the native GH receptor of rabbit liver cytosol and the PRL receptor of mammary gland. Co-incubation with GH-receptor MAb inhibited {sup 125}I-hGH binding only to the higher MW (120,000) species, whereas the PRL-receptor MAb inhibited only the lower MW (60,000) species, thus establishing definitively the hormonal specificities of the two binding proteins. The presence of both GH- and PRL-specific binding subunits in cytosol was confirmed using covalent cross-linking techniques. No GH binding protein was detected in kidney membranes. The presence of naturally soluble, receptor-like binding proteins for GH and PRL in kidney cytosol preparations raises the possibility of their playing a role in the intracellular regulation of kidney function and/or metabolism.

Herington, A.C.; Stevenson, J.L.; Ymer, S.I. (Prince Henry's Hospital, Melbourne (Australia))

1988-09-01T23:59:59.000Z

264

Binding of He{sub n}V clusters to ?-Fe grain boundaries  

SciTech Connect (OSTI)

The objective of this research is to explore the formation/binding energetics and length scales associated with the interaction between He{sub n}V clusters and grain boundaries in bcc ?-Fe. In this work, we calculated formation/binding energies for 18 He atoms in a monovacancy at all potential grain boundary (GB) sites within 15? of the ten grain boundaries selected (122106 simulations total). The present results provide detailed information about the interaction energies and length scales of 18 He atoms with grain boundaries for the structures examined. A number of interesting new findings emerge from the present study. First, the ?3(112) twin GB has significantly lower binding energies for all He{sub n}V clusters than all other boundaries in this study. For all grain boundary sites, the effect of the local environment surrounding each site on the He{sub n}V formation and binding energies decreases with an increasing number of He atoms in the He{sub n}V cluster. Based on the calculated dataset, we formulated a model to capture the evolution of the formation and binding energy of He{sub n}V clusters as a function of distance from the GB center, utilizing only constants related to the maximum binding energy and the length scale.

Tschopp, M. A., E-mail: mark.a.tschopp.civ@mail.mil [U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States); Gao, F. [Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Solanki, K. N. [Arizona State University, Tempe, Arizona 85287 (United States)

2014-06-21T23:59:59.000Z

265

Nucleotide Binding Site Communication in Arabidopsis thaliana Adenosine 5;-Phosphosulfate Kinase  

SciTech Connect (OSTI)

Adenosine 5{prime}-phosphosulfate kinase (APSK) catalyzes the ATP-dependent synthesis of adenosine 3{prime}-phosphate 5{prime}-phosphosulfate (PAPS), which is an essential metabolite for sulfur assimilation in prokaryotes and eukaryotes. Using APSK from Arabidopsis thaliana, we examine the energetics of nucleotide binary and ternary complex formation and probe active site features that coordinate the order of ligand addition. Calorimetric analysis shows that binding can occur first at either nucleotide site, but that initial interaction at the ATP/ADP site was favored and enhanced affinity for APS in the second site by 50-fold. The thermodynamics of the two possible binding models (i.e. ATP first versus APS first) differs and implies that active site structural changes guide the order of nucleotide addition. The ligand binding analysis also supports an earlier suggestion of intermolecular interactions in the dimeric APSK structure. Crystallographic, site-directed mutagenesis, and energetic analyses of oxyanion recognition by the P-loop in the ATP/ADP binding site and the role of Asp136, which bridges the ATP/ADP and APS/PAPS binding sites, suggest how the ordered nucleotide binding sequence and structural changes are dynamically coordinated for catalysis.

Ravilious, Geoffrey E.; Jez, Joseph M. (WU)

2012-08-31T23:59:59.000Z

266

Internal strain regulates the nucleotide binding site of the kinesin leading head  

E-Print Network [OSTI]

In the presence of ATP, kinesin proceeds along the protofilament of microtubule by alternated binding of two motor domains on the tubulin binding sites. Since the processivity of kinesin is much higher than other motor proteins, it has been speculated that there exists a mechanism for allosteric regulation between the two monomers. Recent experiments suggest that ATP binding to the leading head domain in kinesin is regulated by the rearward strain built on the neck-linker. We test this hypothesis by explicitly modeling a $C_{\\alpha}$-based kinesin structure whose both motor domains are bound on the tubulin binding sites. The equilibrium structures of kinesin on the microtubule show disordered and ordered neck-linker configurations for the leading and the trailing head, respectively. The comparison of the structures between the two heads shows that several native contacts present at the nucleotide binding site in the leading head are less intact than those in the binding site of the rear head. The network of n...

Hyeon, Changbong; 10.1073/pnas.0610939104

2009-01-01T23:59:59.000Z

267

Structural basis for the evolutionary inactivation of Ca[superscript 2+] binding to synaptotagmin 4  

SciTech Connect (OSTI)

The neuronal protein synaptotagmin 1 functions as a Ca{sup 2+} sensor in exocytosis via two Ca{sup 2+}-binding C{sub 2} domains. The very similar synaptotagmin 4, which includes all the predicted Ca{sup 2+}-binding residues in the C{sub 2}B domain but not in the C{sub 2}A domain, is also thought to function as a neuronal Ca{sup 2+} sensor. Here we show that, unexpectedly, both C{sub 2} domains of fly synaptotagmin 4 exhibit Ca{sup 2+}-dependent phospholipid binding, whereas neither C{sub 2} domain of rat synaptotagmin 4 binds Ca{sup 2+} or phospholipids efficiently. Crystallography reveals that changes in the orientations of critical Ca{sup 2+} ligands, and perhaps their flexibility, render the rat synaptotagmin 4 C{sub 2}B domain unable to form full Ca{sup 2+}-binding sites. These results indicate that synaptotagmin 4 is a Ca{sup 2+} sensor in the fly but not in the rat, that the Ca{sup 2+}-binding properties of C{sub 2} domains cannot be reliably predicted from sequence analyses, and that proteins clearly identified as orthologs may nevertheless have markedly different functional properties.

Dai, Han; Shin, Ok-Ho; Machius, Mischa; Tomchick, Diana R.; Sdhof, Thomas C.; Rizo, Josep (U. of Texas-SMED)

2010-11-16T23:59:59.000Z

268

Divergence of Pumilio/fem-3 mRNA Binding Factor (PUF) Protein Specificity through Variations in an RNA-binding  

E-Print Network [OSTI]

sequence feature. Importantly, other PUF proteins lack the pocket and so do not discriminate upstream bases. A structure-based alignment reveals that these proteins lack key residues that would contact the cytosineDivergence of Pumilio/fem-3 mRNA Binding Factor (PUF) Protein Specificity through Variations

Sheridan, Jennifer

269

Nonspecific transcription factor binding reduces variability in transcription factor and target protein expression  

E-Print Network [OSTI]

Transcription factors (TFs) interact with a multitude of binding sites on DNA and partner proteins inside cells. We investigate how nonspecific binding/unbinding to such decoy binding sites affects the magnitude and time-scale of random fluctuations in TF copy numbers arising from stochastic gene expression. A stochastic model of TF gene expression, together with decoy site interactions is formulated. Distributions for the total (bound and unbound) and free (unbound) TF levels are derived by analytically solving the chemical master equation under physiologically relevant assumptions. Our results show that increasing the number of decoy binding sides considerably reduces stochasticity in free TF copy numbers. The TF autocorrelation function reveals that decoy sites can either enhance or shorten the time-scale of TF fluctuations depending on model parameters. To understand how noise in TF abundances propagates downstream, a TF target gene is included in the model. Intriguingly, we find that noise in the expression of the target gene decreases with increasing decoy sites for linear TF-target protein dose-responses, even in regimes where decoy sites enhance TF autocorrelation times. Moreover, counterintuitive noise transmissions arise for nonlinear dose-responses. In summary, our study highlights the critical role of molecular sequestration by decoy binding sites in regulating the stochastic dynamics of TFs and target proteins at the single-cell level.

Mohammad Soltani; Pavol Bokes; Zachary Fox; Abhyudai Singh

2015-04-14T23:59:59.000Z

270

Analytic, non-perturbative, gauge-invariant quantum chromodynamics: Nucleon scattering and binding potentials  

SciTech Connect (OSTI)

Removal of the quenched approximation in the mechanism which produced an analytic estimate of quark-binding potentials, along with a reasonable conjecture of the color structure of the nucleon formed by such a binding potential, is shown to generate an effective nucleon scattering and binding potential. The mass-scale factor on the order of the pion mass, previously introduced to define the transverse imprecision of quark coordinates, is again used, while the strength of the potential is proportional to the square of a renormalized quantum chromodynamics (QCD) coupling constant. The potential so derived does not include corrections due to spin, angular momentum, nucleon structure, and electroweak interactions; rather, it is qualitative in nature, showing how Nuclear Physics can arise from fundamental QCD. -- Highlights: Nucleonnucleon forces are derived qualitatively from basic realistic quantum chromodynamics. An effective nucleon binding is obtained from the simplest unquenched approximation. A model deuteron binding energy of ?2.2 MeV follows with ?{sub s,R}=12.5.

Fried, H.M. [Physics Department, Brown University, Providence, RI 02912 (United States)] [Physics Department, Brown University, Providence, RI 02912 (United States); Gabellini, Y.; Grandou, T. [Universit de Nice Sophia-Antipolis, Institut Non Linaire de Nice, UMR 6618 CNRS, 06560 Valbonne (France)] [Universit de Nice Sophia-Antipolis, Institut Non Linaire de Nice, UMR 6618 CNRS, 06560 Valbonne (France); Sheu, Y.-M., E-mail: ymsheu@alumni.brown.edu [Universit de Nice Sophia-Antipolis, Institut Non Linaire de Nice, UMR 6618 CNRS, 06560 Valbonne (France)

2013-11-15T23:59:59.000Z

271

Analysis of the hormone-binding domain of steroid receptors using chimeras generated by homologous recombination  

SciTech Connect (OSTI)

The glucocorticoid receptor and the mineralocorticoid receptor are members of the steroid receptor family that exhibit ligand cross-reactivity. Specificity of steroid receptor action is investigated in the present work by the construction and characterization of chimeras between the glucocorticoid receptor and the mineralocorticoid receptor. We used an innovative approach to make novel steroid receptor proteins in vivo that in general, contrary to our expectations, show increased ligand specificity compared to the parental receptors. We describe a receptor that is specific for the potent synthetic glucocorticoid triamcinolone acetonide and does not bind aldosterone. A further set of chimeras has an increased ability to discriminate between ligands, responding potently to mineralocorticoids and only very weakly to synthetic glucocorticoids. A chimera with the fusion site in the hinge highlights the importance of the region between the DNA-binding and the hormone-binding domains since, unlike both the glucocorticoid and mineralocorticoid receptors, it only responds to mineralocorticoids. One chimera has reduced specificity in that it acts as a general corticoid receptor, responding to glucocorticoids and mineralocorticoids with similar potency and efficacy. Our data suggest that regions of the glucocorticoid and mineralocorticoid receptor hormone-binding domains are functionally non-reciprocal. We present transcriptional, hormone-binding, and structure-modeling evidence that suggests that receptor-specific interactions within and across domains mediate aspects of specificity in transcriptional responses to steroids.

Martinez, Elisabeth D. [Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, Washington, DC 20057 (United States); Pattabiraman, Nagarajan [Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, Washington, DC 20057 (United States); Department of Oncology, Georgetown University School of Medicine, Washington, DC 20057 (United States); Danielsen, Mark [Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, Washington, DC 20057 (United States)]. E-mail: dan@bc.georgetown.edu

2005-08-15T23:59:59.000Z

272

Association of Copper to Riboflavin Binding Protein; Characterization by EPR and XAS  

SciTech Connect (OSTI)

The association of copper to Riboflavin Binding Protein (RBP) from egg white has been studied by electron paramagnetic resonance (EPR) and X-ray absorption (XAS) spectroscopies. The type II site contains a mix of copper I and II in an oxygen rich environment. The association of copper to Riboflavin Binding Protein (RBP) from egg white has been studied by electron paramagnetic resonance (EPR) and X-ray absorption (XAS) spectroscopies in order to provide insight into how this essential protein may transport and store copper in avian embryos. Riboflavin Binding Protein, RBP, purified from avian egg white, has been shown to bind copper in a 1:1 molar ratio when dialyzed against copper(II) [1]. While the egg is a unique environment and quite rich in copper, the mechanisms by which this copper is delivered during development and stored for eventual use remain unclear [2]. Since RBP is already identified in the active transport of the cofactor riboflavin to the egg, evidence of its copper binding ability may suggest an additional role for RBP in the transport and storage of copper.

Smith,S.; Bencze, K.; Wasiukanis, K.; Stemmler, T.; Benore-Parsons, M.

2008-01-01T23:59:59.000Z

273

The effect of heat stress on 1,25-dihydroxycholecalciferol induced calcium-binding protein in laying hens  

E-Print Network [OSTI]

atoms of calcium per molecule of protein (Wasserman and Taylor, 1968), and although it has a high specificity for calcium, it may also bind strontium and barium. A mammalian intestinal calcium- binding protein having a molecular weight...THE EFFECT OF HEAT STRESS ON 1, 25-DIHYDROXYCHOLECALCIFEROL INDUCED CALCIUM-BINDING PROTEIN IN LAYING HENS A Thesis by BONNIE HARRIET KAY SCHAEFFER Submitted to the Office of Graduate Studies Texas AErM University in partial fulfillment...

Schaeffer, Bonnie Harriet Kay

2012-06-07T23:59:59.000Z

274

Different antagonist binding properties of rat pancreatic and cardiac muscarinic receptors  

SciTech Connect (OSTI)

The antagonist binding properties of rat pancreatic and cardiac muscarinic receptors were compared. In both tissues pirenzepine (PZ) had a low affinity for muscarinic receptors labelled by (/sup 3/H)N-methylscopolamine ((/sup 3/)NMS) (K/sub D/ values of 140 and 280nM, respectively, in pancreatic and cardiac homogenates). The binding properties of pancreatic and cardiac receptors were, however, markedly different. This was indicated by different affinities for dicyclomine, (11-(/(2-((diethylamino)-methyl)-1-piperidinyl/acetyl)-5, 11-dihydro-6H-pyrido(2,3-b)(1,4) benzodiazepin-6-on)(AFDX-116), 4-diphenylacetoxy-N-methyl-piperidine methobromide (4-DAMP) and hexahydrosiladifenidol (HHSiD). Pancreatic and cardiac muscarinic receptros also showed different (/sup 3/H)NMS association and dissociation rates. These results support the concept of M2 receptor subtypes have different binding kinetic properties. 20 references, 3 figures, 1 table.

Waelbroeck, M.; Camus, J.; Winand, J.; Christophe, J.

1987-11-09T23:59:59.000Z

275

Beyond position weight matrices: nucleotide correlations in transcription factor binding sites and their description  

E-Print Network [OSTI]

The identification of transcription factor binding sites (TFBSs) on genomic DNA is of crucial importance for understanding and predicting regulatory elements in gene networks. TFBS motifs are commonly described by Position Weight Matrices (PWMs), in which each DNA base pair independently contributes to the transcription factor (TF) binding, despite mounting evidence of interdependence between base pairs positions. The recent availability of genome-wide data on TF-bound DNA regions offers the possibility to revisit this question in detail for TF binding {\\em in vivo}. Here, we use available fly and mouse ChIPseq data, and show that the independent model generally does not reproduce the observed statistics of TFBS, generalizing previous observations. We further show that TFBS description and predictability can be systematically improved by taking into account pairwise correlations in the TFBS via the principle of maximum entropy. The resulting pairwise interaction model is formally equivalent to the disordered ...

Santolini, Marc; Hakim, Vincent

2013-01-01T23:59:59.000Z

276

Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint  

SciTech Connect (OSTI)

Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin ({sup 10}Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three {sup 10}Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibody combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the {beta} strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these {beta} strand interactions, indicating that these nonloop residues can expand the available binding footprint.

Ramamurthy, Vidhyashankar; Krystek, Jr., Stanley R.; Bush, Alexander; Wei, Anzhi; Emanuel, Stuart L.; Gupta, Ruchira Das; Janjua, Ahsen; Cheng, Lin; Murdock, Melissa; Abramczyk, Bozena; Cohen, Daniel; Lin, Zheng; Morin, Paul; Davis, Jonathan H.; Dabritz, Michael; McLaughlin, Douglas C.; Russo, Katie A.; Chao, Ginger; Wright, Martin C.; Jenny, Victoria A.; Engle, Linda J.; Furfine, Eric; Sheriff, Steven (BMS)

2014-10-02T23:59:59.000Z

277

LINC Complexes Form by Binding of Three KASH Peptides to Domain Interfaces of Trimeric SUN Proteins  

SciTech Connect (OSTI)

Linker of nucleoskeleton and cytoskeleton (LINC) complexes span the nuclear envelope and are composed of KASH and SUN proteins residing in the outer and inner nuclear membrane, respectively. LINC formation relies on direct binding of KASH and SUN in the perinuclear space. Thereby, molecular tethers are formed that can transmit forces for chromosome movements, nuclear migration, and anchorage. We present crystal structures of the human SUN2-KASH1/2 complex, the core of the LINC complex. The SUN2 domain is rigidly attached to a trimeric coiled coil that prepositions it to bind three KASH peptides. The peptides bind in three deep and expansive grooves formed between adjacent SUN domains, effectively acting as molecular glue. In addition, a disulfide between conserved cysteines on SUN and KASH covalently links both proteins. The structure provides the basis of LINC complex formation and suggests a model for how LINC complexes might arrange into higher-order clusters to enhance force-coupling.

Sosa, Brian A.; Rothballer, Andrea; Kutay, Ulrike; Schwartz, Thomas U. (MIT); (ETH Zurich)

2012-08-31T23:59:59.000Z

278

Molecular imaging of water binding state and diffusion in breast cancer using diffuse optical spectroscopy and diffusion weighted MRI  

E-Print Network [OSTI]

Molecular imaging of water binding state and diffusion inChung et al. , In vivo water state measurements in breastby measuring tis- sue water state using diffuse optical

Chung, So Hyun; Yu, Hon; Su, Min-Ying; Cerussi, Albert E.; Tromberg, Bruce J.

2012-01-01T23:59:59.000Z

279

Human Biliverdin Reductase Is a Leucine Zipper-like DNA-binding Protein and Functions in Transcriptional Activation of Heme  

E-Print Network [OSTI]

BVR DNA complex formation; and (e) purified preparations of hBVR or hHO-1 do not bind to DNA with two AP-1

Zulfiqar Ahmad

280

Expansion of the NRL Tight-Binding Method to Include f-orbitals and Application in Thorium and Actinium .  

E-Print Network [OSTI]

??The current NRL Tight-Binding suite of programs was designed to only include s, p, and d orbitals in the basis. Because of this limitation, materials (more)

Durgavich, Joel

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


281

Kits and methods of detection using cellulose binding domain fusion proteins  

DOE Patents [OSTI]

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL)

1998-01-01T23:59:59.000Z

282

Kits and methods of detection using cellulose binding domain fusion proteins  

DOE Patents [OSTI]

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

Shoseyov, O.; Yosef, K.

1998-04-14T23:59:59.000Z

283

Epigallocatechin gallate, the main polyphenol in green tea, binds to the T-cell receptor,  

E-Print Network [OSTI]

Epigallocatechin gallate, the main polyphenol in green tea, binds to the T-cell receptor, CD4D,b and William T. Shearer, MD, PhDb Sheffield, United Kingdom, and Houston, Tex Background: The green tea that is one of the main active components of green tea. Among the properties ascribed to EGCG

Williamson, Mike P.

284

Using electrospray ionization FTICR mass spectrometry to study competitive binding of inhibitors to carbonic anhydrase  

SciTech Connect (OSTI)

We report a method based on mass spectrometry for the characterization of noncovalent complexes of proteins with mixtures of ligands; this method is relevant to the study of drug leads and may be useful in screening libraries for tight-binding compounds. This study describes the competitive binding of inhibitors derived from para-substituted benzenesulfonamides to bovine carbonic anhydrase II (BCAII, EC 4.2.1.1) using this technique. Relative binding constants and structural information for a mixture of inhibitors can be obtained in a single experiment using ESI-FTICR-MS. The work demonstrates that ESI-MS has significant potential for measuring relative binding affinities and characterizing the structures of ligands associated noncovalently to proteins. We have detected noncovalent complexes in the gas phase for ligands having values of K{sub b} as low as 1.7 x 10{sup 6} M{sup -1} in solution. The technique also allowed identification of tightbinding ligands from small libraries. The structures of inhibitors having similar masses can be identified by the high-resolution and multistep dissociation mass spectrometry of which FTICR is uniquely capable. This range of capabilities for ESI-FTICR-MS should be widely useful in medicinal chemistry. 22 refs., 2 figs.

Cheng, X.; Chen, R.; Bruce, J.E.; Schwartz, B.L.; Anderson, G.A.; Hofstadler, S.A.; Gale, D.C.; Smith, R.D. [Pacific Northwest Lab., Richland, WA (United States); Gao, J.; Sigal, G.B.; Mammen, M.; Whitesides, G.M. [Harvard Univ., Cambridge, MA (United States)

1995-08-30T23:59:59.000Z

285

IN VITRO METABOLISM OF ZERANOL: EVALUATION OF COVALENT BINDING TO MICROSOMAL PROTEIN  

E-Print Network [OSTI]

). In contrast, for zeranol there is no information about the production of reactive metabolites of reactive metabolite production and of possible covalent binding of zeranol metabolite(s) to proteins using using a Beckmann ultracentrifuge (rotor 50). The microsomal pellet was suspended in 10 volumes of KCI

Paris-Sud XI, Université de

286

Serendipitous alkylation of a Plk1 ligand uncovers a new binding channel  

E-Print Network [OSTI]

We obtained unanticipated synthetic byproducts from alkylation of the ?[superscript 1] nitrogen (N3) of the histidine imidazole ring of the polo-like kinase-1 (Plk1) polo-box domain (PBD)-binding peptide PLHSpT. For the ...

Lim, Dan

287

Annu. Rev. Biophys. Biomol. Struct. 1998. 27:10531 MINOR GROOVE-BINDING  

E-Print Network [OSTI]

by architectural proteins that typically lack the potential to activate transcription or carry out recombinationAnnu. Rev. Biophys. Biomol. Struct. 1998. 27:10531 MINOR GROOVE-BINDING ARCHITECTURAL PROTEINS protein, HMG-box proteins, integration host factor, HMG I(Y), DNA bending ABSTRACT To date, high

Clore, G. Marius

288

Structural Basis for Simultaneous Binding of Two Carboxy-terminal Peptides of Plant Glutamate  

E-Print Network [OSTI]

of glutamate decarboxylase (GAD) by calcium-bound calmodulin (CaM) is required for normal plant growth through- otic cell-cycle rely on fine-tuned intracellular calcium (Ca2þ ) regulation for normal operation. Proteins containing the Ca2þ -binding EF-hand (helix-loop-helix) motif are known to be involved

Ikura, Mitsuhiko

289

Grafting odorant binding proteins on diamond bio-MEMS R. Manai a,  

E-Print Network [OSTI]

. Beside, cantilevers based on polycrystalline diamond surfaces are very promising as chemical transducers. Here two methods were investigated for chemically grafting porcine OBPs onto polycrystalline diamond1 Grafting odorant binding proteins on diamond bio-MEMS R. Manai a, *, E. Scorsone a , L. Rousseau

Boyer, Edmond

290

Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon  

E-Print Network [OSTI]

Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon (Cdc6)/Origin Replication Complex subunit 1 (Orc1) proteins share sequence homology with eukaryotic DNA under- stand whether Cdc6/Orc1 functions in an eukaryotic or bacterial-like manner, we have

Berger, James M.

291

Disordered graphene and boron nitride in a microwave tight-binding analogue S. Barkhofen,1  

E-Print Network [OSTI]

Disordered graphene and boron nitride in a microwave tight-binding analogue S. Barkhofen,1 M Sophia-Antipolis, 06108 Nice, France (Dated: December 20, 2012) Experiments on hexagonal graphene of the high flexibility of the discs positions, consequences of the disorder introduced in the graphene

Paris-Sud XI, Université de

292

Notch and MAML-1 Complexation Do Not Detectably Alter the DNA Binding Specificity of the Transcription  

E-Print Network [OSTI]

States of America Abstract Background: Canonical Notch signaling is initiated when ligand binding induces of Health/National Human Genome Research Institute to M.L.B. and grant # R01 CA092433 to S.C.B. The funders-mail: sblacklow@partners.org (SCB); mlbulyk@receptor.med.harvard.edu (MLB) a Current address: Cibio Centro

Bulyk, Martha L.

293

Estimating ProteinLigand Binding Free Energy: Atomic Solvation Parameters for Partition Coefficient and  

E-Print Network [OSTI]

on the assumption that the overall solvation free energy is the sum of all atomic solvation contributions: Gs iAi (1Estimating Protein­Ligand Binding Free Energy: Atomic Solvation Parameters for Partition Coefficient and Solvation Free Energy Calculation Jianfeng Pei,1,2 Qi Wang,1,2 Jiaju Zhou,3 and Luhua Lai1

Luhua, Lai

294

MODELING OF CAPILLARY FORCES AND BINDING SITES FOR FLUIDIC SELF-ASSEMBLY  

E-Print Network [OSTI]

MODELING OF CAPILLARY FORCES AND BINDING SITES FOR FLUIDIC SELF-ASSEMBLY Karl F. Böhringer 1-1774 ABSTRACT Massively parallel self-assembly is emerging as an efficient, low-cost alternative to conventional pick-and-place assembly of microfabricated components. The fluidic self-assembly technique we have

295

Eur. J. Biochem. 78, 585-598 (1977) Binding of Modified Adenine Nucleotides  

E-Print Network [OSTI]

Eur. J. Biochem. 78, 585-598 (1977) Binding of Modified Adenine Nucleotides to Isolated Coupling) 1. Fluorescent nucleotides (1,N6-ethenoadenosine diphosphate and triphosphate, EADP and EATP)replace the natural nucleotides rather efficiently (65- 85%) in several chloroplast reactions (ADP inhibition

Govindjee

296

Quantum confined Stark effect in Gaussian quantum wells: A tight-binding study  

SciTech Connect (OSTI)

The main characteristics of the quantum confined Stark effect (QCSE) are studied theoretically in quantum wells of Gaussian profile. The semi-empirical tight-binding model and the Green function formalism are applied in the numerical calculations. A comparison of the QCSE in quantum wells with different kinds of confining potential is presented.

Ramrez-Morales, A.; Martnez-Orozco, J. C.; Rodrguez-Vargas, I. [Unidad Acadmica de Fsica, Universidad Autnoma de Zacatecas, Calzada Solidaridad Esquina Con Paseo La Bufa S/N, 98060 Zacatecas, Zac. (Mexico)

2014-05-15T23:59:59.000Z

297

Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding and Binding Stability  

E-Print Network [OSTI]

Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding that macromolecular crowding can increase protein folding stability, but depending on details of the models (e.g., how on the effects of macro- molecular crowding on protein folding and binding stability has been reached. Crowders

Weston, Ken

298

Ligand binding proteins: roles in ligand transfer and activation of nuclear receptors  

E-Print Network [OSTI]

different cellular functions: steroidogenic acute regulatory protein (StAR), hepatocyte nuclear factor-4a (HNF-4a) and acyl-CoA binding protein (ACBP). First, StAR mediates delivery of cholesterol to inner mitochondrial membrane in steroidogenesis by a...

Petrescu, Anca Daniela

2004-09-30T23:59:59.000Z

299

Characterization of network morphology in anion binding hydrogels used for wastewater remediation  

E-Print Network [OSTI]

Characterization of network morphology in anion binding hydrogels used for wastewater remediation wastewater effluents. The sorbent used was crosslinked polyamine (PAA$HCl) polymeric hydrogels. The surface of crosslinking. q 2005 Elsevier Ltd. All rights reserved. Keywords: Hydrogel; Atomic force microscopy; Wastewater

Rubloff, Gary W.

300

Structural Basis for p300 Taz2-p53 TAD1 Binding and Modulation by Phosphorylation  

E-Print Network [OSTI]

Structure Article Structural Basis for p300 Taz2-p53 TAD1 Binding and Modulation by Phosphorylation to interact with p53 through its N-terminal transactivation domain (TAD) (Avantaggiati et al., 1997; Grossman et al., 1998). The p53 TAD can be divided into two subdomains, TAD1 (composed of residues 1

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


301

Europium-Doped TiO2 Hollow Nanoshells: Two-Photon Imaging of Cell Binding  

E-Print Network [OSTI]

Europium-Doped TiO2 Hollow Nanoshells: Two-Photon Imaging of Cell Binding Sergio Sandoval,,,§ Jian Laboratory, § Moores Cancer Center, Department of Chemistry & Biochemistry, Department of Nano method to fabricate luminescent monodisperse 200 nm europium-doped hollow TiO2 nanoshell (NS) particles

Kummel, Andrew C.

302

Methanobactin: a copper binding compound having antibiotic and antioxidant activity isolated from methanotrophic bacteria  

DOE Patents [OSTI]

A means and method for treating bacterial infection, providing antioxidant activity, and chelating copper using a copper binding compound produced by methanotrophic bacteria is described. The compound, known as methanobactin, is the first of a new class of antibiotics having gram-positive activity. Methanobactin has been sequenced, and its structural formula determined.

DiSpirito, Alan A. (Ames, IA); Zahn, James A. (Harbor Beach, MI); Graham, David W. (Lawrence, KS); Kim, Hyung J. (St. Paul, MN); Alterman, Michail (Lawrence, KS); Larive, Cynthia (Lawrence, KS)

2007-04-03T23:59:59.000Z

303

Binding energies and radii of N > Z nuclei in the n,p-networks model  

E-Print Network [OSTI]

A nuclear model is extended to estimate binding energies and radii of neutron-rich nuclei. These calculations have been made for some representative examples of even-Z and odd-Z nuclei with nucleon numbers lower than sixty. A comparison of results with experimental data supports the value and development of the model in nuclear studies.

I. Casinos

2009-03-09T23:59:59.000Z

304

The First Example of a Nitrile Hydratase Model Complex that Reversibly Binds Nitriles  

E-Print Network [OSTI]

with both methanol and acetonitrile to afford a six-coordinate solvent-bound complex. Competitive binding for acetonitrile (H ) -6.2((0.2) kcal/mol, S ) -29.4((0.8) eu), benzonitrile (-4.2((0.6) kcal/mol, S ) -18((3) eu-temperature electronic absorption spectroscopy. Ligand exchange kinetics were examined for acetonitrile, iso

Kaminsky, Werner

305

Agonist-Activated Glucocorticoid Receptor Inhibits Binding of Heat Shock Factor 1 to the Heat Shock  

E-Print Network [OSTI]

Agonist-Activated Glucocorticoid Receptor Inhibits Binding of Heat Shock Factor 1 to the Heat Shock- cocorticoid receptor (GR) signaling in stressed cells will cause inhibition of the heat shock re- sponse as mediated by heat shock transcription factor 1 (HSF1). In that work, a full-length human heat shock protein

Abraham, Nader G.

306

A new protein folding screen: Application to the ligand binding domains of a glutamate and kainate  

E-Print Network [OSTI]

A new protein folding screen: Application to the ligand binding domains of a glutamate and kainate of determining and evaluating protein folding conditions, we have designed a new fractional factorial protein folding screen. The screen includes 12 factors shown by previous experiments to enhance protein folding

Lebendiker, Mario

307

Tumor necrosis factor: specific binding and internalization in sensitive and resistant cells  

SciTech Connect (OSTI)

Highly purified, Escherichia coli-derived recombinant human tumor necrosis factor (TNF) was labeled with /sup 125/I and employed to determine receptor binding, internalization, and intracellular degradation in murine L929 cells (highly sensitive to the cytotoxic action of TNF) and in diploid human FS-4 cells (resistant to TNF cytotoxicity). /sup 125/I-labeled TNF bound specifically to high-affinity receptors on both L929 and FS-4 cells. Scatchard analysis of the binding data indicated the presence of 2200 binding sites per L929 cell and 7500 binding sites per FS-4 cell. The calculated dissociation constants are 6.1 x 10/sup -10/ M and 3.2 x 10/sup -10/ M for L929 and FS-4 cells, respectively. In both L929 and FS-4 cells, incubation at 37/sup 0/C resulted in a rapid internalization of the bulk of the cell-bound TNF, followed by the appearance of trichloroacetic acid-soluble /sup 125/I radioactivity in the tissue culture medium, due to degradation of TNF. Degradation but not cellular uptake of TNF was inhibited in the presence of chloroquine (an inhibitor of lysosomal proteases) in both L929 and FS-4 cells, suggesting that degradation occurs intracellularly, probably within lysosomes. These results show that resistance of FS-4 cells to TNF cytotoxicity is not due to a lack of receptors or their inability to internalize and degrade TNF.

Tsujimoto, M.; Yip, Y.K.; Vilcek, J.

1985-11-01T23:59:59.000Z

308

Computational design of an endo-1,4-[beta]-xylanase ligand binding site  

SciTech Connect (OSTI)

The field of computational protein design has experienced important recent success. However, the de novo computational design of high-affinity protein-ligand interfaces is still largely an open challenge. Using the Rosetta program, we attempted the in silico design of a high-affinity protein interface to a small peptide ligand. We chose the thermophilic endo-1,4-{beta}-xylanase from Nonomuraea flexuosa as the protein scaffold on which to perform our designs. Over the course of the study, 12 proteins derived from this scaffold were produced and assayed for binding to the target ligand. Unfortunately, none of the designed proteins displayed evidence of high-affinity binding. Structural characterization of four designed proteins revealed that although the predicted structure of the protein model was highly accurate, this structural accuracy did not translate into accurate prediction of binding affinity. Crystallographic analyses indicate that the lack of binding affinity is possibly due to unaccounted for protein dynamics in the 'thumb' region of our design scaffold intrinsic to the family 11 {beta}-xylanase fold. Further computational analysis revealed two specific, single amino acid substitutions responsible for an observed change in backbone conformation, and decreased dynamic stability of the catalytic cleft. These findings offer new insight into the dynamic and structural determinants of the {beta}-xylanase proteins.

Morin, Andrew; Kaufmann, Kristian W.; Fortenberry, Carie; Harp, Joel M.; Mizoue, Laura S.; Meiler, Jens (Vanderbilt)

2012-09-05T23:59:59.000Z

309

Box: Interdependent Modes of Binding in a Two-Nanometer-Long Synthetic Receptor  

E-Print Network [OSTI]

,6-dinitrotoluene, 1,2,4- trichlorobenzene, and both the 9,10- and 1,4-anthraquinone molecules. Moreover, Ex2 Box4 the different modes of binding of Ex2 Box4+ with anthracene, 9,10-anthraquinone, and 1,4-anthraquinone in order

Goddard III, William A.

310

Strip, Bind, and Search: A Method for Identifying Abnormal Energy Consumption in Buildings  

E-Print Network [OSTI]

towards reducing the building's en- ergy consumption is to prevent electricity waste due to the improperStrip, Bind, and Search: A Method for Identifying Abnormal Energy Consumption in Buildings Romain, operators are relying more on historical data pro- cessing to uncover opportunities for energy-savings. How

California at Berkeley, University of

311

Hydrogen-impurity binding energy in vanadium and niobium A. Mokrani and C. Demangeat  

E-Print Network [OSTI]

2243 Hydrogen-impurity binding energy in vanadium and niobium A. Mokrani and C. Demangeat IPCMS, UM by the hydrogen) contribution, ii) the band structure contribution, iii) the electron-electron interaction without. Strong H-H repulsion is observed when the hydrogen atoms are at first nearest neighbouring positions

Boyer, Edmond

312

Heart- and liver-type fatty acid binding proteins in lipid and glucose metabolism  

E-Print Network [OSTI]

Heart-type Fatty Acid-Binding Protein (H-FABP) is required for high rates of skeletal muscle long chain fatty acid (LCFA) oxidation and esterification. Here we assessed whether H-FABP affects soleus muscle glucose uptake when measured in vitro...

Erol, Erdal

2004-11-15T23:59:59.000Z

313

Original article Increase of plasma eCG binding rate after  

E-Print Network [OSTI]

Original article Increase of plasma eCG binding rate after administration of repeated high dose of eCG to cows Pierre V. DRIONa*, Rudy DE ROOVERb, Jean-Yves HOUTAINc, Edmond M. MCNAMARAd, Benoît chorionic gonadotrophin (eCG) is still used to promote follicular growth in cat- tle and, more recently

Paris-Sud XI, Université de

314

Theory of Free Energy and Entropy in Noncovalent Binding HUAN-XIANG ZHOU AND MICHAEL K. GILSON  

E-Print Network [OSTI]

S1 Theory of Free Energy and Entropy in Noncovalent Binding HUAN-XIANG ZHOU AND MICHAEL K. GILSON 1 in a form that supports the present formulation of the theory of noncovalent binding. The free energy, F, provides a measure of the stability of a system at thermal equilibrium: the lower the free energy

Weston, Ken

315

ATP Utilization by Yeast Replication Factor C II. MULTIPLE STEPWISE ATP BINDING EVENTS ARE REQUIRED TO LOAD PROLIFERATING CELL  

E-Print Network [OSTI]

ATP Utilization by Yeast Replication Factor C II. MULTIPLE STEPWISE ATP BINDING EVENTS ARE REQUIRED of adenosine (3-thiotriphosphate) (ATP S), a nonhydrolyzable analog of ATP, to replication factor C with a N-terminal truncation ( 2­273) of the Rfc1 sub- unit (RFC) was studied by filter binding. RFC alone bound 1.8 ATP

Burgers, Peter M.

316

Dirac Point and Edge States in a Microwave Realization of Tight-Binding Graphene-like Structures  

E-Print Network [OSTI]

Dirac Point and Edge States in a Microwave Realization of Tight-Binding Graphene-like Structures U-binding graphene-like structures. The structures are realized using disks with a high index of refraction properties, mechan- ically as electronically. Another realization is graphene, a one-atom-thick allotrope

Boyer, Edmond

317

Oligomeric Status and Nucleotide Binding Properties of the Plastid ATP/ADP Transporter 1: Toward a Molecular  

E-Print Network [OSTI]

Oligomeric Status and Nucleotide Binding Properties of the Plastid ATP/ADP Transporter 1: Toward, was confirmed to be essential for nucleotide steady-state transport. Nucleotide binding studies and analysis is not essential for multimerization, but probably plays a regulatory role, controlling the nucleotide exchange

Paris-Sud XI, Université de

318

The Glutamate Switch of Bacteriophage T7 DNA Helicase ROLE IN COUPLING NUCLEOTIDE TRIPHOSPHATE (NTP) AND DNA BINDING TO NTP  

E-Print Network [OSTI]

The Glutamate Switch of Bacteriophage T7 DNA Helicase ROLE IN COUPLING NUCLEOTIDE TRIPHOSPHATE (NTP also creates nucleotide-binding sites located at the interfaces of the sub- units. DNA binding of a bound nucleoside 5 -triphosphate. However, in the absence of a nucleotide, Glu-343 changes orientation

Richardson, Charles C.

319

1997 Oxford University Press49945002 Nucleic Acids Research, 1997, Vol. 25, No. 24 Information analysis of Fis binding sites  

E-Print Network [OSTI]

analysis of Fis binding sites Paul N. Hengen1, Stacy L. Bartram1,2,+, Lisa E. Stewart1 and Thomas D 30, 1997 ABSTRACT Originally discovered in the bacteriophage Mu DNA inversion system gin, Fis (Factor for Fis to locate its binding sites, we collected a set of 60 experimentally defined wild-type Fis DNA

Schneider, Thomas D.

320

Identification of a putative calcium-binding protein as a dioxin-responsive gene in zebrafish and rainbow trout  

E-Print Network [OSTI]

Identification of a putative calcium-binding protein as a dioxin-responsive gene in zebrafish; accepted 16 October 2002 Abstract 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD, dioxin) is a widespread in zebrafish and rainbow trout that dioxin increases expression of this EF-hand calcium-binding protein gene

Tullos, Desiree

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


321

Understanding Weak Binding for Phospho(enol)pyruvate to the Allosteric Site of Phosphofructokinase from Lactobacillus delbrueckii subspecies bulgaricus  

E-Print Network [OSTI]

diphosphate (MgADP). PEP and MgADP bind to the same allosteric binding site but exhibit opposite effects, PEP acting as an inhibitor and MgADP an activator. In 2005, Parichatttanakul, et al. solved the first crystal structure of LbPFK to 1.87 A resolution...

Ferguson, Scarlett Blair

2012-10-19T23:59:59.000Z

322

PAPER www.rsc.org/obc | Organic & Biomolecular Chemistry RNA binding and thiolytic stability of a quinoline-containing  

E-Print Network [OSTI]

as the intercalation domain. A quinoline-containing HTP is shown to bind selectively to duplex RNA binding sites influences the affinity of these compounds for RNA targets. Our original HTP design used 9- anilinoacridines a new HTP design that uses quinoline for intercalation. A high yielding synthesis to a new quinoline

Beal, Peter A.

323

Vacancies and small vacancy clusters in BCC transition metals : calculation of binding energy, atomic relaxation and electronic  

E-Print Network [OSTI]

921 Vacancies and small vacancy clusters in BCC transition metals : calculation of binding energy(E) and gi(03C9), for vacancy-type lattice defects in BCC transition metals : The short-range repulsive energies between neighbouring atomic sites are simulated by a Born-Mayer potential. Binding energies of di-vacancies

Paris-Sud XI, Université de

324

A Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors  

SciTech Connect (OSTI)

GspB is a serine-rich repeat (SRR) adhesin of Streptococcus gordonii that mediates binding of this organism to human platelets via its interaction with sialyl-T antigen on the receptor GPIb{alpha}. This interaction appears to be a major virulence determinant in the pathogenesis of infective endocarditis. To address the mechanism by which GspB recognizes its carbohydrate ligand, we determined the high-resolution x-ray crystal structure of the GspB binding region (GspB{sub BR}), both alone and in complex with a disaccharide precursor to sialyl-T antigen. Analysis of the GspB{sub BR} structure revealed that it is comprised of three independently folded subdomains or modules: (1) an Ig-fold resembling a CnaA domain from prokaryotic pathogens; (2) a second Ig-fold resembling the binding region of mammalian Siglecs; (3) a subdomain of unique fold. The disaccharide was found to bind in a pocket within the Siglec subdomain, but at a site distinct from that observed in mammalian Siglecs. Confirming the biological relevance of this binding pocket, we produced three isogenic variants of S. gordonii, each containing a single point mutation of a residue lining this binding pocket. These variants have reduced binding to carbohydrates of GPIb{alpha}. Further examination of purified GspB{sub BR}-R484E showed reduced binding to sialyl-T antigen while S. gordonii harboring this mutation did not efficiently bind platelets and showed a significant reduction in virulence, as measured by an animal model of endocarditis. Analysis of other SRR proteins revealed that the predicted binding regions of these adhesins also had a modular organization, with those known to bind carbohydrate receptors having modules homologous to the Siglec and Unique subdomains of GspBBR. This suggests that the binding specificity of the SRR family of adhesins is determined by the type and organization of discrete modules within the binding domains, which may affect the tropism of organisms for different tissues.

Pyburn, Tasia M.; Bensing, Barbara A.; Xiong, Yan Q.; Melancon, Bruce J.; Tomasiak, Thomas M.; Ward, Nicholas J.; Yankovskaya, Victoria; Oliver, Kevin M.; Cecchini, Gary; Sulikowski, Gary A.; Tyska, Matthew J.; Sullam, Paul M.; Iverson, T.M. (VA); (UCLA); (Vanderbilt); (UCSF)

2014-10-02T23:59:59.000Z

325

High-Affinity and Cooperative Binding of Oxidized Calmodulin by Methionine Sulfoxide Reductase  

SciTech Connect (OSTI)

Methionines play an important role in modulating protein-protein interactions associated with intracellular signaling, and their reversible oxidation to form methionine sulfoxides [Met(O)] in calmodulin (CaM) and other signaling proteins has been suggested to couple cellular redox changes to protein function changes through the action of methionine sulfoxide reductases (Msr). Prior measurements indicate the full recovery of target protein activation upon the stereospecific reduction of oxidized CaM by MsrA, where the formation of the S-stereoisomer of Met(O) selectively inhibits the CaM-dependent activation of the Ca-ATPase. However, the physiological substrates of MsrA remain unclear, as neither the binding specificities nor affinities of protein targets have been measured. To assess the specificity of binding and its possible importance in the maintenance of CaM function, we have measured the kinetics of repair and the binding affinity between oxidized CaM and MsrA. Reduction of Met(O) in fully oxidized CaM by MsrA is sensitive to protein folding, as repair of the intact protein is incomplete, with > 6 Met(O) remaining in each CaM following MsrA reduction. In contrast, following proteolytic digestion, MsrA is able to fully reduce one-half of the oxidized methionines, indicating that Met(O) within folded proteins are not substrates for MsrA repair. Further, in comparison to free Met(O), the turnover number and Km for oxidized CaM (CaMox) are substantially smaller, indicating that the binding interaction retards Msr recycling to reduce steady-state enzyme activity. Mutation of the active site (i.e., C72S) in MsrA permitted equilibrium-binding measurements using both ensemble and single-molecule measurements obtained by fluorescence correlation spectroscopy (FCS). Multiple MsrA bind tightly to CaMox (Kd = 70 +- 10 nM) with an affinity that is three orders of magnitude greater than the Michaelis constant (KM = 71 +- 8 micromolar). These results indicate that MsrA selectively reduces surface-exposed Met(O) within unstructured sequences and suggest that only a small subset of oxidized proteins are substrates for MsrA, which may selectively modulate the function of key signaling proteins as part of an adaptive response to oxidative stress.

Xiong, Yijia; Chen, Baowei; Smallwood, Heather S.; Urbauer, Ramona J.; Markillie, Lye Meng; Galeva, Nadezhda A.; Williams, Todd D.; Squier, Thomas C.

2006-12-12T23:59:59.000Z

326

Accurate Analysis of Large Datasets of Protein-Ligand Binding Geometries Using a Linear Clustering Method Based on MapReduce  

E-Print Network [OSTI]

are traditionally scored based on energy values. A protein-ligand complex selected because Accurate Analysis of Large Datasets of Protein-Ligand Binding Geometries for classifying protein-ligand binding geometries in molecular docking. We analyze results

Maccabe, Barney

327

Translation Initiation Factors eIF-iso4G and eIF-4B Interact with the Poly(A)-binding Protein and Increase Its RNA Binding Activity*  

E-Print Network [OSTI]

Translation Initiation Factors eIF-iso4G and eIF-4B Interact with the Poly(A)-binding Protein (eIF-4F and eIF-iso4F) and eIF-4B, bind to the poly(A)-binding protein (PABP) both in the presence and absence of poly(A) RNA. The interactions between PABP and eIF- 4F, eIF-iso4F, and eIF-4B were measured

Tullos, Desiree

328

Promiscuous 8Alkoxyadenosines in the Guide Strand of an SiRNA: Modulation of Silencing Efficacy and Off-Pathway Protein Binding  

E-Print Network [OSTI]

and Off-Pathway Protein Binding Uday Ghanty, Erik Fostvedt, Rachel Valenzuela, Peter A. Beal, and Cynthia

Beal, Peter A.

329

The cooperative binding of spermine to SSB protein-poly(dT) complexes  

E-Print Network [OSTI]

mode conformation. The intrinsic binding constant (B) to the (SSB) binding mode is dependent upon NaC1 concentration, having values of 1. 80x10 M in 0. 1 mM NaC1, 1. 40x10 M in 5mM NaC1, and 6. 57x10 M in 10 mM NaCl, respectively. The allosteric... equilibrium constant (L) between the two SSB protein-ssDNA conformations is 1. 00 x 10 in 0. 1 mM NaC1, 5. 00 in 5 mM NaC1, and 5. 50 x 10 in 10 mM NaC1 indicating that cooperativity decreases as NaC1 concentration increases. Na+ acts as a competitor...

Wei, Tai-Fen

1988-01-01T23:59:59.000Z

330

Nucleic acids encoding phloem small RNA-binding proteins and transgenic plants comprising them  

DOE Patents [OSTI]

The present invention provides a polynucleotide sequence encoding a component of the protein machinery involved in small RNA trafficking, Cucurbita maxima phloem small RNA-binding protein (CmPSRB 1), and the corresponding polypeptide sequence. The invention also provides genetic constructs and transgenic plants comprising the polynucleotide sequence encoding a phloem small RNA-binding protein to alter (e.g., prevent, reduce or elevate) non-cell autonomous signaling events in the plants involving small RNA metabolism. These signaling events are involved in a broad spectrum of plant physiological and biochemical processes, including, for example, systemic resistance to pathogens, responses to environmental stresses, e.g., heat, drought, salinity, and systemic gene silencing (e.g., viral infections).

Lucas, William J.; Yoo, Byung-Chun; Lough, Tony J.; Varkonyi-Gasic, Erika

2007-03-13T23:59:59.000Z

331

Capture and release of mixed acid gasses with binding organic liquids  

DOE Patents [OSTI]

Reversible acid-gas binding organic liquid systems that permit separation and capture of one or more of several acid gases from a mixed gas stream, transport of the liquid, release of the acid gases from the ionic liquid and reuse of the liquid to bind more acid gas with significant energy savings compared to current aqueous systems. These systems utilize acid gas capture compounds made up of strong bases and weak acids that form salts when reacted with a selected acid gas, and which release these gases when a preselected triggering event occurs. The various new materials that make up this system can also be included in various other applications such as chemical sensors, chemical reactants, scrubbers, and separators that allow for the specific and separate removal of desired materials from a gas stream such as flue gas.

Heldebrant, David J. (Richland, WA); Yonker, Clement R. (Kennewick, WA)

2010-09-21T23:59:59.000Z

332

Quenching methods for background reduction in luminescence-based probe-target binding assays  

DOE Patents [OSTI]

Background luminescence is reduced from a solution containing unbound luminescent probes, each having a first molecule that attaches to a target molecule and having an attached luminescent moiety, and luminescent probe/target adducts. Quenching capture reagent molecules are formed that are capable of forming an adduct with the unbound luminescent probes and having an attached quencher material effective to quench luminescence of the luminescent moiety. The quencher material of the capture reagent molecules is added to a solution of the luminescent probe/target adducts and binds in a proximity to the luminescent moiety of the unbound luminescent probes to quench luminescence from the luminescent moiety when the luminescent moiety is exposed to exciting illumination. The quencher capture reagent does not bind to probe molecules that are bound to target molecules and the probe/target adduct emission is not quenched.

Cai, Hong (Los Alamos, NM); Goodwin, Peter M (Los Alamos, NM); Keller, Richard A. (Los Alamos, NM); Nolan, Rhiannon L. (Santa Fe, NM)

2007-04-10T23:59:59.000Z

333

Alignment of RNA molecules: Binding energy and statistical properties of random sequences  

SciTech Connect (OSTI)

A new statistical approach to the problem of pairwise alignment of RNA sequences is proposed. The problem is analyzed for a pair of interacting polymers forming an RNA-like hierarchical cloverleaf structures. An alignment is characterized by the numbers of matches, mismatches, and gaps. A weight function is assigned to each alignment; this function is interpreted as a free energy taking into account both direct monomer-monomer interactions and a combinatorial contribution due to formation of various cloverleaf secondary structures. The binding free energy is determined for a pair of RNA molecules. Statistical properties are discussed, including fluctuations of the binding energy between a pair of RNA molecules and loop length distribution in a complex. Based on an analysis of the free energy per nucleotide pair complexes of random RNAs as a function of the number of nucleotide types c, a hypothesis is put forward about the exclusivity of the alphabet c = 4 used by nature.

Valba, O. V., E-mail: valbaolga@gmail.com [Moscow Institute of Physics and Technology (State University) (Russian Federation); Nechaev, S. K., E-mail: sergei.nechaev@gmail.com [Universite Paris Sud, LPTMS (France); Tamm, M. V., E-mail: thumm.m@gmail.com [Moscow State University (Russian Federation)

2012-02-15T23:59:59.000Z

334

Selective electrostatic binding of ions by monolayers of mercaptan derivatives adsorbed to gold substrates  

SciTech Connect (OSTI)

A single, self-assembled monolayer of organic material is used to impart pH-dependent electrostatic-based recognition capability to an Au electrode. The results show that 4-aminothiophenol and related mercaptans change the surface characteristics of naked Au toward the adsorption of positively and negatively charged ions as a function of pH. For example, anthraquinone-2,6-disulfonate irreversibly adsorbs to naked Au surfaces over a broad range of pH. However, a preadsorbed monolayer of 4-aminothiophenol prevents adsorption of anthraquinone-2,6-disulfonate at high pH but electrostatically binds it at low pH. The principle of pH-dependent binding is general for a number of amine-, carboxylic acid-, and pyridine-terminated mercaptan derivatives adsorbed to Au surfaces.

Sun, Li; Johnson, B.; Wade, T.; Crooks, R.M. (Univ. of New Mexico, Albuquerque (USA))

1990-12-27T23:59:59.000Z

335

Binding energy for hydrogen-like atoms in the Nelson model without cutoffs  

E-Print Network [OSTI]

In the Nelson model particles interact through a scalar massless field. For hydrogen-like atoms there is a nucleus of infinite mass and charge $Ze$, $Z > 0$, fixed at the origin and an electron of mass $m$ and charge $e$. This system forms a bound state with binding energy $E_{\\rm bin} = me^4Z^2/2$ to leading order in $e$. We investigate the radiative corrections to the binding energy and prove upper and lower bounds which imply that $ E_{\\rm bin} = me^4 Z^2/2 + c_0 e^6 + \\Ow(e^7 \\ln e)$ with explicit coefficient $c_0$ and independent of the ultraviolet cutoff. $c_0$ can be computed by perturbation theory, which however is only formal since for the Nelson Hamiltonian the smallest eigenvalue sits exactly at the bottom of the continuous spectrum.

Christian Hainzl; Masao Hirokawa; Herbert Spohn

2003-12-10T23:59:59.000Z

336

Binding hotspots of BAZ2B bromodomain: histone interaction revealed by solution NMR driven docking  

E-Print Network [OSTI]

, Dow Street, Dundee, DD1 5EH, UK Corresponding Author * To whom correspondence should be addressed: Alessio Ciulli, Phone: +44 1382 386230, Fax: +44 1382 386373, Email: a.ciulli@dundee.ac.uk Funding Source Statement: This work was supported... spectroscopy and docking simulations. The resulting models were validated with site-directed mutagenesis and peptide binding studies using ITC. EXPERIMENTAL PROCEDURES Protein expression Escherichia coli Rosetta competent cells were transformed with a p...

Ferguson, Fleur M.; Dias, David M.; Rodrigues, Joao P. G. L. M.; Wienk, Hans; Bonvin, Alexandre M. J. J.; Abell, Chris; Ciulli, Alessio

2014-09-30T23:59:59.000Z

337

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Thermodynamics of calmodulin binding to  

E-Print Network [OSTI]

and skeletal muscle ryanodine receptor ion channels Gerhard Meissner,* Daniel A. Pasek, Naohiro Yamaguchi . A no- table property of the RyRs is that they interact with both the Ca21 -free (apoCaM) and Ca21 to the intact receptors indi- cates that the RyRs have a single, high-affinity binding domain for apoCaM and Ca

Dokholyan, Nikolay V.

338

Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Frauke Gra1ter,, Sonja M. Schwarzl,, Annick Dejaegere,| Stefan Fischer,*, and  

E-Print Network [OSTI]

Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Mechanics Frauke of the complexes are predicted (the "docking" problem) as well as in how the free energy is calculated from)solvation during the binding process.3 Typically, binding free energies calculated with these methods have average

Gräter, Frauke

339

Phospholipase A2 Engineering. Deletion of the C-Terminus Segment Changes Substrate Specificity and Uncouples Calcium and Substrate Binding at the  

E-Print Network [OSTI]

channel, and the calcium binding loop are perturbed, but the global conformation is not changed and Uncouples Calcium and Substrate Binding at the Zwitterionic Interface, Baohua Huang,,§ Bao-Zhu Yu,| Joseph and the uncoupling between substrate and calcium binding are interesting and significant. One of the important

Tsai, Ming-Daw

340

Calsensin: A Novel Calcium-binding Protein Expressed in a Subset of Peripheral Leech Neurons Fasciculating in a Single Axon Tract  

E-Print Network [OSTI]

helix-loop-helix domains. The calcium-binding domains are likely to be functional in vivo since a fusionCalsensin: A Novel Calcium-binding Protein Expressed in a Subset of Peripheral Leech Neurons. We have used this antibody to clone a novel EF-hand calcium-binding protein, calsensin, by screening

Johansen, Jorgen

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


341

Sm-like protein Hfq: Location of the ATP-binding site and the effect of ATP on HfqRNA complexes  

E-Print Network [OSTI]

Sm-like protein Hfq: Location of the ATP-binding site and the effect of ATP on Hfq­RNA complexes the first evidence indicating that Hfq is an ATP-binding protein. Using a combination of biochemical and genetic techniques, we have now determined a plausible ATP-binding site in Hfq and tested Hfq's ATP

Mura, Cameron

342

The N-terminus of TDP-43 promotes its oligomerization and enhances DNA binding affinity  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer The N-terminus of TDP-43 contains an independently folded structural domain (NTD). Black-Right-Pointing-Pointer The structural domains of TDP-43 are arranged in a beads-on-a-string fashion. Black-Right-Pointing-Pointer The NTD promotes TDP-43 oligomerization in a concentration-dependent manner. Black-Right-Pointing-Pointer The NTD may assist nucleic acid-binding activity of TDP-43. -- Abstract: TDP-43 is a DNA/RNA-binding protein associated with different neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-U). Here, the structural and physical properties of the N-terminus on TDP-43 have been carefully characterized through a combination of nuclear magnetic resonance (NMR), circular dichroism (CD) and fluorescence anisotropy studies. We demonstrate for the first time the importance of the N-terminus in promoting TDP-43 oligomerization and enhancing its DNA-binding affinity. An unidentified structural domain in the N-terminus is also disclosed. Our findings provide insights into the N-terminal domain function of TDP-43.

Chang, Chung-ke [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China)] [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Wu, Tzong-Huah [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China) [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biochemistry, Academia Sinica, Taipei 115, Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan (China); Wu, Chu-Ya [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China) [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Graduate Institute of Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan (China); Chiang, Ming-hui; Toh, Elsie Khai-Woon [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China)] [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Hsu, Yin-Chih; Lin, Ku-Feng [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China)] [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Liao, Yu-heng [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China)] [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Huang, Tai-huang, E-mail: bmthh@gate.sinica.edu.tw [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China) [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Department of Physics, National Taiwan Normal University, Taipei 106, Taiwan (China); Huang, Joseph Jen-Tse, E-mail: jthuang@chem.sinica.edu.tw [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China)

2012-08-24T23:59:59.000Z

343

Binding Energies and Radii of the Nuclei with N >=Z in an Alpha-Cluster Model  

E-Print Network [OSTI]

Using the surface tension energy put in dependence on the number of alpha-clusters in the core in a phenomenological model representing a nucleus as a core and a nuclear molecule on its surface leads to widening the number of isotopes to be described from the narrow strip of beta-stability to the isotopes with N >= Z. The number of alpha-clusters in the molecule is obtained from the analysis of experimental binding energies and the specific density of the core binding energy \\rho and the radii are calculated. It is shown that for the isotopes of one Z with growing A the number of alpha-clusters of the molecule decreases mostly to 3 and \\rho increases to reach a saturation value within \\rho = 2.5 \\div 2.7 MeV/fm^3 at the beta - stable isotopes, so the narrow strip of the binding energies of the beta - stable isotopes with Z <= 84 is outlined by a function of one variable Z.

G. K. Nie

2008-07-01T23:59:59.000Z

344

Complexities in human herpesvirus-6A and -6B binding to host cells  

SciTech Connect (OSTI)

Human herpesvirus-6A and -6B uses the cellular receptor CD46 for fusion and infection of the host cell. The viral glycoprotein complex gH-gL from HHV-6A binds to the short consensus repeat 2 and 3 in CD46. Although all the major isoforms of CD46 bind the virus, certain isoforms may have higher affinity than others for the virus. Within recent years, elucidation of the viral complex has identified additional HHV-6A and -6B specific glycoproteins. Thus, gH-gL associates with a gQ1-gQ2 dimer to form a heterotetrameric complex. In addition, a novel complex consisting of gH-gL-gO has been described that does not bind CD46. Accumulating evidence suggests that an additional HHV-6A and -6B receptor exists. The previous simple picture of HHV-6A/B-host cell contact therefore includes more layers of complexities on both the viral and the host cell side of the interaction.

Pedersen, Simon Metz [Institute of Medical Microbiology and Immunology, The Bartholin Building, University of Aarhus, DK-8000 Aarhus C (Denmark); Hoellsberg, Per [Institute of Medical Microbiology and Immunology, The Bartholin Building, University of Aarhus, DK-8000 Aarhus C (Denmark)]. E-mail: ph@microbiology.au.dk

2006-12-20T23:59:59.000Z

345

A Novel, ;Double-Clamp; Binding Mode for Human Heme Oxygenase-1 Inhibition  

SciTech Connect (OSTI)

The development of heme oxygenase (HO) inhibitors is critical in dissecting and understanding the HO system and for potential therapeutic applications. We have established a program to design and optimize HO inhibitors using structure-activity relationships in conjunction with X-ray crystallographic analyses. One of our previous complex crystal structures revealed a putative secondary hydrophobic binding pocket which could be exploited for a new design strategy by introducing a functional group that would fit into this potential site. To test this hypothesis and gain further insights into the structural basis of inhibitor binding, we have synthesized and characterized 1-(1H-imidazol-1-yl)-4,4-diphenyl-2-butanone (QC-308). Using a carbon monoxide (CO) formation assay on rat spleen microsomes, the compound was found to be {approx}15 times more potent (IC{sub 50} = 0.27{+-}0.07 {mu}M) than its monophenyl analogue, which is already a potent compound in its own right (QC-65; IC{sub 50} = 4.0{+-}1.8 {mu}M). The crystal structure of hHO-1 with QC-308 revealed that the second phenyl group in the western region of the compound is indeed accommodated by a definitive secondary proximal hydrophobic pocket. Thus, the two phenyl moieties are each stabilized by distinct hydrophobic pockets. This 'double-clamp' binding offers additional inhibitor stabilization and provides a new route for improvement of human heme oxygenase inhibitors.

Rahman, Mona N.; Vlahakis, Jason Z.; Vukomanovic, Dragic; Lee, Wallace; Szarek, Walter A.; Nakatsu, Kanji; Jia, Zongchao (Queens)

2012-08-01T23:59:59.000Z

346

Biological activities of binding site specific monoclonal antibodies to prolactin receptors of rabbit mammary gland  

SciTech Connect (OSTI)

The biological activity of three monoclonal antibodies (mAbs) against the rabbit mammary prolactin (PRL) receptor (M110, A82, and A917) were investigated using explants of rabbit mammary gland. The three mAbs which were all able to inhibit the binding of SVI-ovine prolactin to its receptor had different biological activities. Two mAbs (M110 and A82) were able to prevent the stimulating effect of PRL on casein synthesis when the molar ratio between the mAb and PRL was 100. One mAb (A917) was able to mimic the action of PRL on both casein and DNA ((TH)thymidine incorporation) synthesis, whereas the other two mAbs were without any stimulatory effect. For this stimulatory effect to be observed, bivalency of the antibody was essential, since monovalent fragments, which were able to inhibit PRL binding, had no agonistic activity. The ability of the mAbs to induce a down-regulation of receptors was also studied. These studies suggest that the binding domain of the receptor might be relatively complex, since only a part of this domain recognized by the antibody with PRL-like activity was able to induce hormonal action. Alternatively, only those antibodies able to microaggregate the receptors may possess PRL-like activity.

Djiane, J.; Dusanter-Fourt, I.; Katoh, M.; Kelly, P.A.

1985-09-25T23:59:59.000Z

347

Identification of FAM96B as a novel prelamin A binding partner  

SciTech Connect (OSTI)

Highlights: We screen the binding protein of prelamin A by yeast two-hybrid screen. FAM96B colocalizes with prelamin A in HEK-293 cells. FAM96B physically interacts with prelamin A. -- Abstract: Prelamin A accumulation causes nuclear abnormalities, impairs nuclear functions, and eventually promotes cellular senescence. However, the underlying mechanism of how prelamin A promotes cellular senescence is still poorly understood. Here we carried out a yeast two-hybrid screen using a human skeletal muscle cDNA library to search for prelamin A binding partners, and identified FAM96B as a prelamin A binding partner. The interaction of FAM96B with prelamin A was confirmed by GST pull-down and co-immunoprecipitation experiments. Furthermore, co-localization experiments by fluorescent confocal microscopy revealed that FAM96B colocalized with prelamin A in HEK-293 cells. Taken together, our data demonstrated the physical interaction between FAM96B and prelamin A, which may provide some clues to the mechanisms of prelamin A in premature aging.

Xiong, Xing-Dong; Wang, Junwen; Zheng, Huiling; Jing, Xia; Liu, Zhenjie [Institute of Aging Research, Guangdong Medical College, Dongguan 523808 (China) [Institute of Aging Research, Guangdong Medical College, Dongguan 523808 (China); Institute of Biochemistry and Molecular Biology, Guangdong Medical College, Zhanjiang 524023 (China); Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan 523808 (China); Zhou, Zhongjun [Institute of Aging Research, Guangdong Medical College, Dongguan 523808 (China) [Institute of Aging Research, Guangdong Medical College, Dongguan 523808 (China); Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong (China); Liu, Xinguang, E-mail: xgliu64@126.com [Institute of Aging Research, Guangdong Medical College, Dongguan 523808 (China) [Institute of Aging Research, Guangdong Medical College, Dongguan 523808 (China); Institute of Biochemistry and Molecular Biology, Guangdong Medical College, Zhanjiang 524023 (China); Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan 523808 (China)

2013-10-11T23:59:59.000Z

348

Enhancing DNA binding rate using optical trapping of high-density gold nanodisks  

SciTech Connect (OSTI)

We present the dynamic study of optical trapping of fluorescent molecules using high-density gold nanodisk arrays. The gold nanodisks were fabricated by electron beam lithography with a diameter of 500 nm and a period of 1 ?m. Dark-field illumination showed ?15 times enhancement of fluorescence near edges of nanodisks. Such enhanced near-field generated an optical trapping force of ?10 fN under 3.58 10{sup 3} W/m{sup 2} illumination intensity as calculated from the Brownian motions of 590 nm polystyrene beads. Kinetic observation of thiolated DNA modified with Cy5 dye showed different binding rates of DNA under different illumination intensity. The binding rate increased from 2.14 10{sup 3} s{sup ?1} (I = 0.7 10{sup 3} W/m{sup 2}) to 1.15 10{sup 5} s{sup ?1} (I = 3.58 10{sup 3} W/m{sup 2}). Both enhanced fluorescence and binding rate indicate that gold nanodisks efficiently improve both detection limit and interaction time for microarrays.

Lin, En-Hung; Pan, Ming-Yang [Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan 30013 (China) [Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan 30013 (China); Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan 11529 (China); Lee, Ming-Chang [Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan 30013 (China)] [Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan 30013 (China); Wei, Pei-Kuen, E-mail: pkwei@sinica.edu.tw [Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan 11529 (China) [Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan 11529 (China); Institute of Biophotonics, National Yang-Ming University, Taipei 11221, Taiwan (China)

2014-03-15T23:59:59.000Z

349

Protein-salt binding data from potentiometric titrations of lysozyme in aqueous solutions containing KCl  

SciTech Connect (OSTI)

An existing method for potentiometric titrations of proteins was improved, tested and applied to titrations of the enzyme hen-egg-white lysozyme in aqueous solutions containing KCl at ionic strengths from 0.1 M to 2.0 M at 25 C. Information about the protein`s net charge dependence on pH and ionic strength were obtained and salt binding numbers for the system were calculated using a linkage concept. For the pH range 2.5--11.5, the net charge slightly but distinctly increases with increasing ionic strength between 0.1 M and 2.0 M. The differences are most distinct in the pH region below 5. Above pH 11.35, the net charge decreases with increasing ionic strength. Preliminary calculation of binding numbers from titration curves at 0.1 M and 1.0 M showed selective association of chloride anions and expulsion of potassium ions at low pH. Ion-binding numbers from this work will be used to evaluate thermodynamic properties and to correlate crystallization or precipitation phase-equilibrium data in terms of a model based on the integral-equation theory of fluids which is currently under development.

Engmann, J.; Blanch, H.W.; Prausnitz, J.M. [Univ. of California, Berkeley, CA (United States). Dept. of Chemical Engineering]|[Lawrence Berkeley National Lab., CA (United States). Chemical Sciences Div.

1997-03-01T23:59:59.000Z

350

Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids  

SciTech Connect (OSTI)

Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized by interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.

Zhukhlistova, N. E.; Balaev, V. V.; Lyashenko, A. V.; Lashkov, A. A., E-mail: alashkov83@gmail.com [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2012-05-15T23:59:59.000Z

351

A Single-Domain Llama Antibody Potently Inhibits the Enzymatic Activity of Botulinum Neurotoxin by Binding to the Non-Catalytic [alpha]-Exosite Binding Region  

SciTech Connect (OSTI)

Ingestion or inhalation of botulinum neurotoxin (BoNT) results in botulism, a severe and frequently fatal disease. Current treatments rely on antitoxins, which, while effective, cannot reverse symptoms once BoNT has entered the neuron. For treatments that can reverse intoxication, interest has focused on developing inhibitors of the enzymatic BoNT light chain (BoNT Lc). Such inhibitors typically mimic substrate and bind in or around the substrate cleavage pocket. To explore the full range of binding sites for serotype A light chain (BoNT/A Lc) inhibitors, we created a library of non-immune llama single-domain VHH (camelid heavy-chain variable region derived from heavy-chain-only antibody) antibodies displayed on the surface of the yeast Saccharomyces cerevisiae. Library selection on BoNT/A Lc yielded 15 yeast-displayed VHH with equilibrium dissociation constants (K{sub d}) from 230 to 0.03 nM measured by flow cytometry. Eight of 15 VHH inhibited the cleavage of substrate SNAP25 (synaptosome-associated protein of 25,000 Da) by BoNT/A Lc. The most potent VHH (Aa1) had a solution K{sub d} for BoNT/A Lc of 1.47 x 10{sup -10} M and an IC{sub 50} (50% inhibitory concentration) of 4.7 x 10{sup -10} M and was resistant to heat denaturation and reducing conditions. To understand the mechanism by which Aa1 inhibited catalysis, we solved the X-ray crystal structure of the BoNT/A Lc-Aa1 VHH complex at 2.6 {angstrom} resolution. The structure reveals that the Aa1 VHH binds in the {alpha}-exosite of the BoNT/A Lc, far from the active site for catalysis. The study validates the utility of non-immune llama VHH libraries as a source of enzyme inhibitors and identifies the BoNT/A Lc {alpha}-exosite as a target for inhibitor development.

Dong, Jianbo; Thompson, Aaron A.; Fan, Yongfeng; Lou, Jianlong; Conrad, Fraser; Ho, Mengfei; Pires-Alves, Melissa; Wilson, Brenda A.; Stevens, Raymond C.; Marks, James D. (UIUC); (Scripps); (UCSF)

2010-08-13T23:59:59.000Z

352

1Lesions in the mRNA cap-binding gene ABA HYPERSENSITIVE 1 suppress FRIGIDA-mediated delayed  

E-Print Network [OSTI]

1Lesions in the mRNA cap-binding gene ABA HYPERSENSITIVE 1 suppress FRIGIDA-mediated delayed morphology were identified in T-DNA and fast-neutron mutant populations. Molecular analysis showed

Raines, Ronald T.

353

Basic residues of human group IIA phospholipase A2 are important for binding to factor Xa and prothrombinase inhibition  

E-Print Network [OSTI]

bridges, and a number of conserved amino acids located in the calcium-binding loop and the catalytic site (14±17 kDa), calcium-dependent catalytic activity, the pre- sence of between five and eight disulfide

Gelb, Michael

354

The HSV-1 ICP27 RGG box specifically binds flexible, GC-rich sequences but not G-quartet structures  

E-Print Network [OSTI]

recognition complex (ORC) proteins to the EBV episomal mini-the binding by EBNA1 to the ORC proteins was RNA dependentrich RNA may be a mechanism for ORC recruitment (41). It is

Corbin-Lickfett, Kara A.; Chen, I-Hsiung Brandon; Cocco, Melanie J.; Sandri-Goldin, Rozanne M.

2009-01-01T23:59:59.000Z

355

Characterization of IgG and IgE Binding to Parvalbumin Derived from Commercially Important Fish Species.  

E-Print Network [OSTI]

??Parvalbumin is a calcium-binding muscle protein that is present in all vertebrates. Despite being a pan-allergen in fish and frog, fish-specific IgE and antiparvalbumin IgG (more)

Lee, Poi-Wah

2012-01-01T23:59:59.000Z

356

Quantitative Estimates on the Binding Energy for Hydrogen in Non-Relativistic QED. II. The spin case  

E-Print Network [OSTI]

The hydrogen binding energy in the Pauli-Fierz model with the spin Zeeman term is determined up to the order alpha cube, where alpha denotes the fine-structure constant.

Jean-Marie Barbaroux; Semjon Vugalter

2013-06-19T23:59:59.000Z

357

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights  

E-Print Network [OSTI]

Background: Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding ...

Gordan, Raluca

358

On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence  

E-Print Network [OSTI]

METHODOLOGY ARTICLE Open Access On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence David S Huen1*, Steven Russell1,2 Abstract Background: In eukaryotes, most DNA-binding proteins exert their action... : Functional Anatomy of Polycomb and Trithorax chromatin landscapes in Drosophila embryos. Plos Biology 2009, 7:e1000013. 7. Solomon MJ, Larsen PL, Varshavsky A: Mapping protein-DNA interactions in vivo with formaldehyde - evidence that histone H4 is retained...

Huen, David S; Russell, Steven R

2010-06-30T23:59:59.000Z

359

Particle trap to sheath non-binding contact for a gas-insulated transmission line having a corrugated outer conductor  

DOE Patents [OSTI]

A non-binding particle trap to outer sheath contact for use in gas insulated transmission lines having a corrugated outer conductor. The non-binding feature of the contact according to the teachings of the invention is accomplished by having a lever arm rotatably attached to a particle trap by a pivot support axis disposed parallel to the direction of travel of the inner conductor/insulator/particle trap assembly.

Fischer, William H. (Pittsburgh, PA)

1984-04-24T23:59:59.000Z

360

XENOBIOTIC REGULATION OF THE ATP BINDING CASSETTE TRANSPORTER ABCB6 AND ITS SIGNIFICANCE TO HEPATIC HEME HOMEOSTASIS  

E-Print Network [OSTI]

.2. Pathologies associated with disruption of heme homeostasis 3 1.3. Cellular heme homeostasis 5 1.4. The human ATP binding cassette transporter subfamily 23 1.5. Mitochondrial ATP binding cassette transporter Abcb6 38 Chapter 2: STATEMENT... OF ABCB6 SUBSTRATES 178 Chapter 8: CONCLUSIONS AND FUTURE DIRECTIONS 207 8.1. Summary and conclusions 208 8.2. Future directions 212 REFERENCES 217 XI LIST OF ABBREVIATIONS Abbreviation Full name 3-AT 3...

Chavan, Hemantkumar Dilip

2013-12-31T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


361

On the origins of enzyme inhibitor selectivity and promiscuity: a case study of protein kinase binding to staurosporine  

E-Print Network [OSTI]

that are highly correlated to binding constants. Most kinases with better binding affinities to staurosporine (dark red) have large gatekeeper residues, e.g. phenylalanine (F), methionine (M). A majority of kinases which are inhibited by ZD-6474 (blue) has... accessible region ................................................................. Figure 44. The MAHORI web-interface allows for various forms of ligand query, e.g. by providing a chemical structure, a SMILES string, a chemical name or a PDB three...

Tanramluk, Duangrudee

2010-02-09T23:59:59.000Z

362

Crystal Structures of the Staphylococcal Toxin SSL5 in Complex With Sialyl-Lewis X Reveal a Conserved Binding Site That Shares Common Features With Viral And Bacterial Sialic Acid-Binding Proteins  

SciTech Connect (OSTI)

Staphylococcus aureus is a significant human pathogen. Among its large repertoire of secreted toxins is a group of staphylococcal superantigen-like proteins (SSLs). These are homologous to superantigens but do not have the same activity. SSL5 is shown here to bind to human granulocytes and to the cell surface receptors for human IgA (Fc alphaRI) and P-selectin [P-selectin glycoprotein ligand-1 (PSGL-1)] in a sialic acid (Sia)-dependent manner. Co-crystallization of SSL5 with the tetrasaccharide sialyl Lewis X (sLe(X)), a key determinant of PSGL-1 binding to P-selectin, led to crystal structures of the SSL5-sLe(X) complex at resolutions of 1.65 and 2.75 A for crystals at two pH values. In both structures, sLe(X) bound to a specific site on the surface of the C-terminal domain of SSL5 in a conformation identical with that bound by P-selectin. Conservation of the key carbohydrate binding residues indicates that this ability to bind human glycans is shared by a substantial subgroup of the SSLs, including SSL2, SSL3, SSL4, SSL5, SSL6, and SSL11. This indicates that the ability to target human glycans is an important property of this group of toxins. Structural comparisons also showed that the Sia binding site in SSL5 contains a substructure that is shared by other Sia binding proteins from bacteria as well as viruses and represents a common binding motif.

Baker, H.M.; Basu, I.; Chung, M.C.; Caradoc-Davies, T.; Fraser, J.D.; Baker, E.N.

2009-06-02T23:59:59.000Z

363

Structural Basis for Nucleotide Binding and Reaction Catalysis in Mevalonate Diphosphate Decarboxylase  

SciTech Connect (OSTI)

Mevalonate diphosphate decarboxylase (MDD) catalyzes the final step of the mevalonate pathway, the Mg{sup 2+}-ATP dependent decarboxylation of mevalonate 5-diphosphate (MVAPP), producing isopentenyl diphosphate (IPP). Synthesis of IPP, an isoprenoid precursor molecule that is a critical intermediate in peptidoglycan and polyisoprenoid biosynthesis, is essential in Gram-positive bacteria (e.g., Staphylococcus, Streptococcus, and Enterococcus spp.), and thus the enzymes of the mevalonate pathway are ideal antimicrobial targets. MDD belongs to the GHMP superfamily of metabolite kinases that have been extensively studied for the past 50 years, yet the crystallization of GHMP kinase ternary complexes has proven to be difficult. To further our understanding of the catalytic mechanism of GHMP kinases with the purpose of developing broad spectrum antimicrobial agents that target the substrate and nucleotide binding sites, we report the crystal structures of wild-type and mutant (S192A and D283A) ternary complexes of Staphylococcus epidermidis MDD. Comparison of apo, MVAPP-bound, and ternary complex wild-type MDD provides structural information about the mode of substrate binding and the catalytic mechanism. Structural characterization of ternary complexes of catalytically deficient MDD S192A and D283A (k{sub cat} decreased 10{sup 3}- and 10{sup 5}-fold, respectively) provides insight into MDD function. The carboxylate side chain of invariant Asp{sup 283} functions as a catalytic base and is essential for the proper orientation of the MVAPP C3-hydroxyl group within the active site funnel. Several MDD amino acids within the conserved phosphate binding loop ('P-loop') provide key interactions, stabilizing the nucleotide triphosphoryl moiety. The crystal structures presented here provide a useful foundation for structure-based drug design.

Barta, Michael L.; McWhorter, William J.; Miziorko, Henry M.; Geisbrecht, Brian V. (UMKC)

2012-09-17T23:59:59.000Z

364

RNA-binding properties and RNA chaperone activity of human peroxiredoxin 1  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer hPrx1 has RNA-binding properties. Black-Right-Pointing-Pointer hPrx1 exhibits helix-destabilizing activity. Black-Right-Pointing-Pointer Cold stress increases hPrx1 level in the nuclear fraction. Black-Right-Pointing-Pointer hPrx1 enhances the viability of cells exposed to cold stress. -- Abstract: Human peroxiredoxin 1 (hPrx1), a member of the peroxiredoxin family, detoxifies peroxide substrates and has been implicated in numerous biological processes, including cell growth, proliferation, differentiation, apoptosis, and redox signaling. To date, Prx1 has not been implicated in RNA metabolism. Here, we investigated the ability of hPrx1 to bind RNA and act as an RNA chaperone. In vitro, hPrx1 bound to RNA and DNA, and unwound nucleic acid duplexes. hPrx1 also acted as a transcription anti-terminator in an assay using an Escherichia coli strain containing a stem-loop structure upstream of the chloramphenicol resistance gene. The overall cellular level of hPrx1 expression was not increased at low temperatures, but the nuclear level of hPrx1 was increased. In addition, hPrx1 overexpression enhanced the survival of cells exposed to cold stress, whereas hPrx1 knockdown significantly reduced cell survival under the same conditions. These findings suggest that hPrx1 may perform biological functions as a RNA-binding protein, which are distinctive from known functions of hPrx1 as a reactive oxygen species scavenger.

Kim, Ji-Hee; Lee, Jeong-Mi; Lee, Hae Na; Kim, Eun-Kyung; Ha, Bin [Lee Gil Ya Cancer and Diabetes Institute, Gachon University (Korea, Republic of)] [Lee Gil Ya Cancer and Diabetes Institute, Gachon University (Korea, Republic of); Ahn, Sung-Min, E-mail: smahn@gachon.ac.kr [Lee Gil Ya Cancer and Diabetes Institute, Gachon University (Korea, Republic of) [Lee Gil Ya Cancer and Diabetes Institute, Gachon University (Korea, Republic of); Department of Translational Medicine, Gachon University Gil Hospital, Incheon (Korea, Republic of); Jang, Ho Hee, E-mail: hhjang@gachon.ac.kr [Lee Gil Ya Cancer and Diabetes Institute, Gachon University (Korea, Republic of); Lee, Sang Yeol [Division of Applied Life Sciences (Brain Korea 21 program), Gyeongsang National University, Jinju 660-701 (Korea, Republic of)] [Division of Applied Life Sciences (Brain Korea 21 program), Gyeongsang National University, Jinju 660-701 (Korea, Republic of)

2012-09-07T23:59:59.000Z

365

Radii and Binding Energies of Nuclei in the Alpha-Cluster Model  

E-Print Network [OSTI]

The alpha-cluster model is based on two assumptions that the proton-neutron pair interactions are responsible for adherence between alpha-clusters and that the NN-interaction in the alpha-clusters is isospin independent. It allows one to estimate the Coulomb energy and the short range inter-cluster bond energy in dependence on the number of clusters. The charge radii are calculated on the number of alpha-clusters too. Unlike the Weizsacker formula in this model the binding energies of alpha-clusters and excess neutrons are estimated separately. The calculated values are in a good agreement with the experimental data.

G. K. Nie

2006-03-22T23:59:59.000Z

366

ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes  

DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. This database of evolutionary conserved regions (ECRs) in vertebrate genomes features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and fugu genomes. (taken from paper in Journal: Bioinformatics, November 7, 2006, pp. 122-124

Loots, Gabriela G. (LLNL); Ovcharenko, I. (LLNL)

367

Binding Effects in High-Energy Scattering Applied to K-Shell Ionization  

E-Print Network [OSTI]

PHYSICA L RE VIEW A VOLUME 11, NUMBER APRIL 1975 Binding effects in high-energy scattering applied to K-shell ionization* J. Binstock and J. F. Reading Physics Department and Cyclotron Institute, Texas ASM University, College Station, Texas 77843... (Received 30 October 1974) The equation describing scattering of a fast ion by a E-shell electron, ihv 881/BZ = exp (iHe Z/k ) V(r, R) exp (-sHeZ/h v) S? where He ( ) =- {0 /2~ e)+ r ?(@ /~e) l8 1n Xo (&)/~&~ 8/8&:?FT+ BT, is solved in the Glauber...

Binstock, J.; Reading, John F.

1975-01-01T23:59:59.000Z

368

Glucose oxidation in heart-type fatty acid binding protein null mice  

E-Print Network [OSTI]

of Genetics Faculty, James R. Wild August 2006 Major Subject: Genetics iii ABSTRACT Glucose Oxidation in Heart-Type Fatty Acid Binding Protein Null Mice. (August 2006) Sean Adhikari, B.S., University of Washington Chair of Advisory... was incubated in media solely containing the above reagents, and the other muscle was incubated in media containing the above reagents supplemented with either 1 mM palmitic acid, 2 mU/mL insulin (Humulin R), 2 mM AICAR, 0.5 mM 2,4- dinitrophenol (DNP), or a...

Adhikari, Sean

2006-10-30T23:59:59.000Z

369

The use of binding arbitration for Arizona's public works disputes as viewed from the contractor's perspective  

E-Print Network [OSTI]

Buildin s and Im rovements include contractual language in their contracts requiring optional binding arbitration for claims under $100, 000. 00. DEDICATION This thesis is dedicated to the contractors who took part in the survey. Their opinions... of the Associated General Contractors of American and Mr. John K. Mangum, Esq. for their direction in helping to define the scope of this research. I would also like to thank Mr. Melvin C. Cohen, Esq. for his suggestions and advise. I am grateful to my brother...

Bluff, Michael Robert

2012-06-07T23:59:59.000Z

370

Identification and functional characterization of lipid binding proteins in liver and adipose tissues of Gallus domesticus  

E-Print Network [OSTI]

; whereas the second hepatic lipid transport protein is most likely liver-FABP (L-FABP). An FABP from chicken adipose cytosol (A-FABP) was purified by membrane ultrafiltration and molecular sieve chromatography. Purification was verified by SDS... via ion exchange chromatography, pH 7. 73. Purification was verified by ligand binding assays and SDS-PAGE. The first protein eluted (designated ns-LTP) had a molecular weight of approximately 14. 5 kDa and the second protein (designated L...

Sams, Gretchen Hubler

1990-01-01T23:59:59.000Z

371

Sm and DNA Binding by dual reactive B cells requires distinct V{sub H}, V{sub {kappa}}, and V{sub H} CDR3 structures  

SciTech Connect (OSTI)

We have previously demonstrated an overlap of the anti-Sm and anti-DNA responses in MRL/Mp-Ipr/Ipr mice. The Ab produced by many anti-Sm hybridomas bind DNA and are encoded by Ig V genes used by anti-DNA hybridomas. In addition, some anti-Sm Ab that bind DNA have acquired mutations that improve DNA binding, indicating that DNA is a selecting Ag in the anti-Sm response. To gain insight into the basis for the dual binding ability of these Ab, we coexpressed the H chain from the anti-Sm hybridoma 2-12 with nine different L chains. Hybridoma 2-12 binds Sm but not DNA, yet expresses the same J558 V{sub H} gene as three anti-Sm hybridomas that bind ssDNA and at least one anti-DNA hybridoma that does not bind Sm. We found that most of the transfectoma Ab bind Sm, but their avidities vary over more than 3 orders of magnitude. Five of the nine transfectoma Ab bind ssDNA, and none bind dsDNA. In general, the ability to bind each Ag follows the binding ability of the hybridoma from which the L chain is derived. H Chain swapping experiments indicate that the H chain, V{sub H} CDR3 in particular contributes to the binding of both Sm and DNA. We conclude that Sm and DNA select for distinct features of V{sub H}, V{sub {kappa}}, and V{sub H} CDR3, suggesting selection by both Ag in the anti-Sm response.

Retter, M.W.; Eisenberg, R.A.; Cohen, P.L. [Univ. of North Carolina, Chapel Hill, NC (United States)] [and others

1995-08-15T23:59:59.000Z

372

Nuclear binding energy and symmetry energy of nuclear matter with modern nucleon-nucleon potentials  

SciTech Connect (OSTI)

Research Highlights: > The nuclear matter is studied within the Brueckner-Hartree-Fock (BHF) approach employing the most recent accurate nucleon-nucleon potentials. > The results come out by approximating the single particle self-consistent potential with a parabolic form. > We discuss the current status of the Coester line, i.e., density and energy of the various saturation points being strongly linearly correlated. > The nuclear symmetry energy is calculated as the difference between the binding energy of pure neutron matter and that of symmetric nuclear matter. - Abstract: The binding energy of nuclear matter at zero temperature in the Brueckner-Hartree-Fock approximation with modern nucleon-nucleon potentials is studied. Both the standard and continuous choices of single particle energies are used. These modern nucleon-nucleon potentials fit the deuteron properties and are phase shifts equivalent. Comparison with other calculations is made. In addition we present results for the symmetry energy obtained with different potentials, which is of great importance in astrophysical calculation.

Hassaneen, Kh.S.A., E-mail: khs_94@yahoo.com [Physics Department, Faculty of Science, Sohag University, Sohag (Egypt); Abo-Elsebaa, H.M.; Sultan, E.A. [Physics Department, Faculty of Science, Sohag University, Sohag (Egypt); Mansour, H.M.M. [Physics Department, Faculty of Science, Cairo University, Giza (Egypt)

2011-03-15T23:59:59.000Z

373

Posizione Matricola Corso di Laurea Magistrale Sede isc. Sede alt. Voto laurea Data nascita 1 765363 I-INGEGNERIA NUCLEARE MI BV 110 05/07/1988  

E-Print Network [OSTI]

765363 I-INGEGNERIA NUCLEARE MI BV 110 05/07/1988 2 766599 I-INGEGNERIA NUCLEARE MI 110 21/03/1988 3 764813 I-INGEGNERIA ELETTRICA MI 110 29/04/1987 4 765411 I-INGEGNERIA CHIMICA MI 110 23/05/1988 5 781546 NANOTECHNOLOGY MI 110 19/08/1989 6 778979 NANOTECHNOLOGY MI 110 21/05/1990 7 764495 I-INGEGNERIA NUCLEARE MI 110

374

Posizione Matricola Corso di Laurea Magistrale Sede isc. Sede alt. Voto laurea Data nascita 1 781330 I-GESTIONE DEL COSTRUITO MI 110 11/08/1988  

E-Print Network [OSTI]

781330 I-GESTIONE DEL COSTRUITO MI 110 11/08/1988 2 783933 I-GESTIONE DEL COSTRUITO MI BV 110 03/09/1987 3 766434 I-INGEGNERIA DEI SISTEMI EDILIZI MI 110 30/08/1988 4 761490 I-INGEGNERIA DEI SISTEMI EDILIZI MI 108 17/08/1989 5 776698 I-GESTIONE DEL COSTRUITO MI MI 106 02/05/1989 6 784798 I-INGEGNERIA DEI

375

Posizione Matricola Corso di Laurea Magistrale Sede isc. Sede alt. Voto laurea Data nascita 1 764721 I-INGEGNERIA MATEMATICA MI 110 05/11/1988  

E-Print Network [OSTI]

764721 I-INGEGNERIA MATEMATICA MI 110 05/11/1988 2 771099 I-INGEGNERIA BIOMEDICA MI 110 19/10/1987 3 783806 I-INGEGNERIA BIOMEDICA MI MI 110 19/05/1989 4 783463 I-INGEGNERIA BIOMEDICA MI MI 110 19/05/1989 5 769961 I-INGEGNERIA BIOMEDICA MI MI 110 10/01/1989 6 764825 I-INGEGNERIA MATEMATICA MI LC 110 22

376

Posizione Matricola Corso di Laurea Magistrale Sede isc. Sede alt. Voto laurea Data nascita 1 782252 A-ARCHITETTURA MI BV 110 07/05/1989  

E-Print Network [OSTI]

782252 A-ARCHITETTURA MI BV 110 07/05/1989 2 766298 A-PIANIFICAZIONE URBANA E POLITICHE TERRITORIALI MI BV 110 20/04/1989 3 770229 A-PIANIFICAZIONE URBANA E POLITICHE TERRITORIALI MI 110 27/06/1988 4 767317 A-ARCHITETTURA MI 110 13/06/1988 5 765987 A-PIANIFICAZIONE URBANA E POLITICHE TERRITORIALI MI 110

377

Posizione Matricola Corso di Luarea magistrale Sede isc. Sede alt. Voto laurea Data nascita 1 783525 I-INGEGNERIA INFORMATICA MI 110 10/04/1989  

E-Print Network [OSTI]

783525 I-INGEGNERIA INFORMATICA MI 110 10/04/1989 2 766724 I-INGEGNERIA ELETTRONICA MI 110 11/01/1989 3 752109 I-INGEGNERIA INFORMATICA MI 110 03/12/1984 4 783081 I-INGEGNERIA INFORMATICA MI BV 110 09/03/1989 5 783397 I-INGEGNERIA DELLE TELECOMUNICAZIONI MI 110 16/02/1988 6 750317 I-INGEGNERIA INFORMATICA MI

378

Posizione Matricola Corso di Laurea Magistrale Sede isc. Sede alt. Voto laurea Data nascita 1 783078 I-INGEGNERIA CIVILE MI CO 110 26/09/1989  

E-Print Network [OSTI]

783078 I-INGEGNERIA CIVILE MI CO 110 26/09/1989 2 783301 I-INGEGNERIA CIVILE MI 110 31/10/1989 3 767166 I-INGEGNERIA PER L'AMBIENTE E IL TERRITORIO MI 110 06/08/1988 4 784194 I-INGEGNERIA PER L'AMBIENTE E IL TERRITORIO MI 110 28/04/1989 5 783920 I-INGEGNERIA CIVILE MI MI 110 31/12/1989 6 782721 I-INGEGNERIA PER L

379

Addendum: Triton and hypertriton binding energies calculated from SU_6 quark-model baryon-baryon interactions  

E-Print Network [OSTI]

Previously we calculated the binding energies of the triton and hypertriton, using an SU_6 quark-model interaction derived from a resonating-group method of two baryon clusters. In contrast to the previous calculations employing the energy-dependent interaction kernel, we present new results using a renormalized interaction, which is now energy independent and reserves all the two-baryon data. The new binding energies are slightly smaller than the previous values. In particular the triton binding energy turns out to be 8.14 MeV with a charge-dependence correction of the two-nucleon force, 190 keV, being included. This indicates that about 350 keV is left for the energy which is to be accounted for by three-body forces.

Y. Fujiwara; Y. Suzuki; M. Kohno; K. Miyagawa

2007-09-29T23:59:59.000Z

380

Transcription Factors Bind Thousands of Active and InactiveRegions in the Drosophila Blastoderm  

SciTech Connect (OSTI)

Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. Here, we use whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior-posterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to highly overlapping sets of several thousand genomic regions in blastoderm embryos. Specific high- and moderate-affinity in vitro recognition sequences for each factor are enriched in bound regions. This enrichment, however, is not sufficient to explain the pattern of binding in vivo and varies in a context-dependent manner, demonstrating that higher-order rules must govern targeting of transcription factors. The more highly bound regions include all of the over forty well-characterized enhancers known to respond to these factors as well as several hundred putative new cis-regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. The new targets include most of the microRNAs (miRNAs) transcribed in the blastoderm, as well as all major zygotically transcribed dorsal-ventral patterning genes, whose expression we show to be quantitatively modulated by anterior-posterior factors. In addition to these highly bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly bound regions; are preferentially found in protein-coding sequences; and are less conserved than highly bound regions. Together these observations suggest that many of these poorly-bound regions are not involved in early-embryonic transcriptional regulation, and a significant proportion may be nonfunctional. Surprisingly, for five of the six factors, their recognition sites are not unambiguously more constrained evolutionarily than the immediate flanking DNA, even in more highly bound and presumably functional regions, indicating that comparative DNA sequence analysis is limited in its ability to identify functional transcription factor targets.

Li, Xiao-Yong; MacArthur, Stewart; Bourgon, Richard; Nix, David; Pollard, Daniel A.; Iyer, Venky N.; Hechmer, Aaron; Simirenko, Lisa; Stapleton, Mark; Luengo Hendriks, Cris L.; Chu, Hou Cheng; Ogawa, Nobuo; Inwood, William; Sementchenko, Victor; Beaton, Amy; Weiszmann, Richard; Celniker, Susan E.; Knowles, David W.; Gingeras, Tom; Speed, Terence P.; Eisen, Michael B.; Biggin, Mark D.

2008-01-10T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


381

Binding energetics of substitutional and interstitial helium and di-helium defects with grain boundary structure in ?-Fe  

SciTech Connect (OSTI)

The formation/binding energetics and length scales associated with the interaction between He atoms and grain boundaries in BCC ?-Fe were explored. Ten different low ? grain boundaries from the ?100? and ?110? symmetric tilt grain boundary systems were used. In this work, we then calculated formation/binding energies for 12 He atoms in the substitutional and interstitial sites (HeV, He{sub 2}V, HeInt, He{sub 2}Int) at all potential grain boundary sites within 15? of the boundary (52?826 simulations total). The present results provide detailed information about the interaction energies and length scales of 12 He atoms with grain boundaries for the structures examined. A number of interesting new findings emerge from the present study. For instance, the ?3(112) twin boundary in BCC Fe possesses a much smaller binding energy than other boundaries, which corresponds in long time dynamics simulations to the ability of an interstitial He defect to break away from the boundary in simulations on the order of nanoseconds. Additionally, positive correlations between the calculated formation/binding energies of the He defects (R?>?0.9) asserts that the local environment surrounding each site strongly influences the He defect energies and that highly accurate quantum mechanics calculations of lower order defects may be an adequate predictor of higher order defects. Various metrics to quantify or classify the local environment were compared with the He defect binding energies. The present work shows that the binding and formation energies for He defects are important for understanding the physics of He diffusion and trapping by grain boundaries, which can be important for modeling He interactions in polycrystalline steels.

Tschopp, M. A., E-mail: mark.tschopp@gatech.edu [Dynamic Research Corporation, (on site at) U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States); Center for Advanced Vehicular Systems, Mississippi State University, Starkville, Mississippi 39762 (United States); Gao, F.; Yang, L. [Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Solanki, K. N. [Arizona State University, School for Engineering of Matter, Transport and Energy, Tempe, Arizona 85287 (United States)

2014-01-21T23:59:59.000Z

382

Crystal structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains  

E-Print Network [OSTI]

binding site. Using atomic absorption spectroscopy and TrpElmer AAnalyst 400 atomic absorption spectrometer (AAS) withthe metal, we employed atomic absorption spectroscopy on the

Zheng, Meiying

2009-01-01T23:59:59.000Z

383

Full $0\\hbar?$ shell model calculation of the binding energies of the $1f_{7/2}$ nuclei  

E-Print Network [OSTI]

Binding energies and other global properties of nuclei in the middle of the $pf$ shell, such as M1, E2 and Gamow-Teller sum rules, have been obtained using a new Shell Model code (NATHAN) written in quasi-spin formalism and using a $j-j$-coupled basis. An extensive comparison is made with the recently available Shell Model Monte Carlo results using the effective interaction KB3. The binding energies for -nearly- all the $1f_{7/2}$ nuclei are compared with the measured (and extrapolated) results.

E. Caurier; G. Martinez-Pinedo; F. Nowacki; A. Poves; J. Retamosa; A. P. Zuker

1998-09-23T23:59:59.000Z

384

Benchmark Theoretical Study of the ?? Binding Energy in the Benzene Dimer  

SciTech Connect (OSTI)

We establish a new estimate for the interaction energy between two benzene molecules in the parallel displaced (PD) conformation by systematically converging (i) the intra- and intermolecular geometry at the minimum geometry, (ii) the expansion of the orbital basis set and (iii) the level of electron correlation. The calculations were performed at the second order Mller - Plesset perturbation (MP2) and the Coupled Cluster including Singles, Doubles and a perturbative estimate of Triples replacements [CCSD(T)] levels of electronic structure theory. At both levels of theory, by including results corrected for Basis Set Superposition Error (BSSE), we have estimated the Complete Basis Set (CBS) limit by employing the family of Dunnings correlation consistent polarized valence basis sets. The largest MP2 calculation was performed with the cc-pV6Z basis set (2,772 basis functions), whereas the largest CCSD(T) calculation with the cc-pV5Z basis set (1,752 basis functions). The cluster geometries were optimized with basis sets up to quadruple-? quality, observing that both its intra- and inter-molecular parts have practically converged with the triple-? quality sets. The use of converged geometries was found to play an important role for obtaining accurate estimates for the CBS limits. Our results demonstrate that the binding energies with the families of the plain (cc-pVnZ) and augmented (aug-cc-pVnZ) sets converge [to within < 0.01 kcal/mol for MP2 and < 0.15 kcal/mol for CCSD(T)] to the same CBS limit. In addition, the average of the uncorrected and BSSEcorrected binding energies was found to converge to the same CBS limit must faster than either of the two constituents (uncorrected or BSSE-corrected binding energies). Due to the fact that the family of augmented basis sets (especially for the larger sets) causes serious linear dependency problems, the plain basis sets (for which no linear dependencies were found) are deemed as a more efficient and straightforward path for obtaining an accurate CBS limit. We considered extrapolations of the uncorrected (?𝐸) and BSSE-corrected (?𝐸!") binding energies, their average value (?𝐸!"#) as well as the average of the latter over the plain and augmented sets (?𝐸!"#) with the cardinal number of the basis set n. Our best estimate of the CCSD(T)/CBS limit for the ?-? interaction energy in the PD benzene dimer is De = 2.65 0.02 kcal/mol. The best CCSD(T)/cc-pV5Z calculated value is 2.62 kcal/mol, just 0.03 kcal/mol away from the CBS limit. For comparison, the MP2/CBS limit estimate is 5.00 0.01 kcal/mol, demonstrating a 90% overbinding with respect to CCSD(T). The Spin-Component-Scaled (SCS) MP2 variant was found to closely reproduce the CCSD(T) results for each basis set, while Scaled-Opposite-Spin (SOS) yielded results that are too low when compared to CCSD(T).

Miliordos, Evangelos; Apra, Edoardo; Xantheas, Sotiris S.

2014-09-04T23:59:59.000Z

385

Visualization of Iron-Binding Micelles in Acidic Recombinant Biomineralization Protein, MamC  

SciTech Connect (OSTI)

Biological macromolecules are utilized in low-temperature synthetic methods to exert precise control over nanoparticle nucleation and placement. They enable low-temperature formation of a variety of functional nanostructured materials with properties often not achieved via conventional synthetic techniques. Here we report on the in situ visualization of a novel acidic bacterial recombinant protein, MamC, commonly present in the magnetosome membrane of several magnetotactic bacteria, including Magnetococcus marinus, strain MC-1. Our findings provide an insight into the self-assembly of MamC and point to formation of the extended protein surface, which is assumed to play an important role in the formation of biotemplated inorganic nanoparticles. The self-organization of MamC is compared to the behavior of another acidic recombinant iron-binding protein, Mms6.

Kashyap, Sanjay [Ames Laboratory; Woehl, Taylor [Ames Laboratory; Valverde-Tercedor, Carmen [University of Granada; Sanchez-Quesada, Miguel [University of Granada; Lopez, Concepcion Jimenez [University of Granada; Prozorov, Tanya [Ames Laboratory

2014-03-07T23:59:59.000Z

386

Binding energy of singlet excitons and charge transfer complexes in MDMO-PPV:PCBM solar cells  

E-Print Network [OSTI]

The influence of an external electric field on the photoluminescence intensity of singlet excitons and charge transfer complexes is investigated for a poly[2-methoxy-5-(3',7'-dimethyloctyloxy)-1,4-phenylenevinylene] (MDMO-PPV) diode and a bulk heterojunction of the PPV in combination with [6,6]-phenyl-C61 butyric acid methylester (PCBM), respectively. The experimental data is related to the dissociation probability derived from the Onsager-Braun model. In this way, a lower limit for the singlet exciton binding energy of MDMO-PPV is determined as (327 +- 30) meV, whereas a significantly lower value of (203 +- 18) meV is extracted for the charge transfer complex in a MDMO-PPV:PCBM blend.

Kern, Julia; Deibel, Carsten; Dyakonov, Vladimir

2011-01-01T23:59:59.000Z

387

3D calculation of Tucson-Melbourne 3NF effect in triton binding energy  

E-Print Network [OSTI]

As an application of the new realistic three-dimensional (3D) formalism reported recently for three-nucleon (3N) bound states, an attempt is made to study the effect of three-nucleon forces (3NFs) in triton binding energy in a non partial wave (PW) approach. The spin-isospin dependent 3N Faddeev integral equations with the inclusion of 3NFs, which are formulated as function of vector Jacobi momenta, specifically the magnitudes of the momenta and the angle between them, are solved with Bonn-B and Tucson-Melbourne NN and 3N forces in operator forms which can be incorporated in our 3D formalism. The comparison with numerical results in both, novel 3D and standard PW schemes, shows that non PW calculations avoid the very involved angular momentum algebra occurring for the permutations and transformations and it is more efficient and less cumbersome for considering the 3NF.

M. R. Hadizadeh; L. Tomio; S. Bayegan

2010-03-24T23:59:59.000Z

388

Atmospheric Oxygen Binding and Hole Doping in Deformed Graphene on a SiO2 Substrate  

E-Print Network [OSTI]

Using micro-Raman spectroscopy and scanning tunneling microscopy, we study the relationship between structural distortion and electrical hole doping of graphene on a silicon dioxide substrate. The observed upshift of the Raman G band represents charge doping and not compressive strain. Two independent factors control the doping: (1) the degree of graphene coupling to the substrate, and (2) exposure to oxygen and moisture. Thermal annealing induces a pronounced structural distortion due to close coupling to SiO2 and activates the ability of diatomic oxygen to accept charge from graphene. Gas flow experiments show that dry oxygen reversibly dopes graphene; doping becomes stronger and more irreversible in the presence of moisture and over long periods of time. We propose that oxygen molecular anions are stabilized by water solvation and electrostatic binding to the silicon dioxide surface.

Sunmin Ryu; Li Liu; Stephane Berciaud; Young-Jun Yu; Haitao Liu; Philip Kim; George W. Flynn; Louis E. Brus

2010-11-13T23:59:59.000Z

389

Phospholamban mutants compete with wild type for SERCA binding in living cells  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer PLB phosphorylation in HEK cells increased FRET between YFP-PLB and CFP-SERCA. Black-Right-Pointing-Pointer Competition: Expressing loss-of-function PLB mutants in the system decreased FRET. Black-Right-Pointing-Pointer The FRET assay could screen potential therapeutic PLB mutants to activate SERCA. -- Abstract: We have used fluorescent fusion proteins stably expressed in HEK cells to detect directly the interaction between the sarcoplasmic reticulum Ca-ATPase (SERCA) and phospholamban (PLB) in living cells, in order to design PLB mutants for gene therapy. Ca{sup 2+} cycling in muscle cells depends strongly on SERCA. Heart failure (HF), which contributes to 12% of US deaths, typically exhibits decreased SERCA activity, and several potential therapies for HF aim to increase SERCA activity. We are investigating the use of LOF-PLB mutants (PLB{sub M}) as gene therapy vectors to increase SERCA activity. Active SERCA1a and WT-PLB, tagged at their N termini with fluorescent proteins (CFP and YFP), were coexpressed in stable HEK cell lines, and fluorescence resonance energy transfer (FRET) was used to detect their interaction directly. Phosphorylation of PLB, induced by forskolin, caused an increase in FRET from CFP-SERCA to YFP-PLB, indicating that SERCA inhibition can be relieved without dissociation of the complex. This suggests that a LOF mutant might bind to SERCA with sufficient affinity to complete effectively with WT-PLB, thus relieving SERCA inhibition. Therefore, we transiently expressed a series of PLB{sub M} in the CFP-SERCA/YFP-PLB cell line, and found decreased FRET, implying competition between PLB{sub M} and WT-PLB for binding to SERCA. These results establish this FRET assay as a rapid and quantitative means of screening PLB{sub M} for optimization of gene therapy to activate SERCA, as needed for gene therapy in HF.

Gruber, Simon J.; Haydon, Suzanne [Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455 (United States)] [Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455 (United States); Thomas, David D., E-mail: ddt@umn.edu [Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455 (United States)

2012-04-06T23:59:59.000Z

390

Structural and Biochemical Determinants of Ligand Binding by the c-di-GMP Riboswitch  

SciTech Connect (OSTI)

The bacterial second messenger c-di-GMP is used in many species to control essential processes that allow the organism to adapt to its environment. The c-di-GMP riboswitch (GEMM) is an important downstream target in this signaling pathway and alters gene expression in response to changing concentrations of c-di-GMP. The riboswitch selectively recognizes its second messenger ligand primarily through contacts with two critical nucleotides. However, these two nucleotides are not the most highly conserved residues within the riboswitch sequence. Instead, nucleotides that stack with c-di-GMP and that form tertiary RNA contacts are the most invariant. Biochemical and structural evidence reveals that the most common natural variants are able to make alternative pairing interactions with both guanine bases of the ligand. Additionally, a high-resolution (2.3 {angstrom}) crystal structure of the native complex reveals that a single metal coordinates the c-di-GMP backbone. Evidence is also provided that after transcription of the first nucleotide on the 3{prime}-side of the P1 helix, which is predicted to be the molecular switch, the aptamer is functional for ligand binding. Although large energetic effects occur when several residues in the RNA are altered, mutations at the most conserved positions, rather than at positions that base pair with c-di-GMP, have the most detrimental effects on binding. Many mutants retain sufficient c-di-GMP affinity for the RNA to remain biologically relevant, which suggests that this motif is quite resilient to mutation.

Smith, K.; Lipchock, S; Livingston,; Shanahan, C; Strobel, S

2010-01-01T23:59:59.000Z

391

Morphine-6-glucuronide: analgesic effects and receptor binding profile in rats  

SciTech Connect (OSTI)

The antinociceptive effects of morphine-6-glucuronide (M6G) were examined in two animal models of pain, the tail immersion test (reflex withdrawal to noxious heat) and the formalin test (behavioral response to minor tissue injury). In the tail immersion test, M6G produced and increase in withdrawal latency that rose rapidly between 0.01 and 0.025 ug ICV or 1 and 2 mg/kg SC. A further increase occurred at doses greater than 0.2 ug ICV or 4 mg/kg SC and was associated with marked catelepsy and cyanosis. Naloxone, 0.1 mg/kg SC, shifted the lower component of the dose-effect relation by a factor of 24. In the formalin test, 0.01 ug M6G ICV produced hyperalgesia, while between 0.05 and 0.2 ug ICV, antinociception increased rapidly without toxicity. The dose effect relations for hyperalgesia and antinociception were shifted to the right by factors of 20- and 3-fold, respectively. By comparison, ICV morphine was 60 (formalin test) to 145-200 (tail immersion test) times less potent than M6G. At sub-nanomolar concentrations, M6G enhanced the binding of (/sup 3/H)-etorphine, (/sup 3/H)-dihydromorphine and (/sup 3/H)-naloxone to rat brain membrane receptors by 20-40%. At higher concentrations, M6G displaced each ligand from binding sites, with K/sub i/ values of about 30 nM, as compared to morphine K/sub i/ values of about 3 nM.

Abbott, F.V.; Palmour, R.M.

1988-01-01T23:59:59.000Z

392

Studies on the binding of 5-N-methylated quindoline derivative to human telomeric G-quadruplex  

SciTech Connect (OSTI)

Research highlights: {yields} Hydrophobic interaction provided an important driving force for the interaction between ligand and G-quadruplex. {yields} Constrained water molecules were released from surface of G-tetrad upon the formation of the complex. {yields} The end-stacking mode for quindoline derivative was validated through UV-vis, ITC, steady-state, and time-resolved fluorescence experiment. {yields} The binding of compound 1 to quadruplex was found to be a temperature-dependent and enthalpy-entropy compensation process. -- Abstract: Quindoline derivatives as telomeric quadruplex ligands have shown good biological activity for telomerase inhibition. In the present study, we used spectroscopic and calorimetric methods to investigate the interactions between a quindoline derivative (5-methyl-11-(2-morpholinoethylamino)-10-H-indolo-[3,2-b]quinolin-5-ium iodide, compound 1) and human telomeric G-quadruplex. The thermodynamic studies using isothermal titration calorimetry (ITC) indicated that their binding process was temperature-dependent and enthalpy-entropy co-driven. The significant negative heat capacity was obtained experimentally from the temperature dependence of enthalpy changes, which was consistent with that from theoretical calculation, and all suggesting significant hydrophobic contribution to the molecular recognition process. Based on the results from UV-vis, ITC, steady-state and time-resolved fluorescence, their binding mode was determined as two ligand molecules stacking on the quartets on both ends of the quadruplex. These results shed light on rational design and development of quindoline derivatives as G-quadruplex binding ligands.

Xu, Wei; Tan, Jia-Heng; Chen, Shuo-Bin; Hou, Jin-Qiang; Li, Ding [School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006 (China)] [School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006 (China); Huang, Zhi-Shu, E-mail: ceshzs@mail.sysu.edu.cn [School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006 (China)] [School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006 (China); Gu, Lian-Quan, E-mail: cesglq@mail.sysu.edu.cn [School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006 (China)] [School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006 (China)

2011-03-18T23:59:59.000Z

393

Nucleoprotein of influenza B virus binds to its type A counterpart and disrupts influenza A viral polymerase complex formation  

SciTech Connect (OSTI)

Highlights: FluB nucleoprotein (BNP) can bind to FluA nucleoprotein (ANP). BNPANP interaction inhibits FluA polymerase activity. BNP binding prevents ANP from forming a functional FluA polymerase complex. Nuclear localization of BNP is necessary for FluA polymerase inhibition. Viral RNA is not required for the BNPANP interaction. -- Abstract: Upon co-infection with influenza B virus (FluB), influenza A virus (FluA) replication is substantially impaired. Previously, we have shown that the nucleoprotein of FluB (BNP) can inhibit FluA polymerase machinery, retarding the growth of FluA. However, the molecular mechanism underlying this inhibitory action awaited further investigation. Here, we provide evidence that BNP hinders the proper formation of FluA polymerase complex by competitively binding to the nucleoprotein of FluA. To exert this inhibitory effect, BNP must be localized in the nucleus. The interaction does not require the presence of the viral RNA but needs an intact BNP RNA-binding motif. The results highlight the novel role of BNP as an anti-influenza A viral agent and provide insights into the mechanism of intertypic interference.

Jaru-ampornpan, Peera, E-mail: peera.jar@biotec.or.th; Narkpuk, Jaraspim; Wanitchang, Asawin; Jongkaewwattana, Anan, E-mail: anan.jon@biotec.or.th

2014-01-03T23:59:59.000Z

394

A Distal Arginine in Oxygen-Sensing Heme-PAS Domains Is Essential to Ligand Binding, Signal Transduction, and Structure  

E-Print Network [OSTI]

loop (the FG loop) with the helix of heme attachment was weakened. Binding of carbon monoxide was nevertheless preserved. Carbon monoxide and nitric oxide regulation, although weak in BjFixL, were abolished basic helix-loop-helix (bHLH) transcription factor and two different groups of microbial enzymes (3, 4

Scott, William

395

Mapping the Phospholipid-binding Surface and Translocation Determinants of the C2 Domain from Cytosolic Phospholipase A2*  

E-Print Network [OSTI]

in living cells. We have identified sets of exposed hydro- phobic residues in loops known as calcium C2 domain, we show that two of the calcium-binding loops, CBR1 and CBR3, penetrate in a calcium to translocate in a calcium-dependent manner from the cytosol to the nuclear envelope and endoplasmic retic- ulum

Williams, Roger L.

396

Effect of lactose feeding on cell renewal, disaccharidase activity and calcium-binding protein content in the intestinal  

E-Print Network [OSTI]

is injected into the lumen of the intestinal ligated loop, the absorption of calcium increases onlyEffect of lactose feeding on cell renewal, disaccharidase activity and calcium-binding protein Edouard Herriot, 69374 Lyon Cedex 2, France. Summary. To determine how lactose increases calcium

Paris-Sud XI, Université de

397

Effect of Polyethylene Glycol, Alkyl, and Oligonucleotide Spacers on the Binding, Secondary Structure, and Self-Assembly of Fractalkine  

E-Print Network [OSTI]

Effect of Polyethylene Glycol, Alkyl, and Oligonucleotide Spacers on the Binding, Secondary-amphiphiles with no spacer (NoSPR), polyethylene glycol (PEG4, PEG8, PEG24), alkyl (C12 and C24), or oligonucleotide (T10 a polyethylene glycol (PEG) or an oligo-T (thymine) spacer is added to the aptamer, especially when attaching

Kokkoli, Efie

398

Metal binding to dissolved organic matter and adsorption to ferrihydrite in shallow peat groundwaters: Application to diamond exploration  

E-Print Network [OSTI]

Metal binding to dissolved organic matter and adsorption to ferrihydrite in shallow peat t The speciation and solubility of kimberlite pathfinder metals (Ni, Nd, Ba and K) in shallow peat ground- waters with kimberlite pathfinder metals and determine the spatial distribution of those metals in shallow peat

399

THE JOURNAL OF CHEMICAL PHYSICS 134, 134701 (2011) Binding of hydrogen on benzene, coronene, and graphene from quantum  

E-Print Network [OSTI]

, and graphene from quantum Monte Carlo calculations Jie Ma,1,2,3 Angelos Michaelides,2,3,4 and Dario Alfè3 the binding energy curves of hydrogen on benzene, coronene, and graphene. The DMC results on benzene agree well with MP2, giving an adsorption energy of 40 meV. For physisorbed hydrogen on graphene, DMC

Alfè, Dario

400

Interactions between ultraviolet light and interleukin-1 on MSH binding in both mouse melanoma and human squamous carcinoma cells  

SciTech Connect (OSTI)

Interactions between beta-melanotropin (MSH), interleukin 1-a (IL-1), and ultraviolet light (UV) were examined in Cloudman S91 mouse melanoma and RHEK human squamous carcinoma cell lines. The following points were established: (1) both cell lines produced IL-1 and their production was stimulated by exposure of the cells to UV; (2) both cell lines possessed high affinity binding sites for MSH, and their ability to bind MSH was modulated by IL-1; (3) IL-1 exhibited both stimulatory and inhibitory effects on MSH binding to Cloudman cells; and (4) the stimulatory effect of IL-1 on MSH binding to melanoma cells was reflected in enhanced cellular responsiveness to MSH regarding tyrosinase activity (E.C. 1.14.18.1) and melanin content. The findings raise the possibility that interactions between keratinocytes and melanocytes may be regulated by IL-1 and MSH, and suggest a possible mechanism for stimulation of cutaneous melanogenesis by solar radiation: enhancement of MSH receptor activity by induction of IL-1.

Birchall, N.; Orlow, S.J.; Kupper, T.; Pawelek, J. (Univ. of Auckland, (New Zealand))

1991-03-29T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


401

The integrity of a cholesterol-binding pocket in NiemannPick C2 protein is necessary to  

E-Print Network [OSTI]

cholesterol accumulation in cells. We find that purified NPC2, a secreted soluble protein, binds cholesterol as important, including one required for efficient secretion. point mutants secretion protein evolution Niemann. At the cellular level, mutant cells accumulate cholesterol and other lipids in aberrant compartments with features

Quake, Stephen R.

402

Ensemble Modeling of Substrate Binding to Cytochromes P450: Analysis of Catalytic Differences between CYP1A Orthologs,  

E-Print Network [OSTI]

Ensemble Modeling of Substrate Binding to Cytochromes P450: Analysis of Catalytic Differences substrates (TCB and B[a]P) as well as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) were docked to multiple observed closer to the heme in ensembles of rat or human CYP1A1 than of killifish CYP1A. Analysis

Vajda, Sandor

403

Free Energy Component Analysis for Drug Design: A Case Study of HIV-1 Protease-Inhibitor Binding  

E-Print Network [OSTI]

Free Energy Component Analysis for Drug Design: A Case Study of HIV-1 Protease-Inhibitor Binding energy component analysis that conveys information on the physicochemical forces driving the protein for a specific protein target if not in the general case. It is here that the free energy component analysis

Jayaram, Bhyravabotla

404

A Double-Deletion Method to Quantifying Incremental Binding Energies in Proteins from Experiment: Example of a Destabilizing Hydrogen  

E-Print Network [OSTI]

A Double-Deletion Method to Quantifying Incremental Binding Energies in Proteins from Experiment: Example of a Destabilizing Hydrogen Bonding Pair Luis A. Campos,*y Santiago Cuesta-Lo´pez,*z Jon Lo of a specific hydrogen bond in apoflavodoxin to protein stability is investigated by combining theory

Sancho, Javier

405

Hydrogen Bonds Involved in Binding the Qi-site Semiquinone in the bc1 Complex, Identified through Deuterium Exchange  

E-Print Network [OSTI]

Hydrogen Bonds Involved in Binding the Qi-site Semiquinone in the bc1 Complex, Identified through them. The strength of interactions indicates that the protons are involved in hydrogen bonds with SQ. The hyperfine cou- plings differ from values typical for in-plane hydrogen bonds previously observed in model

Crofts, Antony R.

406

ATP Utilization by Yeast Replication Factor C III. THE ATP-BINDING DOMAINS OF Rfc2, Rfc3, AND Rfc4 ARE ESSENTIAL FOR DNA RECOGNITION AND  

E-Print Network [OSTI]

ATP Utilization by Yeast Replication Factor C III. THE ATP-BINDING DOMAINS OF Rfc2, Rfc3, AND Rfc4 lysine in the Walker A motif of the ATP- binding domain encoded by the yeast RFC1, RFC2, RFC3, and RFC4 loading activity. In addition to their defects in ATP hydrolysis, these complexes were defective for DNA

Burgers, Peter M.

407

Involvement of ATP synthase residues aArg-376, bArg-182, and bLys-155 in Pi binding  

E-Print Network [OSTI]

Involvement of ATP synthase residues aArg-376, bArg-182, and bLys-155 in Pi binding Zulfiqar AhmadArg-182 are catalytically important ATP synthase residues that were proposed to be in- volved in substrate Pi binding and subsequent steps of ATP syn- thesis [Senior, A.E., Nadanaciva, S. and Weber, J. (2002

Zulfiqar Ahmad

408

Letters to the Editor Resonance assignments of 30 kDa complexes of TFIID subunit TAF1 with TATA-binding protein  

E-Print Network [OSTI]

occupies TATA binding concave surface of TBP thereby inhibiting the DNA-binding activity of TBP. In yeast y- mined. We report backbone 1 H, 13 C and 15 N chemical shifts of TBP-yTAND1-2 and TBP-dTAND1 complexes Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02115, USA; e Division

Ikura, Mitsuhiko

409

A tight-binding potential for atomistic simulations of carbon interacting with transition metals: Application to the Ni-C system  

E-Print Network [OSTI]

for transition metals, carbon, and transition metal carbides, which has been optimized through a systematicA tight-binding potential for atomistic simulations of carbon interacting with transition metals of the transition metal, is used to obtain a transferable tight-binding model of the carbon-carbon, metal-metal

Paris-Sud XI, Université de

410

The Exact Form of the Green's Function of the Hckel (Tight Binding) Model  

E-Print Network [OSTI]

The applications of the H\\"uckel (tight binding) model are ubiquitous in quantum chemistry and solid state physics. The matrix representation is isomorphic to an unoriented vertex adjacency matrix of a bipartite graph, which is also the Laplacian matrix plus twice the identity. In this paper, we analytically calculate the determinant and, when it exists, the inverse of this matrix in connection with the Green's function, $\\mathbf{G}$, of the $N\\times N$ H\\"uckel matrix for linear chains and cyclic systems. For an open linear chain we prove that $\\mathbf{G}$ is a real symmetric matrix whose entries are $G\\left(r,s\\right)=\\left(-1\\right)^{\\frac{r+s-1}{2}}$ when $ $$r$ is even and $s

Ramis Movassagh; Yuta Tsuji; Roald Hoffmann

2014-08-13T23:59:59.000Z

411

Binding of copper and nickel to cavities in silicon formed by helium ion implantation  

SciTech Connect (OSTI)

Cavities formed in Si by He ion implantation and annealing are shown to be strong traps for Cu and Ni impurities. Experiments utilizing ion-beam analysis and transmission electron microscopy indicate that Cu is trapped at the internal surfaces of cavities up to {approximately}1 monolayer coverage with a binding energy of 2.2{plus_minus}0.2 eV relative to solution. This is greater than the heat of solution from the precipitated Cu{sub 3}Si phase, determined to be 1.7 eV in agreement with earlier work. Copper at cavity-wall sites is reversibly replaced by H during heating in H{sub 2} gas, indicating the relative stability of the two surface terminations. Initial results for Ni impurities indicate that trapping at cavities is again energetically preferred to silicide formation. The saturation coverage of Ni on the internal surfaces, however, is an order of magnitude smaller for Ni than Cu, consistent with published studies of external-surface adsorption. These results suggest that cavity trapping may getter metallic impurities in Si more effectively than methods based on silicide precipitation.

Myers, S.M.; Follstaedt, D.M.; Bishop, D.M.

1993-12-01T23:59:59.000Z

412

Natural and accelerated CO{sub 2} binding kinetics in cement paste at different relative humidities  

SciTech Connect (OSTI)

Natural carbonation and accelerated carbonation are compared in terms of CO{sub 2} combination. Thermogravimetrical analysis, neutron diffraction and weight measurements were used to quantify the amounts of CO{sub 2} in samples exposed to different CO{sub 2} and relative humidity (RH) conditions. An exponential equation is proposed to describe temporal evolution: combination rates and maximum values are obtained both for natural and accelerated processes. The influence of RH in these parameters is analyzed. At 100% CO{sub 2} an increase of RH from 53 to 75% diminishes the combination rate considerably, but increases slightly the maximum CO{sub 2} binding. At 0.5% CO{sub 2} both the rate and the maximum are higher for intermediate RH, with a linear relation between both variables. Equivalences between the different processes have been calculated: the amount of CO{sub 2} combined in 1 h at 100% CO{sub 2} and 65% RH carbonation is equivalent to approximately 36 days of natural exposure outside and 54 days inside.

Galan, Isabel, E-mail: isabelgalan@abdn.ac.uk [University of Aberdeen, Department of Chemistry, Meston Walk, AB24 3UE (United Kingdom)] [University of Aberdeen, Department of Chemistry, Meston Walk, AB24 3UE (United Kingdom); Andrade, Carmen; Castellote, Marta [Eduardo Torroja Institute CSIC, Serrano Galvache 4, 28033 Madrid (Spain)] [Eduardo Torroja Institute CSIC, Serrano Galvache 4, 28033 Madrid (Spain)

2013-07-15T23:59:59.000Z

413

Intestinal-fatty acid binding protein and lipid transport in human intestinal epithelial cells  

SciTech Connect (OSTI)

Intestinal-fatty acid binding protein (I-FABP) is a 14-15 kDa cytoplasmic molecule highly expressed in the enterocyte. Although different functions have been proposed for various FABP family members, the specific function of I-FABP in human intestine remains unclear. Here, we studied the role of I-FABP in molecularly modified normal human intestinal epithelial cells (HIEC-6). cDNA transfection resulted in 90-fold I-FABP overexpression compared to cells treated with empty pQCXIP vector. The high-resolution immunogold technique revealed labeling mainly in the cytosol and confirmed the marked phenotype abundance of I-FABP in cDNA transfected cells. I-FABP overexpression was not associated with alterations in cell proliferation and viability. Studies using these transfected cells cultured with [{sup 14}C]oleic acid did not reveal higher efficiency in de novo synthesis or secretion of triglycerides, phospholipids, and cholesteryl esters compared to cells treated with empty pQCXIP vector only. Similarly, the incubation with [{sup 35}S]methionine did not disclose a superiority in the biogenesis of apolipoproteins (apo) A-I, A-IV, B-48, and B-100. Finally, cells transfected with I-FABP did not exhibit an increased production of chylomicrons, VLDL, LDL, and HDL. Our observations establish that I-FABP overexpression in normal HIEC-6 is not related to cell proliferation, lipid esterification, apo synthesis, and lipoprotein assembly, and, therefore, exclude its role in intestinal fat transport.

Montoudis, Alain [Department of Nutrition, Universite de Montreal and Research Center, CHU Sainte Justine, 3175 Cote Ste-Catherine, Montreal, Que., H3T 1C5 (Canada); Delvin, Edgard [Department of Biochemistry, Universite de Montreal and Research Center, CHU Sainte Justine, 3175 Cote Ste-Catherine, Montreal, Que., H3T 1C5 (Canada); Canadian Institute of Health Research, Group of the Functional Development and Physiopathology of the Digestive Tract, and Department of Anatomy and Cellular Biology, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, Que., Canada J1H 5N4 (Canada); Menard, Daniel [Department of Pathology and Cell Biology, Universite de Montreal and Research Center, CHU Sainte Justine, 3175 Cote Ste-Catherine, Montreal, Que., H3T 1C5 (Canada); Canadian Institute of Health Research, Group of the Functional Development and Physiopathology of the Digestive Tract, and Department of Anatomy and Cellular Biology, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, Que., J1H 5N4 (Canada)] (and others)

2006-01-06T23:59:59.000Z

414

The Cotton Kinesin-Like Calmodulin-Binding Protein Associates with Cortical Microtubles in Cotton Fibers  

SciTech Connect (OSTI)

Microtubules in interphase plant cells form a cortical array, which is critical for plant cell morphogenesis. Genetic studies imply that the minus end-directed microtubule motor kinesin-like calmodulin-binding protein (KCBP) plays a role in trichome morphogenesis in Arabidopsis. However, it was not clear whether this motor interacted with interphase microtubules. In cotton (Gossypium hirsutum) fibers, cortical microtubules undergo dramatic reorganization during fiber development. In this study, cDNA clones of the cotton KCBP homolog GhKCBP were isolated from a cotton fiber-specific cDNA library. During cotton fiber development from 10 to 21 DPA, the GhKCBP protein level gradually decreases. By immunofluorescence, GhKCBP was detected as puncta along cortical microtubules in fiber cells of different developmental stages. Thus the results provide evidence that GhKCBP plays a role in interphase cell growth likely by interacting with cortical microtubules. In contrast to fibers, in dividing cells of cotton, GhKCBP localized to the nucleus, the microtubule preprophase band, mitotic spindle, and the phragmoplast. Therefore KCBP likely exerts multiple roles in cell division and cell growth in flowering plants.

Preuss, Mary L.; Delmar, Deborah P.; Liu, Bo

2003-05-01T23:59:59.000Z

415

Coordination-resolved local bond contraction and electron binding-energy entrapment of Si atomic clusters and solid skins  

SciTech Connect (OSTI)

Consistency between x-ray photoelectron spectroscopy measurements and density-function theory calculations confirms our bond order-length-strength notation-incorporated tight-binding theory predictions on the quantum entrapment of Si solid skin and atomic clusters. It has been revealed that bond-order deficiency shortens and strengthens the Si-Si bond, which results in the local densification and quantum entrapment of the core and valence electrons. Unifying Si clusters and Si(001) and (111) skins, this mechanism has led to quantification of the 2p binding energy of 96.089?eV for an isolated Si atom, and their bulk shifts of 2.461?eV. Findings evidence the significance of atomic undercoordination that is of great importance to device performance.

Bo, Maolin; Huang, Yongli; Zhang, Ting [Key Laboratory of Low-Dimensional Materials and Application Technologies, Xiangtan University, Hunan 411105 (China); Wang, Yan, E-mail: ywang8@hnust.edu.cn, E-mail: ecqsun@ntu.edu.sg [Key Laboratory of Low-Dimensional Materials and Application Technologies, Xiangtan University, Hunan 411105 (China); School of Information and Electronic Engineering, Hunan University of Science and Technology, Hunan 411201 (China); Zhang, Xi [School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798 (Singapore); Li, Can [Center for Coordination Bond Engineering, School of Materials Science and Engineering, China Jiliang University, Hangzhou 330018 (China); Sun, Chang Q., E-mail: ywang8@hnust.edu.cn, E-mail: ecqsun@ntu.edu.sg [Key Laboratory of Low-Dimensional Materials and Application Technologies, Xiangtan University, Hunan 411105 (China); School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798 (Singapore); Center for Coordination Bond Engineering, School of Materials Science and Engineering, China Jiliang University, Hangzhou 330018 (China)

2014-04-14T23:59:59.000Z

416

Crystal Structure of 12-Lipoxygenase Catalytic-Domain-Inhibitor Complex Identifies a Substrate-Binding Channel for Catalysis  

SciTech Connect (OSTI)

Lipoxygenases are critical enzymes in the biosynthesis of families of bioactive lipids including compounds with important roles in the initiation and resolution of inflammation and in associated diseases such as diabetes, cardiovascular disease, and cancer. Crystals diffracting to high resolution (1.9 {angstrom}) were obtained for a complex between the catalytic domain of leukocyte 12-lipoxygenase and the isoform-specific inhibitor, 4-(2-oxapentadeca-4-yne)phenylpropanoic acid (OPP). In the three-dimensional structure of the complex, the inhibitor occupied a new U-shaped channel open at one end to the surface of the protein and extending past the redox-active iron site that is essential for catalysis. In models, the channel accommodated arachidonic acid, defining the binding site for the substrate of the catalyzed reaction. There was a void adjacent to the OPP binding site connecting to the surface of the enzyme and providing a plausible access channel for the other substrate, oxygen.

Xu, Shu; Mueser, Timothy C.; Marnett, Lawrence J.; Funk, Jr., Max O. (Toledo); (Vanderbilt)

2014-10-02T23:59:59.000Z

417

TIN2 Binds TRF1 and TRF2 Simultaneously and Stabilizes the TRF2 Complex on Telomeres*  

E-Print Network [OSTI]

TIN2 Binds TRF1 and TRF2 Simultaneously and Stabilizes the TRF2 Complex on Telomeres* Received interacting partner, TIN2, as well as PIP1 and POT1 and regulates telomere-length homeo- stasis. The TRF2 that TRF1, TIN2, PIP1, and POT1 are associated with the TRF2-hRap1 complex. Gel filtration identified a TRF

de Lange, Titia

418

Structural and Functional Basis of CXCL12 (stromal cell-derived factor-1 alpha) Binding to Heparin  

SciTech Connect (OSTI)

CXCL12 (SDF-1a) and CXCR4 are critical for embryonic development and cellular migration in adults. These proteins are involved in HIV-1 infection, cancer metastasis, and WHIM disease. Sequestration and presentation of CXCL12 to CXCR4 by glycosaminoglycans (GAGs) is proposed to be important for receptor activation. Mutagenesis has identified CXCL12 residues that bind to heparin. However, the molecular details of this interaction have not yet been determined. Here we demonstrate that soluble heparin and heparan sulfate negatively affect CXCL12-mediated in vitro chemotaxis. We also show that a cluster of basic residues in the dimer interface is required for chemotaxis and is a target for inhibition by heparin. We present structural evidence for binding of an unsaturated heparin disaccharide to CXCL12 attained through solution NMR spectroscopy and x-ray crystallography. Increasing concentrations of the disaccharide altered the two-dimensional 1H-15N-HSQC spectra of CXCL12, which identified two clusters of residues. One cluster corresponds to {beta}-strands in the dimer interface. The second includes the amino-terminal loop and the a-helix. In the x-ray structure two unsaturated disaccharides are present. One is in the dimer interface with direct contacts between residues His25, Lys27, and Arg41 of CXCL12 and the heparin disaccharide. The second disaccharide contacts Ala20, Arg21, Asn30, and Lys64. This is the first x-ray structure of a CXC class chemokine in complex with glycosaminoglycans. Based on the observation of two heparin binding sites, we propose a mechanism in which GAGs bind around CXCL12 dimers as they sequester and present CXCL12 to CXCR4.

Murphy,J.; Cho, Y.; Sachpatzidis, A.; Fan, C.; Hodsdon, M.; Lolis, E.

2007-01-01T23:59:59.000Z

419

Characterization of the 3' terminal 42 nucleotide host protein binding element of the mouse hepatitis virus 3' untranslated region  

E-Print Network [OSTI]

Schematic representation of the defined secondary structures of the MHV 3' UTR including the pseudoknot identified in BCoV??..????????. 21 8 Identified binding sites of known host proteins in the MHV genome and complementary RNA... of complement (25). M protein has been shown to interact with genome associated N protein in pre-Golgi complexes, which is the site of virion assembly and release (69). Work by Nguyen and Hogue demonstrated that BCoV M interacts with HE and S proteins...

Johnson, Reed Findley

2004-09-30T23:59:59.000Z

420

Homotypic clusters of transcription factor binding sites: a model system for understanding the physical mechanics of gene expression  

E-Print Network [OSTI]

architectures influence the physical mechanisms that ultimately lead to transcription. A first step towards developing a more mechanistic view of CRE organization is to dissect common and simple organizational patterns [1]. One of themost common CRE build- ing... ,25,26].With this new technology, it is possible to experimentally test how different TF binding site organizations influ- ence gene expression. Even with the development of techniques to synthesize DNA more efficiently, it is still very difficult to study how...

Ezer, Daphne; Zabet, Nicolae Radu; Adryan, Boris

2014-08-01T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


421

Influence of Linker Structure on the Anion Binding Affinity of Biscyclopeptides  

SciTech Connect (OSTI)

A systematic analysis is presented on the influence of the linking unit between two cyclopeptide rings on the affinity of such biscyclopeptide-based anion receptors in aqueous solvent mixtures. Although the differences in the affinity and selectivity of these receptors toward a given anion are not very pronounced, there are profound differences in the thermodynamics of anion complexation. Enthalpic and entropic contributions both (1) play a role in determining the binding affinity and (2) show significant variation as the linking structure is changed. A decrease in conformational rigidity of the linker improves the entropic advantage for complex formation, but not necessarily the overall complex stability. This effect may be due, in part, to the fact that structural constraints within more rigid linkers might prevent efficient interactions between the host and guest. The optimal linker, which exhibits both favourable enthalpic and entropic contributions, was identified using de novo structure-based design methods as implemented in the HostDesigner software. The submitted manuscript has been authored by a contractor of the U. S. Government under contract No. DE-AC05-00OR22725. Accordingly, the U. S. Government retains a non-exclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for the U. S. Government purposes. This research was sponsored by the following program of the U. S. Department of Energy, Office of Science: the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (ORNL FWP No. ERKKC08. Oak Ridge National Laboratory is managed and operated by UT-Battelle, LLC under contract number DE-AC05-00OR22725 with the U. S. Department of Energy.

Reyheller, Carsten [Technische Universitat Kaiserlautern; Hay, Benjamin [ORNL; Kubik, Stefan [Technische Universitat Kaiserlautern

2007-01-01T23:59:59.000Z

422

Deep Atomic Binding (DAB) Hypothesis: A New Approach of Fission Product Chemistry  

SciTech Connect (OSTI)

Former studies assumed that, after fission process occurs, the highly ionized new born atoms (20-22 positive charge), ionize the media in which they pass through before becoming stable atoms in a manner similar to 4-MeV ?-particles. Via ordinary chemical reactions with the surroundings, each stable atom has a probability to form chemical compound. Since there are about 35 different elemental atoms created through fission processes, a large number of chemical species were suggested to be formed. But, these suggested chemical species were not found in the environment after actual releases of FP during accidents like TMI (USA, 1979), and Chernobyl (former USSR, 1986), also the models based on these suggested reactions and species could not interpret the behavior of these actual species. It is assumed here that the ionization states of the new born atoms and the long term high temperature were not dealt with in an appropriate way and they were the reasons of former models failure. Our new approach of Deep Atomic Binding (DAB) based on the following: 1-The new born atoms which are highly ionized, 10-12 electrons associated with each nucleus, having a large probability to create bonds between them to form molecules. These bonds are at the L, or M shells, and we call it DAB. 2-The molecules stay in the reactor at high temperatures for long periods, so they undergo many stages of composition and decomposition to form giant molecules. By applying DAB approach, field data from Chernobyl, TMI and nuclear detonations could be interpreted with a wide coincidence resulted. (author)

Ajlouni, Abdul-Wali M.S. [Ministry of Energy and Mineral Resources (Jordan)

2006-07-01T23:59:59.000Z

423

Cadmium binding studies to the earthworm Lumbricus rubellus metallothionein by electrospray mass spectrometry and circular dichroism spectroscopy  

SciTech Connect (OSTI)

The earthworm Lumbricus rubellus has been found to inhabit cadmium-rich soils and accumulate cadmium within its tissues. Two metallothionein (MT) isoforms (1 and 2) have been identified and cloned from L. rubellus. In this study, we address the metalation status, metal coordination, and structure of recombinant MT-2 from L. rubellus using electrospray ionization mass spectrometry (ESI-MS), UV absorption, and circular dichroism (CD) spectroscopy. This is the first study to show the detailed mass and CD spectral properties for the important cadmium-containing earthworm MT. We report that the 20-cysteine L. rubellus MT-2 binds seven Cd{sup 2+} ions. UV absorption and CD spectroscopy and ESI-MS pH titrations show a distinct biphasic demetalation reaction, which we propose results from the presence of two metal-thiolate binding domains. We propose stoichiometries of Cd{sub 3}Cys{sub 9} and Cd{sub 4}Cys{sub 11} based on the presence of 20 cysteines split into two isolated regions of the sequence with 11 cysteines in the N-terminal and 9 cysteines in the C-terminal. The CD spectrum reported is distinctly different from any other metallothionein known suggesting quite different binding site structure for the peptide.

Ngu, Thanh T. [Department of Chemistry, University of Western Ontario, London, Ont., N6A 5B7 (Canada); Sturzenbaum, Stephen R. [School of Biomedical and Health Sciences, King's College, London, SE1 9NH (United Kingdom); Stillman, Martin J. [Department of Chemistry, University of Western Ontario, London, Ont., N6A 5B7 (Canada)]. E-mail: Martin.Stillman@uwo.ca

2006-12-08T23:59:59.000Z

424

Evidence for separate substrate binding sites for hydrogen peroxide and cumene hydroperoxide (CHP) in the oxidation of ethanol by catalase  

SciTech Connect (OSTI)

The oxidation of ethanol by purified bovine liver catalase (Sigma, C-40) can be supported by H/sub 2/O/sub 2/ or by CHP. The time course of the H/sub 2/O/sub 2/ supported reaction (using glucose/glucose oxidase as the H/sub 2/O/sub 2/ source) was linear for at least one hr, whereas the rate of acetaldehyde formation in the CHP (4.2 mM) supported reaction decreased with time. When catalase was exposed o CHP for 5 min before the addition of ethanol, the rate of CHP supported ethanol oxidation was reduced by more than 90% compared to incubations where the addition of ethanol preceded that of CHP. In the CHP inhibited state, the peroxidative activity of catalase was not restored by further addition of CHP or ethanol; however, addition of fresh catalase yielded its expected activity. Significantly, the CHP inhibited enzyme was equally effective as the untreated enzyme in catalyzing (a) the oxidation of ethanol in the presence H/sub 2/O/sub 2/ supported peroxidative activity as well as catalytic activity by CHP inhibited catalase points to separate binding sites for H/sub 2/O/sub 2/ and CHP in this reaction. Alternatively, CHP may bind adjacent to a common peroxide active site, thereby sterically impeding the binding of CHP - but not of H/sub 2/O/sub 2/ - to this active site.

DeMaster, E.G.; Nagasawa,ss H.T.

1986-03-01T23:59:59.000Z

425

Identification and characterization of (/sup 3/H)-rauwolscine binding to alpha2-adrenoceptors in the canine saphenous vein  

SciTech Connect (OSTI)

The biochemical exploration of the alpha2-adrenergic receptors was investigated in the canine saphenous vein using the highly selective alpha2-adrenergic antagonist rauwolscine as a tritiated ligand. Following an enzymatic digestive pretreatment, the authors isolated a purified smooth muscle cell membranes fraction from saphenous veins in quantity sufficient to permit them to study the venous alpha2-adrenoreceptor content. The binding of tritiated rauwolscine was rapid, specific, saturable and reversible. The presence of high affinity sites with a density of binding Bmax of 125.2 /+ -/ 43.1 fmol/mg protein was demonstrated on a unique class of non interacting sites. The kinetically derived Kd was 1.28 nM, in good agreement with the value obtained from saturation isotherms. The pharmacological profile of these sites was assessed by the comparison of the potency of alpha-adrenergic agonists and antagonists to inhibit 1 nM (/sup 3/H)-rauwolscine. Their efficacy was respectively: rauwolscine > phentolamine > RX 781094 > clonidine >> prazosin > (-)-phenylephrine > (-)-noradrenaline. The results showed that (/sup 3/H)-rauwolscine bound specifically to sites in their membranal preparation, which had the pharmacological characteristics of the alpha2-adrenoceptors. The correlation between biochemical and pharmacological data revealed the usefulness of binding methods in the further study of adrenergic mechanisms in the canine saphenous vein.

Gout, B.

1988-01-01T23:59:59.000Z

426

Protein-only mechanism induces self-perpetuating changes in the activity of neuronal Aplysia cytoplasmic polyadenylation element binding protein (CPEB)  

E-Print Network [OSTI]

Neuronal cytoplasmic polyadenylation element binding protein (CPEB) plays a critical role in maintaining the functional and morphological long-lasting synaptic changes that underlie learning and memory. It can undergo a ...

Heinrich, Sven U.

427

Mechanism of Binding and Internalization of ICAM-1-derived Cyclic Peptides by LFA-1 on the Surface of T-cells: A Potential Method for Targeted Drug Delivery  

E-Print Network [OSTI]

Purpose Peptides derived from the Domain 1 of the adhesion molecule ICAM-1(1-21) are being developed as targeting ligands for LFA-1 receptors expressed on activated T-cells. This work aims to elucidate the binding and ...

Anderson, Meagan E.; Siahaan, Teruna J.

2003-10-01T23:59:59.000Z

428

This article was processed using the L a T E X macro package with LLNCS style brain manages to circumvent the binding problem altogether with the help of  

E-Print Network [OSTI]

recordings, optical imaging using voltage sensitive dyes, EEG or MEG. We suggest that the spatial resolution to circumvent the binding problem altogether with the help of combination­coding cells, in spite of all

Triesch, Jochen

429

Binding of misonidazole to V79 spheroids and fragments of Dunning rat prostatic and human colon carcinomas in vitro: diffusion of oxygen and reactive metabolites  

SciTech Connect (OSTI)

Differences were noted previously in the binding of /sup 14/C-Misonidazole (MISO) to V79 and EMT6 spheroids when incubated at low oxygen levels. Further data reported here indicate that the K/sub m/ for the inhibition of binding by oxygen is lower in V79 than EMT6 spheroids, so that part of the non-uniformity of binding to V79 spheroids can be explained by diffusion of small amounts of oxygen through the entire rim of viable cells. Diffusion of reactive metabolites of MISO out of the spheroid previously was considered an unlikely explanation. Further evidence to support this interpretation is presented here. Patterns of binding of /sup 3/H-MISO to Dunning and human colon carcinomas are presented which are consistent with the interpretation that most of the reactive metabolites are confined to the cell in which they are produced.

Franko, A.J.; Koch, C.J.

1984-08-01T23:59:59.000Z

430

Characterization of the Allosteric Properties of Thermus thermophilus Phosphofructokinase and the Sources of Strong Inhibitor Binding Affinity and Weak Inhibitory Response  

E-Print Network [OSTI]

Characterization of allosteric properties of phosphofructokinase from the extreme thermophile Thermus thermophilus (TtPFK) using thermodynamic linkage analysis revealed several peculiarities. Inhibition and activation of Fru-6-P binding...

Shubina-McGresham, Maria

2012-10-19T23:59:59.000Z

431

Structure and interactions of the C-terminal metal binding domain of Archaeoglobus fulgidus CopA  

SciTech Connect (OSTI)

The Cu(+)-ATPase CopA from Archaeoglobus fulgidus belongs to the P(1B) family of the P-type ATPases. These integral membrane proteins couple the energy of ATP hydrolysis to heavy metal ion translocation across membranes. A defining feature of P(1B-1)-type ATPases is the presence of soluble metal binding domains at the N-terminus (N-MBDs). The N-MBDs exhibit a conserved ferredoxin-like fold, similar to that of soluble copper chaperones, and bind metal ions via a conserved CXXC motif. The N-MBDs enable Cu(+) regulation of turnover rates apparently through Cu-sensitive interactions with catalytic domains. A. fulgidus CopA is unusual in that it contains both an N-terminal MBD and a C-terminal MBD (C-MBD). The functional role of the unique C-MBD has not been established. Here, we report the crystal structure of the apo, oxidized C-MBD to 2.0 A resolution. In the structure, two C-MBD monomers form a domain-swapped dimer, which has not been observed previously for similar domains. In addition, the interaction of the C-MBD with the other cytoplasmic domains of CopA, the ATP binding domain (ATPBD) and actuator domain (A-domain), has been investigated. Interestingly, the C-MBD interacts specifically with both of these domains, independent of the presence of Cu(+) or nucleotides. These data reinforce the uniqueness of the C-MBD and suggest a distinct structural role for the C-MBD in CopA transport.

Agarwal, S.; Hong, D.; Desai, N.K.; H.Sazinsky, M.; Argello, J.M.; Rosenzweig, A.C. (NWU)

2010-08-13T23:59:59.000Z

432

Crystal structure of the Candida albicans Kar3 kinesin motor domain fused to maltose-binding protein  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer The Candida albicans Kar3 motor domain structure was solved as a maltose-binding protein fusion. Black-Right-Pointing-Pointer The electrostatic surface and part of the ATPase pocket of the motor domain differs markedly from other kinesins. Black-Right-Pointing-Pointer The MBP-Kar3 interface highlights a new site for intramolecular or intermolecular interactions. -- Abstract: In the human fungal pathogen Candida albicans, the Kinesin-14 motor protein Kar3 (CaKar3) is critical for normal mitotic division, nuclear fusion during mating, and morphogenic transition from the commensal yeast form to the virulent hyphal form. As a first step towards detailed characterization of this motor of potential medical significance, we have crystallized and determined the X-ray structure of the motor domain of CaKar3 as a maltose-binding protein (MBP) fusion. The structure shows strong conservation of overall motor domain topology to other Kar3 kinesins, but with some prominent differences in one of the motifs that compose the nucleotide-binding pocket and the surface charge distribution. The MBP and Kar3 modules are arranged such that MBP interacts with the Kar3 motor domain core at the same site where the neck linker of conventional kinesins docks during the 'ATP state' of the mechanochemical cycle. This site differs from the Kar3 neck-core interface in the recent structure of the ScKar3Vik1 heterodimer. The position of MBP is also completely distinct from the Vik1 subunit in this complex. This may suggest that the site of MBP interaction on the CaKar3 motor domain provides an interface for the neck, or perhaps a partner subunit, at an intermediate state of its motile cycle that has not yet been observed for Kinesin-14 motors.

Delorme, Caroline; Joshi, Monika [Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6 (Canada)] [Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6 (Canada); Allingham, John S., E-mail: allinghj@queensu.ca [Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6 (Canada)

2012-11-30T23:59:59.000Z

433

Near-infrared fluorescence glucose sensing based on glucose/galactose-binding protein coupled to 651-Blue Oxazine  

SciTech Connect (OSTI)

Highlights: We showed that the NIR fluorophore, 651-Blue Oxazine, is solvatochromic (polarity sensitive). Blue Oxazine was covalently attached to mutants of glucose/galactose-binding protein (GBP). Fluorescence intensity of GBP-Blue Oxazine increased with addition of glucose. Fluorescence from bead-immobilised GBP-Blue Oxazine was detectable through skin in vitro. This shows proof-of-concept for non-invasive glucose sensing using GBP-Blue Oxazine. -- Abstract: Near-infrared (NIR) fluorescent dyes that are environmentally sensitive or solvatochromic are useful tools for protein labelling in in vivo biosensor applications such as glucose monitoring in diabetes since their spectral properties are mostly independent of tissue autofluorescence and light scattering, and they offer potential for non-invasive analyte sensing. We showed that the fluorophore 651-Blue Oxazine is polarity-sensitive, with a marked reduction in NIR fluorescence on increasing solvent polarity. Mutants of glucose/galactose-binding protein (GBP) used as the glucose receptor were site-specifically and covalently labelled with Blue Oxazine using click chemistry. Mutants H152C/A213R and H152C/A213R/L238S showed fluorescence increases of 15% and 21% on addition of saturating glucose concentrations and binding constants of 6 and 25 mM respectively. Fluorescence responses to glucose were preserved when GBP-Blue Oxazine was immobilised to agarose beads, and the beads were excited by NIR light through a mouse skin preparation studied in vitro. We conclude GBP-Blue Oxazine shows proof-of-concept as a non-invasive continuous glucose sensing system.

Khan, Faaizah; Pickup, John C., E-mail: john.pickup@kcl.ac.uk

2013-08-30T23:59:59.000Z

434

Investigation of metal-ion binding in the four-way junction construct of the hairpin ribozyme  

E-Print Network [OSTI]

sugar (Figure 1- 6).2 Numerous crystal structures of RNA molecules and even isolated nitrogenous bases have revealed these typical metal-RNA interactions.1 Metal ions, such as Mn2+, [Co(NH3)6]3+, Cd2+, Hg2+, Tb3+ and other lanthanides have served....14 Tb3+ has been found to inhibit the function of RNA systems by displacing critical Mg2+ ions.15 In 9 addition, the luminescence of Tb3+ and other lanthanides have been used to locate metal binding sites and to determine relative affinities...

Buckelew, Aurelie Lina

2005-08-29T23:59:59.000Z

435

Comparison of Chlorpyrifos-Oxon and Paraoxon Acetylcholinesterase Inhibition Dynamics: Potential role of a peripheral binding site  

SciTech Connect (OSTI)

The primary mechanism of action for organophosphorus (OP) insecticides involves the inhibition of acetylcholinesterase (AChE) by oxygenated metabolites (oxons). This inhibition has been attributed to the phosphorylation of the serine hydroxyl group located in the active site of the AChE molecule. The rate of phosphorylation is described by the bimolecular inhibitory rate constant (ki), which has been utilized for quantification of OP inhibitory capacity. It has been previously proposed that a peripheral binding site exists on the AChE molecule, which when occupied, reduces the capacity of additional oxon molecules to phosphorylate the active site. The objective of the current study was to evaluate the interaction of chlorpyrifos oxon (CPO) and paraoxon (PO) with rat brain AChE using a modified Ellman assay in conjunction with a pharmacodynamic model to further assess the dynamics of AChE inhibition and the potential role of a peripheral binding site. The ki for AChE inhibition determined at oxon concentrations of 5 x 10{sup -4} 100 nM were 0.212 and 0.0216 nM-1h-1 for CPO and PO, respectively. The spontaneous reactivation rates of the inhibited AChE for CPO and PO were 0.087 and 0.078 h-1, respectively. In contrast, the ki estimated at a low oxon concentration (1 pM) were {approx} 1,000 and 10,000 -fold higher than those determined at high CPO and PO concentrations, respectively. At these low concentrations, the ki estimates were approximately similar for both CPO and PO (180 and 250 nM-1h-1, respectively). This implies that at low exposure concentrations, both oxons exhibited similar inhibitory potency in contrast to the marked difference exhibited at higher concentrations, which is consistent with the presence of a peripheral binding site on the AChE enzyme. These results support the potential importance of a secondary binding site associated with AChE kinetics, particularly at low environmentally relevant concentrations.

Kousba, Ahmed A.; Sultatos, L G.; Poet, Torka S.; Timchalk, Chuck

2004-08-02T23:59:59.000Z

436

Roles of the Tetrahymena thermophila type I element binding factor, TIF1, in DNA replication and genome stability  

E-Print Network [OSTI]

like to thank Dr. Robert Wells, Dr. Van Wilson and Dr. Yi Wei Jiang, for their comments and criticism and for taking the time to serve on my committee. I would also like to thank my friends and colleagues, Swati Saha, Mohammad Mohammad, Audrey Nicholson...RNA promoter (Reischmann et al., 1999). Several possibly trans-acting proteins have been discovered that bind these essential elements (Mohammad et al., 2000; Mohammad et al., 2003). This section describes in detail what is known about these cis and trans...

Morrison, Tara Laine

2005-11-01T23:59:59.000Z

437

Acyl CoA Binding Protein (ACBP) Gene Ablation Induces Pre-Implantation Embryonic Lethality in Mice  

E-Print Network [OSTI]

fulfillment of the requirement for the degree of MASTER OF SCIENCE Approved by: Co-Chairs of Committee, Ann B. Kier Friedhelm Schroeder Committee Member, Ian R.Tizard Head of Department, Linda L. Logan December 2010 Major Subject... Long Chain Acyl CoA Dehydrogenase ACBP Acyl CoA Binding Protein Atp1b1 Na+, K+-ATPase (ATPase, Na+/K+ transporting beta 1 polypeptide) Atp2a2 Ca++-ATPase (endoplasmic reticulum) Capn2 m-Calpain CoA Coenzyme A CPT1 Carnitine...

Landrock, Danilo

2012-02-14T23:59:59.000Z

438

November 2014 Office of Sponsored Programs  

E-Print Network [OSTI]

Systems Center (ISC) Director: Ming Leu Environmental Research Center for Emerging Contaminants (ERCEC

Missouri-Rolla, University of

439

H2-M polymorphism in mice susceptible to collagen-induced arthritis involves the peptide binding groove  

SciTech Connect (OSTI)

The ability to develop type II collagen (CII)-induced arthritis (CIA) in mice is associated with the major histocompatibility I-A gene and with as yet poorly defined regulatory molecules of the major histocompatibility complex (MHC) class II antigen processing and presentation pathway. H2-M molecules are thought to be involved in the loading of antigenic peptides into the MHC class II binding cleft. We sequenced H2-Ma, H2-Mb1, and H2-Mb2 genes from CIA-susceptible and -resistant mouse strains and identified four different Ma and Mb2 alleles, and three different Mb1 alleles defined by polymorphic residues within the predicted peptide binding groove. Most CIA-resistant mouse strains share common Ma, Mb1, and Mb2 alleles. In contrast, H2-M alleles designated Ma-III, Ma-IV, Mb1-III, and Mb2-IV could be exclusively identified in the CIA-susceptible H2{sup r} and H2{sup q} haplotypes, suggesting that allelic H2-M molecules may modulate the composition of different CII peptides loaded onto MHC class II molecules, presumably presenting {open_quotes}arthritogenic{close_quotes} epitopes to T lymphocytes. 42 refs., 4 figs., 3 tabs.

Walter, W.; Loos, M.; Maeurer, M.J. [Johannes Gutenberg Univ., Mainz (Germany)] [Johannes Gutenberg Univ., Mainz (Germany)

1996-12-31T23:59:59.000Z

440

Mycobacterium tuberculosis lipoprotein LprG (Rv1411c) binds triacylated glycolipid agonists of Toll-like receptor 2  

SciTech Connect (OSTI)

Knockout of lprG results in decreased virulence of Mycobacterium tuberculosis (MTB) in mice. MTB lipoprotein LprG has TLR2 agonist activity, which is thought to be dependent on its N-terminal triacylation. Unexpectedly, here we find that nonacylated LprG retains TLR2 activity. Moreover, we show LprG association with triacylated glycolipid TLR2 agonists lipoarabinomannan, lipomannan and phosphatidylinositol mannosides (which share core structures). Binding of triacylated species was specific to LprG (not LprA) and increased LprG TLR2 agonist activity; conversely, association of glycolipids with LprG enhanced their recognition by TLR2. The crystal structure of LprG in complex with phosphatidylinositol mannoside revealed a hydrophobic pocket that accommodates the three alkyl chains of the ligand. In conclusion, we demonstrate a glycolipid binding function of LprG that enhances recognition of triacylated MTB glycolipids by TLR2 and may affect glycolipid assembly or transport for bacterial cell wall biogenesis.

Drage, Michael G.; Tsai, Han-Chun; Pecora, Nicole D.; Cheng, Tan-Yun; Arida, Ahmad R.; Shukla, Supriya; Rojas, Roxana E.; Seshadri, Chetan; Moody, D. Branch; Boom, W. Henry; Sacchettini, James C.; Harding, Clifford V. (Case Western); (BWH); (TAM)

2010-09-27T23:59:59.000Z

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


441

ATP-binding cassette-like transporters are involved in the transport of lignin precursors across plasma and vacuolar membranes  

SciTech Connect (OSTI)

Lignin is a complex biopolymer derived primarily from the condensation of three monomeric precursors, the monolignols. The synthesis of monolignols occurs in the cytoplasm. To reach the cell wall where they are oxidized and polymerized, they must be transported across the cell membrane. However, the molecular mechanisms underlying the transport process are unclear. There are conflicting views about whether the transport of these precursors occurs by passive diffusion or is an energized active process; further, we know little about what chemical forms are required. Using isolated plasma and vacuolar membrane vesicles prepared from Arabidopsis, together with applying different transporter inhibitors in the assays, we examined the uptake of monolignols and their derivatives by these native membrane vesicles. We demonstrate that the transport of lignin precursors across plasmalemma and their sequestration into vacuoles are ATP-dependent primary-transport processes, involving ATP-binding cassette-like transporters. Moreover, we show that both plasma and vacuolar membrane vesicles selectively transport different forms of lignin precursors. In the presence of ATP, the inverted plasma membrane vesicles preferentially take up monolignol aglycones, whereas the vacuolar vesicles are more specific for glucoconjugates, suggesting that the different ATP-binding cassette-like transporters recognize different chemical forms in conveying them to distinct sites, and that glucosylation of monolignols is necessary for their vacuolar storage but not required for direct transport into the cell wall in Arabidopsis.

Miao, Y.C.; Liu, C.

2010-12-28T23:59:59.000Z

442

Physical origins of weak H{sub 2} binding on carbon nanostructures: Insight from ab initio studies of chemically functionalized graphene nanoribbons  

SciTech Connect (OSTI)

We have performed ab initio density functional theory calculations, incorporating London dispersion corrections, to study the absorption of molecular hydrogen on zigzag graphene nanoribbons whose edges have been functionalized by OH, NH{sub 2}, COOH, NO{sub 2}, or H{sub 2}PO{sub 3}. We find that hydrogen molecules always preferentially bind at or near the functionalized edge, and display induced dipole moments. Binding is generally enhanced by the presence of polar functional groups. The largest gains are observed for groups with oxygen lone pairs that can facilitate local charge reorganization, with the biggest single enhancement in adsorption energy found for strong functionalization by H{sub 2}PO{sub 3} (115 meV/H{sub 2} versus 52 meV/H{sub 2} on bare graphene). We show that for binding on the outer edge near the functional group, the presence of the group can introduce appreciable contributions from Debye interactions and higher-order multipole electrostatic terms, in addition to the dominant London dispersion interactions. For those functional groups that contain the OH moiety, the adsorption energy is linearly proportional to the number of lone pairs on oxygen atoms. Mixed functionalization with two different functional groups on a graphene edge can also have a synergistic effect, particularly when electron-donating and electron-withdrawing groups are combined. For binding on the inner edge somewhat farther from the functional group, most of the binding again arises from London interactions; however, there is also significant charge redistribution in the ? manifold, which directly reflects the electron donating or withdrawing capacity of the functional group. Our results offer insight into the specific origins of weak binding of gas molecules on graphene, and suggest that edge functionalization could perhaps be used in combination with other strategies to increase the uptake of hydrogen in graphene. They also have relevance for the storage of hydrogen in porous carbon materials, such as activated carbons.

Ulman, Kanchan; Bhaumik, Debarati [Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064 (India)] [Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064 (India); Wood, Brandon C. [Quantum Simulations Group, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, California 94550 (United States)] [Quantum Simulations Group, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, California 94550 (United States); Narasimhan, Shobhana [Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064 (India) [Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064 (India); Sheikh Saqr Laboratory, ICMS, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064 (India)

2014-05-07T23:59:59.000Z

443

Tight-binding Tight-binding  

E-Print Network [OSTI]

.2 Nicolas 7) Tc* = 1.35 Tt* = 0.68 9) rc = 2.5 5.5 b. 6,10) SPC/E, TIP4P CC SPC/E (Extended Simple Point Lennard-Jones 9 14.3 Jorgenson TIP4P 12) 14.3 HOH 2 SPC/E TIP4P TIP4P Jorgenson OPLS (optimized potential for liquid simulations) 13) CC (Carravetta-Clementi) 14) TIP4P (14.8) Lennard-Jones SPC/E, TIP4P, CC 1.85 D

Maruyama, Shigeo

444

Mass spectrometric characterization of sequence-specific complexes of DNA and transcription factor PU.1 DNA binding domain  

SciTech Connect (OSTI)

Electrospray ionization mass spectrometry (ESI-MS) has been used to study the noncovalent interaction of the 13.5-kDa DNA binding domain of PU.1 (PU.1-DBD) with specific double-stranded DNA (dsDNA) target molecules. Mixtures of PU.1-DBD protein and wildtype target DNA sequence yielded ESI-MS spectra showing only protein-dsDNA complex ions of 1:1 stoichiometry and free dsDNA. When PU.1-DBD protein, wild type target DNA, and a mutant target DNA lacking the consensus sequence were mixed, only the 1:1 complex with the wild-type DNA was observed, consistent with gel electrophoresis mobility shift assay results, demonstrating the observation of sequence-specific protein-dsDNA complexes using ESI-MS. 22 refs., 5 figs., 1 tab.

Cheng, Xueheng; Harms, A.C.; Bruce, J.E. [Pacific Northwest National Lab., Richland, WA (United States)] [and others] [Pacific Northwest National Lab., Richland, WA (United States); and others

1996-07-15T23:59:59.000Z

445

Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method  

E-Print Network [OSTI]

Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply the method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density fu...

Lutsker, Vitalij; Niehaus, Thomas A

2015-01-01T23:59:59.000Z

446

Binding of soluble immune complexes to adult Schistosoma mansoni: evidence for IgG-Fc and complement receptors  

E-Print Network [OSTI]

minus C 3 Mouse C5-def. Anti-C Anti-C m Anti-C m Anti-C Anti-Cm Anti-C m a CVF- cobra venom factor-treated; HIA- heat inactivated; zymosan- zymosan-treated; minus C 3- commercial serum minus complement C 3; C5-def. - complement C5 deficient...G of the complex and could be part1ally blocked by preincubation of schistosomes in heat-aggregated IgG or an isolated Fc preparation. AgAbC binding was dependent on active C 3 in the complement source but did not require an 1ntact Fc on the ant1body...

Tarleton, Ricky Lee

1980-01-01T23:59:59.000Z

447

Communication: Towards the binding energy and vibrational red shift of the simplest organic hydrogen bond: Harmonic constraints for methanol dimer  

SciTech Connect (OSTI)

The discrepancy between experimental and harmonically predicted shifts of the OH stretching fundamental of methanol upon hydrogen bonding to a second methanol unit is too large to be blamed mostly on diagonal and off-diagonal anharmonicity corrections. It is shown that a decisive contribution comes from post-MP2 electron correlation effects, which appear not to be captured by any of the popular density functionals. We also identify that the major deficiency is in the description of the donor OH bond. Together with estimates for the electronic and harmonically zero-point corrected dimer binding energies, this work provides essential constraints for a quantitative description of this simple hydrogen bond. The spectroscopic dissociation energy is predicted to be larger than 18 kJ/mol and the harmonic OH-stretching fundamental shifts by about ?121 cm{sup ?1} upon dimerization, somewhat more than in the anharmonic experiment (?111 cm{sup ?1})

Heger, Matthias; Suhm, Martin A.; Mata, Ricardo A., E-mail: rmata@gwdg.de [Georg-August-Universitt Gttingen, Institut fr Physikalische Chemie, Tammannstr. 6, 37077 Gttingen (Germany)

2014-09-14T23:59:59.000Z

448

CCAAT/enhancer binding protein {beta} deletion increases mitochondrial function and protects mice from LXR-induced hepatic steatosis  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer LXR agonist activation increases liver TG accumulation by increasing lipogenesis. Black-Right-Pointing-Pointer C/EBP{beta}{sup -/-} mouse prevents LXR activation-mediated induction of hepatic lipogenesis. Black-Right-Pointing-Pointer C/EBP{beta} deletion increases mitochondrial transport chain function. Black-Right-Pointing-Pointer Beneficial effects of LXR activation on liver cholesterol metabolism did not change. Black-Right-Pointing-Pointer C/EBP{beta} inhibition might have important therapeutic potential. -- Abstract: Drugs designed specifically to activate liver X receptors (LXRs) have beneficial effects on lowering cholesterol metabolism and inflammation but unfortunately lead to severe hepatic steatosis. The transcription factor CCAAT/enhancer binding protein beta (C/EBP{beta}) is an important regulator of liver gene expression but little is known about its involvement in LXR-based steatosis and cholesterol metabolism. The present study investigated the role of C/EBP{beta} expression in LXR agonist (T0901317)-mediated alteration of hepatic triglyceride (TG) and lipogenesis in mice. C/EBP{beta} deletion in mice prevented LXR agonist-mediated induction of lipogenic gene expression in liver in conjunction with significant reduction of liver TG accumulation. Surprisingly, C/EBP{beta}{sup -/-} mice showed a major increase in liver mitochondrial electron chain function compared to WT mice. Furthermore, LXR activation in C/EBP{beta}{sup -/-} mice increased the expression of liver ATP-binding cassette transporter ABCG1, a gene implicated in cholesterol efflux and reducing blood levels of total and LDL-cholesterol. Together, these findings establish a central role for C/EBP{beta} in the LXR-mediated steatosis and mitochondrial function, without impairing the influence of LXR activation on lowering LDL and increasing HDL-cholesterol. Inactivation of C/EBP{beta} might therefore be an important therapeutic strategy to prevent LXR activation-mediated adverse effects on liver TG metabolism without disrupting its beneficial effects on cholesterol metabolism.

Rahman, Shaikh M., E-mail: rmizanoor@hotmail.com [Department of Pediatrics, School of Medicine, University of Colorado Denver, Aurora, CO 80045 (United States); Choudhury, Mahua; Janssen, Rachel C.; Baquero, Karalee C. [Department of Pediatrics, School of Medicine, University of Colorado Denver, Aurora, CO 80045 (United States)] [Department of Pediatrics, School of Medicine, University of Colorado Denver, Aurora, CO 80045 (United States); Miyazaki, Makoto [Division of Renal Diseases and Hypertension, School of Medicine, University of Colorado Denver, Aurora, CO 80045 (United States)] [Division of Renal Diseases and Hypertension, School of Medicine, University of Colorado Denver, Aurora, CO 80045 (United States); Friedman, Jacob E. [Department of Pediatrics, School of Medicine, University of Colorado Denver, Aurora, CO 80045 (United States) [Department of Pediatrics, School of Medicine, University of Colorado Denver, Aurora, CO 80045 (United States); Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO 80045 (United States)

2013-01-04T23:59:59.000Z

449

Multiple Glycogen-binding Sites in Eukaryotic Glycogen Synthase Are Required for High Catalytic Efficiency toward Glycogen  

SciTech Connect (OSTI)

Glycogen synthase is a rate-limiting enzyme in the biosynthesis of glycogen and has an essential role in glucose homeostasis. The three-dimensional structures of yeast glycogen synthase (Gsy2p) complexed with maltooctaose identified four conserved maltodextrin-binding sites distributed across the surface of the enzyme. Site-1 is positioned on the N-terminal domain, site-2 and site-3 are present on the C-terminal domain, and site-4 is located in an interdomain cleft adjacent to the active site. Mutation of these surface sites decreased glycogen binding and catalytic efficiency toward glycogen. Mutations within site-1 and site-2 reduced the V{sub max}/S{sub 0.5} for glycogen by 40- and 70-fold, respectively. Combined mutation of site-1 and site-2 decreased the V{sub max}/S{sub 0.5} for glycogen by >3000-fold. Consistent with the in vitro data, glycogen accumulation in glycogen synthase-deficient yeast cells ({Delta}gsy1-gsy2) transformed with the site-1, site-2, combined site-1/site-2, or site-4 mutant form of Gsy2p was decreased by up to 40-fold. In contrast to the glycogen results, the ability to utilize maltooctaose as an in vitro substrate was unaffected in the site-2 mutant, moderately affected in the site-1 mutant, and almost completely abolished in the site-4 mutant. These data show that the ability to utilize maltooctaose as a substrate can be independent of the ability to utilize glycogen. Our data support the hypothesis that site-1 and site-2 provide a 'toehold mechanism,' keeping glycogen synthase tightly associated with the glycogen particle, whereas site-4 is more closely associated with positioning of the nonreducing end during catalysis.

Baskaran, Sulochanadevi; Chikwana, Vimbai M.; Contreras, Christopher J.; Davis, Keri D.; Wilson, Wayne A.; DePaoli-Roach, Anna A.; Roach, Peter J.; Hurley, Thomas D. (Indiana-Med); (Des Moines U)

2012-12-10T23:59:59.000Z

450

Testin, a novel binding partner of the calcium-sensing receptor, enhances receptor-mediated Rho-kinase signalling  

SciTech Connect (OSTI)

Highlights: {yields} A yeast two-hybrid screen revealed testin bound to the calcium-sensing receptor. {yields} The second zinc finger of LIM domain 1 of testin is critical for interaction. {yields} Testin bound to a region of the receptor tail important for cell signalling. {yields} Testin and receptor interaction was confirmed in mammalian (HEK293) cells. {yields} Overexpression of testin enhanced receptor-mediated Rho signalling in HEK293 cells. -- Abstract: The calcium-sensing receptor (CaR) plays an integral role in calcium homeostasis and the regulation of other cellular functions including cell proliferation and cytoskeletal organisation. The multifunctional nature of the CaR is manifested through ligand-dependent stimulation of different signalling pathways that are also regulated by partner binding proteins. Following a yeast two-hybrid library screen using the intracellular tail of the CaR as bait, we identified several novel binding partners including the focal adhesion protein, testin. Testin has not previously been shown to interact with cell surface receptors. The sites of interaction between the CaR and testin were mapped to the membrane proximal region of the receptor tail and the second zinc-finger of LIM domain 1 of testin, the integrity of which was found to be critical for the CaR-testin interaction. The CaR-testin association was confirmed in HEK293 cells by coimmunoprecipitation and confocal microscopy studies. Ectopic expression of testin in HEK293 cells stably expressing the CaR enhanced CaR-stimulated Rho activity but had no effect on CaR-stimulated ERK signalling. These results suggest an interplay between the CaR and testin in the regulation of CaR-mediated Rho signalling with possible effects on the cytoskeleton.

Magno, Aaron L. [Western Australian Institute for Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia 6009 (Australia) [Western Australian Institute for Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia 6009 (Australia); Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, Western Australia 6009 (Australia); Ingley, Evan [Western Australian Institute for Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia 6009 (Australia)] [Western Australian Institute for Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia 6009 (Australia); Brown, Suzanne J. [Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, Western Australia 6009 (Australia)] [Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, Western Australia 6009 (Australia); Conigrave, Arthur D. [School of Molecular Bioscience, University of Sydney, New South Wales 2000 (Australia)] [School of Molecular Bioscience, University of Sydney, New South Wales 2000 (Australia); Ratajczak, Thomas [Western Australian Institute for Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia 6009 (Australia) [Western Australian Institute for Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia 6009 (Australia); Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, Western Australia 6009 (Australia); Ward, Bryan K., E-mail: bryanw@cyllene.uwa.edu.au [Western Australian Institute for Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia 6009 (Australia); Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, Western Australia 6009 (Australia)

2011-09-09T23:59:59.000Z

451

Identification of High Affinity Polo-like Kinase 1 (Plk1) Polo-box Domain Binding Peptides Using Oxime-Based Diversification  

E-Print Network [OSTI]

In an effort to develop improved binding antagonists of the polo-like kinase 1 (Plk1) polo-box domain (PBD), we optimized interactions of the known high affinity 5-mer peptide PLHSpT using oxime-based post solid-phase ...

Liu, Fa

452

J. Phys. Chem. 1994, 98, 5113-5111 5773 Free Energy of Solvation, Interaction, and Binding of Arbitrary Charge Distributions Imbedded in  

E-Print Network [OSTI]

J. Phys. Chem. 1994, 98, 5113-5111 5773 Free Energy of Solvation, Interaction, and Binding in a continuum solvent. Background Attempts seeking analytical solutions to the hydration free energies solvation free energies of arbitrary charge distributions with an overall spherical symmetry. This theory

Jayaram, Bhyravabotla

453

Efficient Initiation of HIV-1 Reverse Transcription in Vitro REQUIREMENT FOR RNA SEQUENCES DOWNSTREAM OF THE PRIMER BINDING SITE ABROGATED BY  

E-Print Network [OSTI]

DOWNSTREAM OF THE PRIMER BINDING SITE ABROGATED BY NUCLEOCAPSID PROTEIN-DEPENDENT PRIMER of viral RNA. Here, we have investigated whether sequences downstream of the PBS play a role in promoting bases downstream of the PBS when tRNA3 Lys or an 18-nt RNA complementary to the PBS (R18), but not an 18

Levin, Judith G.

454

The EF-hand motif is the most common calcium-binding motif found in proteins. Several high-resolution structures  

E-Print Network [OSTI]

. This sequence forms a loop that can accommodate calcium or magnesium with distinct geometries: magnesium is usu637 The EF-hand motif is the most common calcium-binding motif found in proteins. Several high matter © 2000 Elsevier Science Ltd. All rights reserved. Introduction Calcium is among life's most

Yue, David

455

Structure of a Glomulin-RBX1-CUL1 Complex: Inhibition of a RING E3 Ligase through Masking of Its E2-Binding Surface  

SciTech Connect (OSTI)

The approximately 300 human cullin-RING ligases (CRLs) are multisubunit E3s in which a RING protein, either RBX1 or RBX2, recruits an E2 to catalyze ubiquitination. RBX1-containing CRLs also can bind Glomulin (GLMN), which binds RBX1's RING domain, regulates the RBX1-CUL1-containing SCF{sup FBW7} complex, and is disrupted in the disease Glomuvenous Malformation. Here we report the crystal structure of a complex between GLMN, RBX1, and a fragment of CUL1. Structural and biochemical analyses reveal that GLMN adopts a HEAT-like repeat fold that tightly binds the E2-interacting surface of RBX1, inhibiting CRL-mediated chain formation by the E2 CDC34. The structure explains the basis for GLMN's selectivity toward RBX1 over RBX2, and how disease-associated mutations disrupt GLMN-RBX1 interactions. Our study reveals a mechanism for RING E3 ligase regulation, whereby an inhibitor blocks E2 access, and raises the possibility that other E3s are likewise controlled by cellular proteins that mask E2-binding surfaces to mediate inhibition.

Duda, David M.; Olszewski, Jennifer L.; Tron, Adriana E.; Hammel, Michal; Lambert, Lester J.; Waddell, M. Brett; Mittag, Tanja; DeCaprio, James A.; Schulman, Brenda A. (BWH); (LBNL); (SJCH); (DFCI)

2012-11-01T23:59:59.000Z

456

The fork head transcription factor Hcm1p participates in the regulation of SPC110, which encodes the calmodulin-binding protein in the  

E-Print Network [OSTI]

The fork head transcription factor Hcm1p participates in the regulation of SPC110, which encodes and abolish the ability of Hcm1p to act as a suppressor of calmodulin mutants. The promoter of SPC110 contains a match to the consensus binding site. Deletion of HCM1 does not affect the basal level of SPC110

Davis, Trisha N.

457

Dynamics of P-binding forms in sediments of a mesotrophic hard-water lake: Insights from non-steady state reactive-transport modeling,  

E-Print Network [OSTI]

Gudimov 1 , George Arhonditsis, Alexey Chesnyuk, Maria Dittrich Department of Physical and Environmental r t i c l e i n f o Article history: Received 6 November 2012 Received in revised form 10 June 2013 the fractionation data of phosphorus binding forms. The impact of the interplay between sedi- mentation fluxes

Arhonditsis, George B.

458

Self-Assembly and Selective Guest Binding of Three-Dimensional Open-Framework Solids from a Macrocyclic Complex as a Trifunctional Metal  

E-Print Network [OSTI]

Self-Assembly and Selective Guest Binding of Three-Dimensional Open- Framework Solids from by the one-pot template condensation re- action of amine and formaldehyde. From the self-assembly of 1-organic coordination networks having specific network topologies and potentially interesting prop- erties.[1±12] Self-assembly

Paik Suh, Myunghyun

459

Volume 242, number 1, 178-182 FEB 06635 December 1988 1H_NMR studies on nucleotide binding to the catalytic sites of  

E-Print Network [OSTI]

Volume 242, number 1, 178-182 FEB 06635 December 1988 1H_NMR studies on nucleotide binding the synconformationin solution,are in the anticonformationwhenboundto F1cata- lyticsites. Fl-ATPase;Nucleotide, a knowledge of the adenine nucleotide conformation Correspondenceaddress:J. Garin, Laboratoirede Biochimie, D6

Clore, G. Marius

460

Age-Related Binding Deficits and the Content of False Memories Keith B. Lyle, Suzanne M. Bloise, and Marcia K. Johnson  

E-Print Network [OSTI]

, and Marcia K. Johnson Yale University The authors examined effects of age-related binding deficits on featureIntyre & Craik, 1987), and location (Chalfonte & Johnson, 1996; Light & Zelinski, 1983; Mitchell, Johnson, Raye with actually experi- enced events (e.g., Balota et al., 1999; Henkel, Johnson, & De Leonardis, 1998; Koutstaal

Johnson, Marcia K.

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


461

Modulation of kinase-inhibitor interactions by auxiliary protein binding: Crystallography studies on Aurora A interactions with VX-680 and with TPX2  

SciTech Connect (OSTI)

VX-680, also known as MK-0457, is an ATP-competitive small molecule inhibitor of the Aurora kinases that has entered phase II clinical trials for the treatment of cancer. We have solved the cocrystal structure of AurA/TPX2/VX-680 at 2.3 {angstrom} resolution. In the crystal structure, VX-680 binds to the active conformation of AurA. The glycine-rich loop in AurA adopts a unique bent conformation, forming a {pi}-{pi} interaction with the phenyl group of VX-680. In contrast, in the published AurA/VX-680 structure, VX-680 binds to AurA in the inactive conformation, interacting with a hydrophobic pocket only present in the inactive conformation. These data suggest that TPX2, a protein cofactor, can alter the binding mode of VX-680 with AurA. More generally, the presence of physiologically relevant cofactor proteins can alter the kinetics, binding interactions, and inhibition of enzymes, and studies with these multiprotein complexes may be beneficial to the discovery and optimization of enzyme inhibitors as therapeutic agents.

Zhao, Baoguang; Smallwood, Angela; Yang, Jingsong; Koretke, Kristin; Nurse, Kelvin; Calamari, Amy; Kirkpatrick, Robert B.; Lai, Zhihong (GSKPA)

2008-10-24T23:59:59.000Z

462

The Zinc Metalloregulatory Protein Synechococcus PCC7942 SmtB Binds a Single Zinc Ion per Monomer with High Affinity in a Tetrahedral Coordination Geometry  

E-Print Network [OSTI]

. Scott, and David P. Giedroc*, Department of Biochemistry and Biophysics, Center for AdVanced metallothionein that functions in the sequestra- tion and metabolism of zinc in Synechococcus (7). Smt-2-12 inverted repeat. Each half-site is characterized by a consensus 5-TGAA sequence to which SmtB binds (9

Scott, Robert A.

463

The Binding of Oxidized Low Density Lipoprotein to Mouse CD36 Is Mediated in Part by Oxidized Phospholipids That Are Associated  

E-Print Network [OSTI]

Friedman¶ , Edward A. Dennis, Joseph L. Witztum, Daniel Steinberg, and Oswald Quehenberger** From ( 50%) both by the reconstituted apoB from OxLDL and by microemulsions prepared from OxLDL lipids and by demonstrating reciprocal inhibition, i.e. apoB from OxLDL inhibited the binding of the OxLDL lipids and vice

Dennis, Edward A.

464

Chemistry & Biology 13, 139147, February 2006 2006 Elsevier Ltd All rights reserved DOI 10.1016/j.chembiol.2005.10.015 Directed Evolution of ATP Binding Proteins  

E-Print Network [OSTI]

.chembiol.2005.10.015 Directed Evolution of ATP Binding Proteins from a Zinc Finger Domain by Using mRNA Display recognize adenosine triphosphate (ATP), dem- onstrating a significant alteration of the function of this protein domain from DNA binding to ATP recogni- tion. Many novel independent sequences were recov- ered

Heller, Eric

465

Crystal Structure of (+)-[delta]-Cadinene Synthase from Gossypium arboreum and Evolutionary Divergence of Metal Binding Motifs for Catalysis  

SciTech Connect (OSTI)

(+)-{delta}-Cadinene synthase (DCS) from Gossypium arboreum (tree cotton) is a sesquiterpene cyclase that catalyzes the cyclization of farnesyl diphosphate in the first committed step of the biosynthesis of gossypol, a phytoalexin that defends the plant from bacterial and fungal pathogens. Here, we report the X-ray crystal structure of unliganded DCS at 2.4 {angstrom} resolution and the structure of its complex with three putative Mg{sup 2+} ions and the substrate analogue inhibitor 2-fluorofarnesyl diphosphate (2F-FPP) at 2.75 {angstrom} resolution. These structures illuminate unusual features that accommodate the trinuclear metal cluster required for substrate binding and catalysis. Like other terpenoid cyclases, DCS contains a characteristic aspartate-rich D{sup 307}DTYD{sup 311} motif on helix D that interacts with Mg{sub A}{sup 2+} and Mg{sub C}{sup 2+}. However, DCS appears to be unique among terpenoid cyclases in that it does not contain the 'NSE/DTE' motif on helix H that specifically chelates Mg{sub B}{sup 2+}, which is usually found as the signature sequence (N,D)D(L,I,V)X(S,T)XXXE (boldface indicates Mg{sub B}{sup 2+} ligands). Instead, DCS contains a second aspartate-rich motif, D{sup 451}DVAE{sup 455}, that interacts with Mg{sub B}{sup 2+}. In this regard, DCS is more similar to the isoprenoid chain elongation enzyme farnesyl diphosphate synthase, which also contains two aspartate-rich motifs, rather than the greater family of terpenoid cyclases. Nevertheless, the structure of the DCS-2F-FPP complex shows that the structure of the trinuclear magnesium cluster is generally similar to that of other terpenoid cyclases despite the alternative Mg{sub B}{sup 2+} binding motif. Analyses of DCS mutants with alanine substitutions in the D{sup 307}DTYD{sup 311} and D{sup 451}DVAE{sup 455} segments reveal the contributions of these segments to catalysis.

Gennadios, Heather A.; Gonzalez, Veronica; Di Costanzo, Luigi; Li, Amang; Yu, Fanglei; Miller, David J.; Allemann, Rudolf K.; Christianson, David W.; (UPENN); (Cardiff); (UC)

2009-09-11T23:59:59.000Z

466

Monte-Carlo simulation of the tight-binding model of graphene with partially screened Coulomb interactions  

E-Print Network [OSTI]

We report on Hybrid-Monte-Carlo simulations of the tight-binding model with long-range Coulomb interactions for the electronic properties of graphene. We investigate the spontaneous breaking of sublattice symmetry corresponding to a transition from the semimetal to an antiferromagnetic insulating phase. Our short-range interactions thereby include the partial screening due to electrons in higher energy states from ab initio calculations based on the constrained random phase approximation [T.O.Wehling {\\it et al.}, Phys.Rev.Lett.{\\bf 106}, 236805 (2011)]. In contrast to a similar previous Monte-Carlo study [M.V.Ulybyshev {\\it et al.}, Phys.Rev.Lett.{\\bf 111}, 056801 (2013)] we also include a phenomenological model which describes the transition to the unscreened bare Coulomb interactions of graphene at half filling in the long-wavelength limit. Our results show, however, that the critical coupling for the antiferromagnetic Mott transition is largely insensitive to the strength of these long-range Coulomb tails. They hence confirm the prediction that suspended graphene remains in the semimetal phase when a realistic static screening of the Coulomb interactions is included.

Dominik Smith; Lorenz von Smekal

2014-03-14T23:59:59.000Z

467

A New Determination of the Binding Energy of Atomic Oxygen on Dust Grain Surfaces: Experimental Results and Simulations  

E-Print Network [OSTI]

The energy to desorb atomic oxygen from an interstellar dust grain surface, $E_{\\rm des}$, is an important controlling parameter in gas-grain models; its value impacts the temperature range over which oxygen resides on a dust grain. However, no prior measurement has been done of the desorption energy. We report the first direct measurement of $E_{\\rm des}$ for atomic oxygen from dust grain analogs. The values of $E_{\\rm des}$ are $1660\\pm 60$~K and $1850\\pm 90$~K for porous amorphous water ice and for a bare amorphous silicate film, respectively, or about twice the value previously adopted in simulations of the chemical evolution of a cloud. We use the new values to study oxygen chemistry as a function of depth in a molecular cloud. For $n=10^4$ cm$^{-3}$ and $G_0$=10$^2$ ($G_0$=1 is the average local interstellar radiation field), the main result of the adoption of the higher oxygen binding energy is that H$_2$O can form on grains at lower visual extinction $A_{\\rm V}$, closer to the cloud surface. A higher ...

He, Jiao; Hopkins, Tyler; Vidali, Gianfranco; Kaufman, Michael J

2015-01-01T23:59:59.000Z

468

Computational study of heterojunction graphene nanoribbon tunneling transistors with p-d orbital tight-binding method  

SciTech Connect (OSTI)

The graphene nanoribbon (GNR) tunneling field effect transistor (TFET) has been a promising candidate for a future low power logic device due to its sub-60?mV/dec subthreshold characteristic and its superior gate control on the channel electrons due to its one-dimensional nature. Even though many theoretical studies have been carried out, it is not clear that GNR TFETs would outperform conventional silicon metal oxide semiconductor field effect transistors (MOSFETs). With rigorous atomistic simulations using the p/d orbital tight-binding model, this study focuses on the optimization of GNR TFETs by tuning the doping density and the size of GNRs. It is found that the optimized GNR TFET can operate at a half of the supply voltage of silicon nanowire MOSFETs in the ballistic limit. However, a study on the effects of edge roughness on the performance of the optimized GNR TFET structure reveals that experimentally feasible edge roughness can deteriorates the on-current performance if the off-current is normalized with the low power requirement specified in the international technology roadmap for semiconductors.

Kim, SungGeun, E-mail: snugkim@gmail.com; Klimeck, Gerhard [Network for Computational Nanotechnology, Purdue University, West Lafayette, Indiana 47907 (United States); Luisier, Mathieu [Integrated Systems Laboratory, Gloriastrasse 35, ETH Zrich, 8092 Zrich (Switzerland); Boykin, Timothy B. [Department of Electrical and Computer Engineering, The University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States)

2014-06-16T23:59:59.000Z

469

Electrostatic binding of bicarbonate and formate in viologen-based redox polymers: importance in catalytic reduction of bicarbonate to formate  

SciTech Connect (OSTI)

The relative importance of electrostatic binding of CO3H and HCO2 in a redox polymer derived from an N,N'-dialkyl-4,4'-bipyridinium monomer has been investigated by Fourier transform infrared (FTIR) spectroscopy. At 298 K and a total concentration of C-containing species of 0.1 M the two species are equally firmly bound in a polymer immobilized on a single-crystal Si electrode surface. When the concentration of C-containing species is 1.0 M, the CO3H ion is more firmly bound by about a factor of 2.5, and at a total concentration of 3.0 M the CO3H ion is about 7 times more firmly bound than the HCO2 ion. The HCO2 and Cl anions are equally firmly bound at 1.0 M total anion concentration. On the basis of the lack of change in the cyclic voltammetry response of a derivatized electrode in 1.0 M Na(CO3H) or Na(HCO2) compared to 1.0 M NaCl, the exchange rate of the C-containing anions does not appear to be a factor that would limit the rate of reduction of the CO3H ion at an electrode modified with the polymer and impregnated with Pd(0).

Andre, J.F.; Wrighton, M.S.

1985-12-04T23:59:59.000Z

470

Study of quark mass dependence of binding energy for light nuclei in 2+1 flavor lattice QCD  

E-Print Network [OSTI]

We investigate the formation of light nuclei with the nuclear mass number less than or equal to four in 2+1 flavor QCD using a non-perturbative improved Wilson quark and Iwasaki gauge actions. The quark mass is decreased from our previous work to the one corresponding to the pion mass of 0.30 GeV. In each multi-nucleon channel, the energy shift of the ground state relative to the assembly of free nucleons is calculated on two volumes, whose spatial extents are 4.3 fm and 5.8 fm. From the volume dependence of the energy shift, we distinguish a bound state of multi nucleons from an attractive scattering state. We find that all the ground states measured in this calculation are bound states. As in the previous studies at larger $m_\\pi$, our result indicates that at $m_\\pi = 0.30$ GeV the effective interaction between nucleons in the light nuclei is relatively stronger than the one in nature, since the results for the binding energies are larger than the experimental values and a bound state appears in the dineutron channel, which is not observed in experiment. Possible sources of this discrepancy from experiment are discussed.

Takeshi Yamazaki; Ken-ichi Ishikawa; Yoshinobu Kuramashi; Akira Ukawa

2015-02-14T23:59:59.000Z

471

hnRNP L binds to CA repeats in the 3'UTR of bcl-2 mRNA  

SciTech Connect (OSTI)

We previously reported that the CA-repeat sequence in the 3'-untranslated region (3'UTR) of bcl-2 mRNA is involved in the decay of bcl-2 mRNA. However, the trans-acting factor for the CA element in bcl-2 mRNA remains unidentified. The heterogeneous nuclear ribonucleoprotein L (hnRNP L), an intron splicing factor, has been reported to bind to CA repeats and CA clusters in the 3'UTR of several genes. We reported herein that the CA repeats of bcl-2 mRNA have the potential to form a distinct ribonuclear protein complex in cytoplasmic extracts of MCF-7 cells, as evidenced by RNA electrophoretic mobility shift assays (REMSA). A super-shift assay using the hnRNP L antibody completely shifted the complex. Immunoprecipitation with the hnRNP L antibody and MCF-7 cells followed by RT-PCR revealed that hnRNP L interacts with endogenous bcl-2 mRNA in vivo. Furthermore, the suppression of hnRNP L in MCF-7 cells by the transfection of siRNA for hnRNP L resulted in a delay in the degradation of RNA transcripts including CA repeats of bcl-2 mRNA in vitro, suggesting that the interaction between hnRNPL and CA repeats of bcl-2 mRNA participates in destabilizing bcl-2 mRNA.

Lee, Dong-Hyoung; Lim, Mi-Hyun; Youn, Dong-Ye [Department of Biochemistry, College of Medicine, The Catholic University of Korea, 505 Banpo-Dong, Seocho-gu, Seoul 137-701 (Korea, Republic of)] [Department of Biochemistry, College of Medicine, The Catholic University of Korea, 505 Banpo-Dong, Seocho-gu, Seoul 137-701 (Korea, Republic of); Jung, Seung Eun [Department of Medical Science, The Graduate School, Yonsei University, Seoul (Korea, Republic of)] [Department of Medical Science, The Graduate School, Yonsei University, Seoul (Korea, Republic of); Ahn, Young Soo [Brain Korea 21 Project for Medical Science, Brain Research Institute, Department of Pharmacology, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Brain Korea 21 Project for Medical Science, Brain Research Institute, Department of Pharmacology, Yonsei University College of Medicine, Seoul (Korea, Republic of); Tsujimoto, Yoshihide [Department of Medical Genetics, Laboratory of Molecular Genetics, Osaka University Medical School, Osaka (Japan)] [Department of Medical Genetics, Laboratory of Molecular Genetics, Osaka University Medical School, Osaka (Japan); Lee, Jeong-Hwa, E-mail: leejh@catholic.ac.kr [Department of Biochemistry, College of Medicine, The Catholic University of Korea, 505 Banpo-Dong, Seocho-gu, Seoul 137-701 (Korea, Republic of)] [Department of Biochemistry, College of Medicine, The Catholic University of Korea, 505 Banpo-Dong, Seocho-gu, Seoul 137-701 (Korea, Republic of)

2009-05-08T23:59:59.000Z

472

Absence of zero-temperature transmission rate of a double-chain tight-binding model for DNA with random sequence of nucleotides in thermodynamic limit  

E-Print Network [OSTI]

The zero-temperature transmission rate spectrum of a double-chain tight-binding model for real DNA is calculated. It is shown that a band of extended-like states exists only for finite chain length with strong inter-chain coupling. While the whole spectrum tends to zero in thermodynamic limit, regardless of the strength of inter-chain coupling. It is also shown that a more faithful model for real DNA with periodic sugar-phosphate chains in backbone structures can be mapped into the above simple double-chain tight-binding model. Combined with above results, the transmission rate of real DNA with long random sequence of nucleotides is expected to be poor.

Gang Xiong; X. R. Wang

2005-12-16T23:59:59.000Z

473

Strong Sulfur Binding with Conducting Magneli-Phase TinO2n-1 Nanomaterials for Improving Lithium-Sulfur Batteries  

E-Print Network [OSTI]

will go through a series of soluble intermediate higher-order polysulfides (Li2S8, Li2S6, and Li2S4 of Li2S2, Li2S, and sulfur.6-8 In order to solve these challenges, there have been recent developmentsStrong Sulfur Binding with Conducting Magneli-Phase TinO2n-1 Nanomaterials for Improving Lithium-Sulfur

Cui, Yi

474

Screening a phage display library for a novel FGF8b-binding peptide with anti-tumor effect on prostate cancer  

SciTech Connect (OSTI)

Fibroblast growth factor 8b (FGF8b) is the major isoform of FGF8 expressed in prostate cancer and it correlates with the stage and grade of the disease. FGF8b has been considered as a potential target for prostate cancer therapy. Here we isolated 12 specific FGF8b-binding phage clones by screening a phage display heptapeptide library with FGF8b. The peptide (HSQAAVP, named as P12) corresponding to one of these clones showed high homology to the immunoglobulin-like (Ig-like) domain II(D2) of high-affinity FGF8b receptor (FGFR3c), contained 3 identical amino acids (AVP) to the authentic FGFR3 D2 sequence aa 163169 (LLAVPAA) directly participating in ligand binding, carried the same charges as its corresponding motif (aa163169) in FGFR3c, suggesting that P12 may have a greater potential to interrupt FGF8b binding to its receptors than other identified heptapeptides do. Functional analysis indicated that synthetic P12 peptides mediate significant inhibition of FGF8b-induced cell proliferation, arrest cell cycle at the G0/G1 phase via suppression of Cyclin D1 and PCNA, and blockade of the activations of Erk1/2 and Akt cascades in both prostate cancer cells and vascular endothelial cells. The results demonstrated that the P12 peptide acting as an FGF8b antagonist may have therapeutic potential in prostate cancer. - Highlights: ? A novel FGF8b-binding peptide P12 was isolated from a phage display library. ? The mechanisms for P12 peptide inhibiting cell proliferation were proposed. ? P12 caused cell cycle arrest at G0/G1 phase via suppression of Cyclin D1 and PCNA. ? P12 suppressed FGF8b-induced activations of Akt and MAP kinases. ? P12 acting as an FGF8b antagonist may have therapeutic potential in prostate cancer.

Wang, Wenhui; Chen, Xilei; Li, Tao; Li, Yanmei; Wang, Ruixue; He, Dan; Luo, Wu [Institute of Tissue Transplantation and Immunology, Jinan University, Guangzhou 510632 (China); Li, Xiaokun [Institute of Tissue Transplantation and Immunology, Jinan University, Guangzhou 510632 (China); School of Pharmaceutical Science, Wenzhou Medical College, Wenzhou 325035 (China); Wu, Xiaoping, E-mail: twxp@jnu.edu.cn [Institute of Tissue Transplantation and Immunology, Jinan University, Guangzhou 510632 (China); School of Pharmaceutical Science, Wenzhou Medical College, Wenzhou 325035 (China)

2013-05-01T23:59:59.000Z

475

Site occupancy and cation binding states in reduced polycrystalline Sr{sub x}Ba{sub 1?x}Nb{sub 2}O{sub 6}  

SciTech Connect (OSTI)

Site occupancy and cation binding states in the proposed thermoelectric n-type oxide Sr{sub x}Ba{sub 1?x}Nb{sub 2}O{sub 6} (SBN100x) were investigated using X-ray photoelectron spectroscopy (XPS). Sr 3d XPS spectra from unreduced polycrystalline SBN100x with various compositions contained two distinct spin-orbit doublets corresponding to Sr occupying either A1 or A2 positions in the SBN lattice; the higher binding energy state was associated with Sr ions at A2 sites, presumably due to their increased coordination over Sr at A1 sites. To gain insight into optimizing the thermoelectric properties of reduced SBN, sintered SBN50 specimens were reduced in Ar/H{sub 2} or N{sub 2}/H{sub 2} ambient. A decrease in the average Nb valence was observed in Nb 3d photoemission through the growth of low-binding energy components after reduction in either environment; evidence of surface NbN formation was apparent with longer reducing times in N{sub 2}/H{sub 2}. Both the single-component Ba 3d emission and the A2 component of the Sr 3d spectra show shifting to lower binding energy as the reduction time is increased, supporting the hypothesis of preferential oxygen vacancy formation adjacent to A2 sites. X-ray diffraction patterns revealed the formation of NbO{sub 2} in both reducing environments; in the case of extended reduction in N{sub 2}/H{sub 2}, NbO{sub 2} is gradually converted to NbN phases. Given the known properties of metallic NbN and semiconducting NbO{sub 2}, the findings obtained here may be used to maximize the thermoelectric performance of SBN via the fabrication of composite structures containing both NbO{sub 2} and NbN.

Dandeneau, Christopher S., E-mail: dandec@u.washington.edu; Yang, YiHsun; Ohuchi, Fumio S. [Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195 (United States)] [Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195 (United States); Krueger, Benjamin W.; Olmstead, Marjorie A. [Department of Physics, University of Washington, Seattle, Washington 98195 (United States)] [Department of Physics, University of Washington, Seattle, Washington 98195 (United States); Bordia, Rajendra K. [Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634 (United States)] [Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634 (United States)

2014-03-10T23:59:59.000Z

476

Cotton Study: Albumin Binding and its Effect on Elastase Activity in the Chronic Non-Healing Wound  

SciTech Connect (OSTI)

Cotton, as it is used in wound dressings is composed of nearly pure cellulose. During the wound-healing process, cotton is exposed to various blood components including water, salts, cells, and blood proteins. Albumin is the most prominent protein in blood. Elastase is an enzyme secreted by white blood cells and takes an active role in tissue reconstruction. In the chronic non-healing wound, elastase is often over-expressed such that this enzyme digests tissue and growth factors, and interferes with the normal healing process. Our goal is to design a cotton wound dressing that will sequester elastase or assist in reducing elastase activity in the presence of other blood proteins such as albumin. The ability of cotton and various cotton derivatives to sequester elastase and albumin has been studied by examining the adsorption of these two proteins separately. We undertook the present work to confirm the binding of albumin to cotton and to quantify the activity of elastase in the presence of various derivatives of cotton. We previously observed a slight increase in elastase activity when exposed to cotton. We also observed a continuous accumulation of albumin on cotton using high-performance liquid chromatography methods. In the present study, we used an open-column-absorption technique coupled with a colorimetric protein assay to confirm losses of albumin to cotton. We have also confirmed increased elastase activity after exposure to cotton. The results are discussed in relation to the porosity of cotton and the use of cotton for treating chronic non-healing wounds.

Castro, N.; Goheen, S.

2005-01-01T23:59:59.000Z

477

Synthesis, characterization and performance of single-component CO2-binding organic liquids (CO2BOL) for post combustion CO2 capture  

SciTech Connect (OSTI)

Carbon dioxide (CO2) emission to the atmosphere will increase significantly with the shift to coal powered plants for energy generation. This increase in CO2 emission will contribute to climate change. There is need to capture and sequester large amounts of CO2 emitted from these coal power plants in order to mitigate the environmental effects. Here we report the synthesis, characterization and system performance of multiple third generation CO2 binding organic liquids (CO2BOLs) as a solvent system for post combustion gas capture. Alkanolguanidines and alkanolamidines are single component CO2BOLs that reversibly bind CO2 chemically as liquid zwitterionic amidinium / guanidinium alkylcarbonates. Three different alkanolguanidines and alkanolamidines were synthesized and studied for CO2 capacity and binding energetics. Solvent performance of these three CO2BOLs was evaluated by batch-wise CO2 uptake and release over multiple cycles. Synthesis of CO2BOLs, characterization, CO2 uptake, selectivity towards CO2 as well as solvent tolerance to water will be discussed.

Koech, Phillip K.; Heldebrant, David J.; Rainbolt, James E.; Zheng, Feng; Smurthwaite, Tricia D.

2010-03-31T23:59:59.000Z

478

Binding of the Respiratory Chain Inhibitor Antimycin to theMitochondrial bc1 Complex: A New Crystal Structure Reveals an AlteredIntramolecular Hydrogen-Bonding Pattern  

SciTech Connect (OSTI)

Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex.Structure-activity-relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding specificity, and suggested that a low pKa for the phenolic OH group and an intramolecular H-bond between that OH and the carbonyl O of the salicylamide linkage are important. Two previous X-ray structures of antimycin bound to vertebrate bc1 complex gave conflicting results. A new structure reported here of the bovine mitochondrial bc1 complex at 2.28Angstrom resolution with antimycin bound, allows us for the first time to reliably describe the binding of antimycin and shows that the intramolecular hydrogen bond described in solution and in the small-molecule structure is replaced by one involving the NH rather than carbonyl O of the amide linkage, with rotation of the amide group relative to the aromatic ring. The phenolic OH and formylamino N form H-bonds with conserved Asp228 of cyt b, and the formylamino O H-bonds via a water molecule to Lys227. A strong density the right size and shape for a diatomic molecule is found between the other side of the dilactone ring and the alpha-A helix.

Huang, Li-shar; Cobessi, David; Tung, Eric Y.; Berry, Edward A.

2005-05-10T23:59:59.000Z

479

Apo calmodulin binding to the L-type voltage-gated calcium channel Ca{sub v}1.2 IQ peptide  

SciTech Connect (OSTI)

The influx of calcium through the L-type voltage-gated calcium channels (LTCCs) is the trigger for the process of calcium-induced calcium release (CICR) from the sarcoplasmic recticulum, an essential step for cardiac contraction. There are two feedback mechanisms that regulate LTCC activity: calcium-dependent inactivation (CDI) and calcium-dependent facilitation (CDF), both of which are mediated by calmodulin (CaM) binding. The IQ domain (aa 1645-1668) housed within the cytoplasmic domain of the LTCC Ca{sub v}1.2 subunit has been shown to bind both calcium-loaded (Ca{sup 2+}CaM ) and calcium-free CaM (apoCaM). Here, we provide new data for the structural basis for the interaction of apoCaM with the IQ peptide using NMR, revealing that the apoCaM C-lobe residues are most significantly perturbed upon complex formation. In addition, we have employed transmission electron microscopy of purified LTCC complexes which shows that both apoCaM and Ca{sup 2+}CaM can bind to the intact channel.

Lian Luyun [School of Biological Sciences, University of Liverpool, P.O. Box 147, Liverpool L69 7ZB (United Kingdom)]. E-mail: lu-yun.lian@liverpool.ac.uk; Myatt, Daniel [School of Medicine, Cardiovascular and Endocrine Sciences, University of Manchester, Manchester M13 9NT (United Kingdom); Kitmitto, Ashraf [School of Medicine, Cardiovascular and Endocrine Sciences, University of Manchester, Manchester M13 9NT (United Kingdom)]. E-mail: ashraf.kitmitto@manchester.ac.uk

2007-02-16T23:59:59.000Z

480

Binding Facility Agreement  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

at the Portsmouth Gaseous Diffusion Plant (PORTS) under the Gaseous Diffusion Plant (GDP) Lease Pursuant to the Lease Agreement Between the United States Department of Energy...

Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


481

Binding Facility Agreement  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

at the Portsmouth Gaseous Diffusion Plant (PORTS) under the Gaseous Diffusion Plant (GDP) Lease Pursuant to the Lease Agreement Between the United States Department oEnergy...

482

bind | The Ames Laboratory  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear SecurityTensile Strain Switched FerromagnetismWaste andAnniversary,Effects of InhomogeneousBig Bendbind Ames

483

In the mIdst of an energy revolutIon, Purdue's world-class researchers lead the charge. we collaborate across a broad range of dIscIPlInes --to develoP  

E-Print Network [OSTI]

In the mIdst of an energy revolutIon, Purdue's world-class researchers lead the charge. we rechargIng IndIana's renewable energy revolutIon #12;enerGY solutions solar The U.S. Department of Energy

Holland, Jeffrey

484

This is a test document showing how utf8.sty makes it possible to put many characters directly into a LaTeX document. Digraphs in Vim exist for many of these characters, and some additional bindings have  

E-Print Network [OSTI]

into a LaTeX document. Digraphs in Vim exist for many of these characters, and some additional bindings have been defined. Thus, should look exactly the same as , and can be typed like Vim. non

Myers, Andrew C.

485

Pb(II) and Hg(II) binding to $de$ $novo$ designed proteins studied by $^{204m}$Pb- and $^{199m}$Hg-Perturbed Angular Correlation of $\\gamma$-rays (PAC) spectroscopy Clues to heavy metal toxicity  

E-Print Network [OSTI]

Pb(II) and Hg(II) binding to $de$ $novo$ designed proteins studied by $^{204m}$Pb- and $^{199m}$Hg-Perturbed Angular Correlation of $\\gamma$-rays (PAC) spectroscopy

CERN. Geneva. ISOLDE and Neutron Time-of-Flight Experiments Committee; Correia, J G

2006-01-01T23:59:59.000Z

486

The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors  

SciTech Connect (OSTI)

Signaling through the programmed death 1 (PD-1) inhibitory receptor upon binding its ligand, PD-L1, suppresses immune responses against autoantigens and tumors and plays an important role in the maintenance of peripheral immune tolerance. Release from PD-1 inhibitory signaling revives 'exhausted' virus-specific T cells in chronic viral infections. Here we present the crystal structure of murine PD-1 in complex with human PD-L1. PD-1 and PD-L1 interact through the conserved front and side of their Ig variable (IgV) domains, as do the IgV domains of antibodies and T cell receptors. This places the loops at the ends of the IgV domains on the same side of the PD-1/PD-L1 complex, forming a surface that is similar to the antigen-binding surface of antibodies and T cell receptors. Mapping conserved residues allowed the identification of residues that are important in forming the PD-1/PD-L1 interface. Based on the structure, we show that some reported loss-of-binding mutations involve the PD-1/PD-L1 interaction but that others compromise protein folding. The PD-1/PD-L1 interaction described here may be blocked by antibodies or by designed small-molecule drugs to lower inhibitory signaling that results in a stronger immune response. The immune receptor-like loops offer a new surface for further study and potentially the design of molecules that would affect PD-1/PD-L1 complex formation and thereby modulate the immune response.

Lin, David Yin-wei; Tanaka, Yoshimasa; Iwasaki, Masashi; Gittis, Apostolos G.; Su, Hua-Poo; Mikami, Bunzo; Okazaki, Taku; Honjo, Tasuku; Minato, Nagahiro; Garboczi, David N. (NIH); (Kyoto)

2008-07-29T23:59:59.000Z

487

Generation of mice deficient in RNA-binding motif protein 3 (RBM3) and characterization of its role in innate immune responses and cell growth  

SciTech Connect (OSTI)

Highlights: {yields} We identified RNA-binding motif protein 3 (RBM3) as CpG-B DNA-binding protein. {yields} RBM3 translocates from the nucleus to the cytoplasm and co-localized with CpG-B DNA. {yields} We newly generated Rbm3-deficient (Rbm3{sup -/-}) mice. {yields} DNA-mediated cytokine gene induction was normally occured in Rbm3{sup -/-} cells. {yields}Rbm3{sup -/-} MEFs showed poorer proliferation rate and increased number of G2-phase cells. -- Abstract: The activation of innate immune responses is critical to host defense against microbial infections, wherein nucleic acid-sensing pattern recognition receptors recognize DNA or RNA from viruses or bacteria and activate downstream signaling pathways. In a search for new DNA-sensing molecules that regulate innate immune responses, we identified RNA-binding motif protein 3 (RBM3), whose role has been implicated in the regulation of cell growth. In this study, we generated Rbm3-deficient (Rbm3{sup -/-}) mice to study the role of RBM3 in immune responses and cell growth. Despite evidence for its interaction with immunogenic DNA in a cell, no overt phenotypic abnormalities were found in cells from Rbm3{sup -/-} mice for the DNA-mediated induction of cytokine genes. Interestingly, however, Rbm3{sup -/-} mouse embryonic fibroblasts (MEFs) showed poorer proliferation rates as compared to control MEFs. Further cell cycle analysis revealed that Rbm3{sup -/-} MEFs have markedly increased number of G2-phase cells, suggesting a hitherto unknown role of RBM3 in the G2-phase control. Thus, these mutant mice and cells may provide new tools with which to study the mechanisms underlying the regulation of cell cycle and oncogenesis.

Matsuda, Atsushi [Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan) [Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan); Core Research for Evolution Science and Technology, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0075 (Japan); Ogawa, Masahiro [Laboratory of Immune Regulation, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 (Japan)] [Laboratory of Immune Regulation, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Yanai, Hideyuki [Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan) [Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan); Core Research for Evolution Science and Technology, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0075 (Japan); Naka, Daiji [ZOEGENE Corp., 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033 (Japan)] [ZOEGENE Corp., 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033 (Japan); Goto, Ayana; Ao, Tomoka [Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)] [Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan); Tanno, Yuji [Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan)] [Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Takeda, Kiyoshi [Laboratory of Immune Regulation, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 (Japan)] [Laboratory of Immune Regulation, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Watanabe, Yoshinori [Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan)] [Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Honda, Kenya [Laboratory of Immune Regulation, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 (Japan)] [Laboratory of Immune Regulation, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Taniguchi, Tadatsugu, E-mail: tada@m.u-tokyo.ac.jp [Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan) [Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan); Core Research for Evolution Science and Technology, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0075 (Japan)

2011-07-22T23:59:59.000Z

488

Changes in the Zero-Point Energy of the Protons as the Source of the Binding Energy of Water to A-Phase DNA  

SciTech Connect (OSTI)

The measured changes in the zero-point kinetic energy of the protons are entirely responsible for the binding energy of water molecules to A phase DNA at the concentration of 6 water molecules/base pair. The changes in kinetic energy can be expected to be a significant contribution to the energy balance in intracellular biological processes and the properties of nano-confined water. The shape of the momentum distribution in the dehydrated A phase is consistent with coherent delocalization of some of the protons in a double well potential, with a separation of the wells of 0.2 Angst .

Reiter, G. F. [Physics Department, University of Houston, Houston, Texas 77204 (United States); Senesi, R. [Dipartimento di Fisica and Centro NAST, Universita degli Studi di Roma 'Tor Vergata', Via della Ricerca Scientifica 1, 00133 Roma (Italy); Mayers, J. [ISIS, Rutherford Appleton Laboratory, Chilton, Didcot (United Kingdom)

2010-10-01T23:59:59.000Z

489

Fontecave and Sandrine Ollagnier de Clemancey, Jean-Marc Latour, Marc  

E-Print Network [OSTI]

have so far revealed three distinct systems responsible for Fe-S cluster biosynthesis, termed NIF, ISC, and SUF, which are encoded by the nif, isc, and suf operon, respec- tively (1­3). The NIF system

Boyer, Edmond

490

Different receptors binding to distinct interfaces on herpes simplex virus gD can trigger events leading to cell fusion and viral entry  

SciTech Connect (OSTI)

One of the herpes simplex virus envelope glycoproteins, designated gD, is the principal determinant of cell recognition for viral entry. Other viral glycoproteins, gB, gH and gL, cooperate with gD to mediate the membrane fusion that is required for viral entry and cell fusion. Membrane fusion is triggered by the binding of gD to one of its receptors. These receptors belong to three different classes of cell surface molecules. This review summarizes recent findings on the structure and function of gD. The results presented indicate that gD may assume more than one conformation, one in the absence of receptor, another when gD is bound to the herpesvirus entry mediator, a member of the TNF receptor family, and a third when gD is bound to nectin-1, a cell adhesion molecule in the immunoglobulin superfamily. Finally, information and ideas are presented about a membrane-proximal region of gD that is required for membrane fusion, but not for receptor binding, and that may have a role in activating the fusogenic activity of gB, gH and gL.

Spear, Patricia G. [Department of Microbiology-Immunology, MC S213, Feinberg School of Medicine, Northwestern University, 320 East Superior Street, Chicago, IL 60611 (United States)]. E-mail: p-spear@northwestern.edu; Manoj, Sharmila [Department of Microbiology-Immunology, MC S213, Feinberg School of Medicine, Northwestern University, 320 East Superior Street, Chicago, IL 60611 (United States); Yoon, Miri [Department of Microbiology-Immunology, MC S213, Feinberg School of Medicine, Northwestern University, 320 East Superior Street, Chicago, IL 60611 (United States); Jogger, Cheryl R. [Department of Microbiology-Immunology, MC S213, Feinberg School of Medicine, Northwestern University, 320 East Superior Street, Chicago, IL 60611 (United States); Zago, Anna [Department of Microbiology-Immunology, MC S213, Feinberg School of Medicine, Northwestern University, 320 East Superior Street, Chicago, IL 60611 (United States); Myscofski, Dawn [Department of Microbiology-Immunology, MC S213, Feinberg School of Medicine, Northwestern University, 320 East Superior Street, Chicago, IL 60611 (United States)

2006-01-05T23:59:59.000Z

491

A self-interaction-free local hybrid functional: Accurate binding energies vis--vis accurate ionization potentials from Kohn-Sham eigenvalues  

SciTech Connect (OSTI)

We present and test a new approximation for the exchange-correlation (xc) energy of Kohn-Sham density functional theory. It combines exact exchange with a compatible non-local correlation functional. The functional is by construction free of one-electron self-interaction, respects constraints derived from uniform coordinate scaling, and has the correct asymptotic behavior of the xc energy density. It contains one parameter that is not determined ab initio. We investigate whether it is possible to construct a functional that yields accurate binding energies and affords other advantages, specifically Kohn-Sham eigenvalues that reliably reflect ionization potentials. Tests for a set of atoms and small molecules show that within our local-hybrid form accurate binding energies can be achieved by proper optimization of the free parameter in our functional, along with an improvement in dissociation energy curves and in Kohn-Sham eigenvalues. However, the correspondence of the latter to experimental ionization potentials is not yet satisfactory, and if we choose to optimize their prediction, a rather different value of the functional's parameter is obtained. We put this finding in a larger context by discussing similar observations for other functionals and possible directions for further functional development that our findings suggest.

Schmidt, Tobias; Kmmel, Stephan [Theoretical Physics IV, University of Bayreuth, 95440 Bayreuth (Germany)] [Theoretical Physics IV, University of Bayreuth, 95440 Bayreuth (Germany); Kraisler, Eli; Makmal, Adi; Kronik, Leeor [Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100 (Israel)] [Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100 (Israel)

2014-05-14T23:59:59.000Z

492

Briefly Bound to Activate: Transient Binding of a Second Catalytic Magnesium Activates the Structure and Dynamics of CDK2 Kinase for Catalysis  

SciTech Connect (OSTI)

We have determined high-resolution crystal structures of a CDK2/Cyclin A transition state complex bound to ADP, substrate peptide, and MgF{sub 3}{sup -}. Compared to previous structures of active CDK2, the catalytic subunit of the kinase adopts a more closed conformation around the active site and now allows observation of a second Mg{sup 2+} ion in the active site. Coupled with a strong [Mg{sup 2+}] effect on in vitro kinase activity, the structures suggest that the transient binding of the second Mg{sup 2+} ion is necessary to achieve maximum rate enhancement of the chemical reaction, and Mg{sup 2+} concentration could represent an important regulator of CDK2 activity in vivo. Molecular dynamics simulations illustrate how the simultaneous binding of substrate peptide, ATP, and two Mg{sup 2+} ions is able to induce a more rigid and closed organization of the active site that functions to orient the phosphates, stabilize the buildup of negative charge, and shield the subsequently activated {gamma}-phosphate from solvent.

Bao, Zhao Qin; Jacobsen, Douglas M.; Young, Matthew A. (Michigan-Med)

2014-10-02T23:59:59.000Z

493

Structural and functional studies of a phosphatidic acid-binding antifungal plant defensin MtDef4: Identification of an RGFRRR motif governing fungal cell entry  

SciTech Connect (OSTI)

A highly conserved plant defensin MtDef4 potently inhibits the growth of a filamentous fungus Fusarium graminearum. MtDef4 is internalized by cells of F. graminearum. To determine its mechanism of fungal cell entry and antifungal action, NMR solution structure of MtDef4 has been determined. The analysis of its structure has revealed a positively charged patch on the surface of the protein consisting of arginine residues in its ?-core signature, a major determinant of the antifungal activity of MtDef4. Here, we report functional analysis of the RGFRRR motif of the ?-core signature of MtDef4. The replacement of RGFRRR to AAAARR or to RGFRAA not only abolishes fungal cell entry but also results in loss of the antifungal activity of MtDef4. MtDef4 binds strongly to phosphatidic acid (PA), a precursor for the biosynthesis of membrane phospholipids and a signaling lipid known to recruit cytosolic proteins to membranes. Mutations of RGFRRR which abolish fungal cell entry of MtDef4 also impair its binding to PA. Our results suggest that RGFRRR motif is a translocation signal for entry of MtDef4 into fungal cells and that this positively charged motif likely mediates interaction of this defensin with PA as part of its antifungal action.

Sagaram, Uma S.; El-Mounadi, Kaoutar; Buchko, Garry W.; Berg, Howard R.; Kaur, Jagdeep; Pandurangi, Raghoottama; Smith, Thomas J.; Shah, Dilip

2013-12-04T23:59:59.000Z

494

Structural dynamics and ssDNA binding activity of the three N-terminal domains of the large subunit of Replication Protein A from small angle X-ray scattering  

SciTech Connect (OSTI)

Replication Protein A (RPA) is the primary eukaryotic ssDNA binding protein utilized in diverse DNA transactions in the cell. RPA is a heterotrimeric protein with seven globular domains connected by flexible linkers, which enable substantial inter-domain motion that is essential to its function. Small angle X-ray scattering (SAXS) experiments on two multi-domain constructs from the N-terminus of the large subunit (RPA70) were used to examine the structural dynamics of these domains and their response to the binding of ssDNA. The SAXS data combined with molecular dynamics simulations reveal substantial interdomain flexibility for both RPA70AB (the tandem high affinity ssDNA binding domains A and B connected by a 10-residue linker) and RPA70NAB (RPA70AB extended by a 70-residue linker to the RPA70N protein interaction domain). Binding of ssDNA to RPA70NAB reduces the interdomain flexibility between the A and B domains, but has no effect on RPA70N. These studies provide the first direct measurements of changes in orientation of these three RPA domains upon binding ssDNA. The results support a model in which RPA70N remains structurally independent of RPA70AB in the DNA bound state and therefore freely available to serve as a protein recruitment module.

Pretto, Dalyir I.; Tsutakawa, Susan; Brosey, Chris A.; Castillo, Amalchi; Chagot, Marie-Eve; Smith, Jarrod A.; Tainer, John A.; Chazin, Walter J.

2010-03-11T23:59:59.000Z

495

Morphology control and characterization of single-walled carbon nanotube counter electrodes in dye sensitized solar cells  

E-Print Network [OSTI]

of the sol Counter electrode ISC[mA/cm2 ] V [V] FF PCE[%] Table 1 I-VSWNT PtISC, mA/cm2 (FF : fill factor) (PCE : power conversion efficiency) ISCFF SWNTPt SWNTPt PtISC SWNT Pt SWNT PCE SWNTFTO VOC V 0.66 V

Maruyama, Shigeo

496

Crystallographic Analysis of Murine Constitutive Androstane Receptor Ligand-Binding Domain Complexed with 5[alpha]-androst-16-en-3[alpha]-ol  

SciTech Connect (OSTI)

The constitutive androstane receptor (CAR) is a member of the nuclear receptor superfamily. In contrast to classical nuclear receptors, which possess small-molecule ligand-inducible activity, CAR exhibits constitutive transcriptional activity in the apparent absence of ligand. CAR is among the most important transcription factors; it coordinately regulates the expression of microsomal cytochrome P450 genes and other drug-metabolizing enzymes. The murine CAR ligand-binding domain (LBD) was coexpressed with the steroid receptor coactivator protein (SRC-1) receptor-interacting domain (RID) in Escherichia coli. The mCAR LBD subunit was purified away from SRC-1 by affinity, anion-exchange and size-exclusion chromatography, crystallized with androstenol and the structure of the complex determined by molecular replacement.

Vincent, J.; Shan, L.; Fan, M.; Brunzelle, J.S.; Forman, B.M.; Fernandez, E.J. (Tennessee-K); (NWU); (CHNMC)

2010-03-08T23:59:59.000Z

497

Water-soluble metal-binding polymers with ultrafiltration: A technology for the removal, concentration, and recovery of metal ions from aqueous streams  

SciTech Connect (OSTI)

The use of water-soluble metal-binding polymers coupled with ultrafiltration (UF) is a technology under development to selectively concentrate and recover valuable or regulated metal-ions from dilute process or waste waters. The polymers have a sufficiently large molecular size that they can be separated and concentrated using commercially available UF technology. The polymers can then be reused by changing the solution conditions to release the metal-ions, which are recovered in a concentrated form for recycle or disposal. Pilot-scale demonstrations have been completed for a variety of waste streams containing low concentrations of metal ions including electroplating wastes (zinc and nickel) and nuclear waste streams (plutonium and americium). Many other potential commercial applications exist including remediation of contaminated solids. An overview of both the pilot-scale demonstrated applications and small scale testing of this technology are presented.

Smith, B.F.; Robison, T.W.; Jarvinen, G.D.

1997-12-31T23:59:59.000Z

498

The Exosporium of B.cereus Contains a Binding Site for gC1qR/p33: Implication in Spore Attachment and/or Entry.  

SciTech Connect (OSTI)

B. cereus, is a member of a genus of aerobic, gram-positive, spore-forming rod-like bacilli, which includes the deadly, B. anthracis. Preliminary experiments have shown that gC1qR binds to B.cereus spores that have been attached to microtiter plates. The present studies were therefore undertaken, to examine if cell surface gC1qR plays a role in B.cereus spore attachment and/or entry. Monolayers of human colon carcinoma (Caco-2) and lung cells were grown to confluency on 6 mm coverslips in shell vials with gentle swirling in a shaker incubator. Then, 2 {micro}l of a suspension of strain SB460 B.cereus spores (3x10{sup 8}/ml, in sterile water), were added and incubated (1-4 h; 36{sup 0} C) in the presence or absence of anti-gC1qR mAb-carbon nanoloops. Examination of these cells by EM revealed that: (1) When B. cereus endospores contacted the apical Caco-2 cell surface, or lung cells, gClqR was simultaneously detectable, indicating upregulation of the molecule. (2) In areas showing spore contact with the cell surface, gClqR expression was often adjacent to the spores in association with microvilli (Caco-2 cells) or cytoskeletal projections (lung cells). (3) Furthermore, the exosporia of the activated and germinating spores were often decorated with mAb-nanoloops. These observations were further corroborated by experiments in which B.cereus spores were readily taken up by monocytes and neutrophils, and this uptake was partially inhibited by mAb 60.11, which recognizes the C1q binding site on gC1qR. Taken together, the data suggest a role, for gC1qR at least in the initial stages of spore attachment and/or entry.

GHEBREHIWET,B.; TANTRAL, L.; TITMUS, M.A.; PANESSA-WARREN, B.J.; TORTORA, G.T.; WONG, S.S.; WARREN, J.B.

2008-01-01T23:59:59.000Z

499

The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3; end of 16S rRNA  

SciTech Connect (OSTI)

Era, composed of a GTPase domain and a K homology domain, is essential for bacterial cell viability. It is required for the maturation of 16S rRNA and assembly of the 30S ribosomal subunit. We showed previously that the protein recognizes nine nucleotides (1531{sup AUCACCUCC}1539) near the 3{prime} end of 16S rRNA, and that this recognition stimulates GTP-hydrolyzing activity of Era. In all three kingdoms of life, the 1530{sup GAUCA}1534 sequence and helix 45 (h45) (nucleotides 1506-1529) are highly conserved. It has been shown that the 1530{sup GA}1531 to 1530{sup AG}1531 double mutation severely affects the viability of bacteria. However, whether Era interacts with G1530 and/or h45 and whether such interactions (if any) contribute to the stimulation of Era's GTPase activity were not known. Here, we report two RNA structures that contain nucleotides 1506-1542 (RNA301), one in complex with Era and GDPNP (GNP), a nonhydrolysable GTP-analogue, and the other in complex with Era, GNP, and the KsgA methyltransferase. The structures show that Era recognizes 10 nucleotides, including G1530, and that Era also binds h45. Moreover, GTPase assay experiments show that G1530 does not stimulate Era's GTPase activity. Rather, A1531 and A1534 are most important for stimulation and h45 further contributes to the stimulation. Although G1530 does not contribute to the intrinsic GTPase activity of Era, its interaction with Era is important for binding and is essential for the protein to function, leading to the discovery of a new cold-sensitive phenotype of Era.

Tu, Chao; Zhou, Xiaomei; Tarasov, Sergey G.; Tropea, Joseph E.; Austin, Brian P.; Waugh, David S.; Court, Donald L.; Ji, Xinhua (NCI)

2012-03-26T23:59:59.000Z

500

Human Sco1 and Sco2 Function as Copper-binding Proteins* Received for publication, June 22, 2005, and in revised form, July 29, 2005 Published, JBC Papers in Press, August 9, 2005, DOI 10.1074/jbc.M506801200  

E-Print Network [OSTI]

Human Sco1 and Sco2 Function as Copper-binding Proteins* Received for publication, June 22, 2005 on copper ion binding. Expression of soluble domains of human Sco1 and Sco2 either in bacteria or the yeast cytoplasm resulted in the recovery of copper-containing proteins. The metallation of human Sco1, but not Sco

Shoubridge, Eric