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Note: This page contains sample records for the topic "u-098 isc bind" from the National Library of EnergyBeta (NLEBeta).
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We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


1

U-098: ISC BIND Deleted Domain Name Resolving Vulnerability | Department of  

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

098: ISC BIND Deleted Domain Name Resolving Vulnerability 098: ISC BIND Deleted Domain Name Resolving Vulnerability U-098: ISC BIND Deleted Domain Name Resolving Vulnerability February 8, 2012 - 7:00am Addthis PROBLEM: A vulnerability has been reported in ISC BIND, which can be exploited by malicious people to bypass certain security restrictions. PLATFORM: ISC BIND 9.2.x ISC BIND 9.3.x ISC BIND 9.4.x ISC BIND 9.5.x ISC BIND 9.6.x ISC BIND 9.7.x ISC BIND 9.8.x ABSTRACT: The vulnerability is caused due to an error within the cache update policy. reference LINKS: Original Advisory Secunia Advisory SA47884 CVE-2012-1033 IMPACT ASSESSMENT: High Discussion: Researchers discovered a vulnerability affecting the large majority of popular DNS implementations which allows a malicious domain name to stay resolvable long after it has been removed from the upper level servers. The

2

U-183: ISC BIND DNS Resource Records Handling Vulnerability | Department of  

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

3: ISC BIND DNS Resource Records Handling Vulnerability 3: ISC BIND DNS Resource Records Handling Vulnerability U-183: ISC BIND DNS Resource Records Handling Vulnerability June 5, 2012 - 7:00am Addthis PROBLEM: A vulnerability has been reported in ISC BIND, which can be exploited by malicious people to disclose potentially sensitive information or cause a DoS (Denial of Service). PLATFORM: Version(s): ISC BIND 9.2.x ISC BIND 9.3.x ISC BIND 9.4.x ISC BIND 9.5.x ISC BIND 9.6.x ISC BIND 9.7.x ISC BIND 9.8.x ISC BIND 9.9.x ABSTRACT: 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. Reference List: Secunia Advisory 49338 CVE-2012-1667 Original Advisory IMPACT ASSESSMENT: High Discussion: Recursive servers may crash or disclose some portion of memory to the

3

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

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

9: ISC Update: BIND 9 Resolver crashes after logging an error 9: ISC Update: BIND 9 Resolver crashes after logging an error in query.c U-039: ISC Update: BIND 9 Resolver crashes after logging an error in query.c November 16, 2011 - 2:30pm Addthis PROBLEM: ISC Update: BIND 9 Resolver crashes after logging an error in query.c. PLATFORM: Versions of BIND, 9.4-ESV, 9.6-ESV, 9.7.x, 9.8.x ABSTRACT: A remote server can cause the target connected client to crash. Organizations across the Internet are reporting crashes interrupting service on BIND 9 nameservers performing recursive queries. Affected servers crash after logging an error in query.c with the following message: "INSIST(! dns_rdataset_isassociated(sigrdataset))" Multiple versions are reported as being affected, including all currently supported release versions of ISC BIND 9. ISC is actively investigating the root cause and

4

V-007: McAfee Firewall Enterprise ISC BIND Record Handling Lockup  

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

7: McAfee Firewall Enterprise ISC BIND Record Handling Lockup 7: McAfee Firewall Enterprise ISC BIND Record Handling Lockup Vulnerability V-007: McAfee Firewall Enterprise ISC BIND Record Handling Lockup Vulnerability October 22, 2012 - 6:00am Addthis PROBLEM: McAfee Firewall Enterprise ISC BIND Record Handling Lockup Vulnerability PLATFORM: Versions 8.2.x prior to 8.2.1P06, and 8.3.x prior to 8.3.0P02 REFERENCE LINKS: Secunia Advisory SA51050 CVE-2012-5166 McAfee Corporate Knowledge Base IMPACT ASSESSMENT: Medium DISCUSSION: The vulnerability is caused due to an error when handling queries for certain records and can be exploited to cause the named process to lockup. IMPACT: If specific combinations of RDATA are loaded into a nameserver, either via cache or an authoritative zone, a subsequent query for a related record

5

U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service  

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

1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service 1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability July 26, 2012 - 7:00am Addthis PROBLEM: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability PLATFORM: BIND 9.6-ESV-R1 through versions 9.6-ESV-R7-P1 BIND 9.7.1 through versions 9.7.6-P1 BIND 9.8.0 through versions 9.8.3-P1 BIND 9.9.0 through versions 9.9.1-P1 ABSTRACT: ISC BIND is prone to a denial-of-service vulnerability. reference LINKS: The Vendor's Advisory CVE-2012-3817 Bugtraq ID: 54658 SecurityTracker Alert ID: 1027296 IMPACT ASSESSMENT: High Discussion: When DNSSEC validation is enabled, does not properly initialize the failing-query cache, which allows remote attackers to cause a denial of

6

U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service  

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

1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service 1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability July 26, 2012 - 7:00am Addthis PROBLEM: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability PLATFORM: BIND 9.6-ESV-R1 through versions 9.6-ESV-R7-P1 BIND 9.7.1 through versions 9.7.6-P1 BIND 9.8.0 through versions 9.8.3-P1 BIND 9.9.0 through versions 9.9.1-P1 ABSTRACT: ISC BIND is prone to a denial-of-service vulnerability. reference LINKS: The Vendor's Advisory CVE-2012-3817 Bugtraq ID: 54658 SecurityTracker Alert ID: 1027296 IMPACT ASSESSMENT: High Discussion: When DNSSEC validation is enabled, does not properly initialize the failing-query cache, which allows remote attackers to cause a denial of

7

U-260: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service |  

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

0: ISC BIND RDATA Processing Flaw Lets Remote Users Deny 0: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service U-260: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service September 14, 2012 - 6:00am Addthis PROBLEM: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service PLATFORM: Version(s): 9.0.x -> 9.6.x, 9.4-ESV->9.4-ESV-R5-P1, 9.6-ESV->9.6-ESV-R7-P2, 9.7.0->9.7.6-P2, 9.8.0->9.8.3-P2, 9.9.0->9.9.1-P2 ABSTRACT: A vulnerability was reported in ISC BIND. reference LINKS: The vendor's advisory SecurityTracker Alert ID: 1027529 Bugtraq ID: 55522 Red Hat Bugzilla - Bug 856754 CVE-2012-4244 IMPACT ASSESSMENT: High Discussion: A remote user can send a query for a record that has RDATA in excess of 65535 bytes to cause named to exit. This can be exploited against recursive servers by causing the server to query for records provided by an

8

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

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

2: ISC BIND Packet Processing Flaw Lets Remote Users Deny 2: ISC BIND Packet Processing Flaw Lets Remote Users Deny Service T-662: ISC BIND Packet Processing Flaw Lets Remote Users Deny Service July 6, 2011 - 7:47am Addthis PROBLEM: A vulnerability was reported in ISC BIND. A remote user can cause denial of service conditions. PLATFORM: 9.6.3, 9.6-ESV-R4, 9.6-ESV-R4-P1, 9.6-ESV-R5b1 9.7.0, 9.7.0-P1, 9.7.0-P2, 9.7.1, 9.7.1-P1, 9.7.1-P2, 9.7.2, 9.7.2-P1, 9.7.2-P2, 9.7.2-P3, 9.7.3, 9.7.3-P1, 9.7.3-P2, 9.7.4b1 9.8.0, 9.8.0-P1, 9.8.0-P2, 9.8.0-P3, 9.8.1b1 ABSTRACT: A defect in the affected BIND 9 versions allows an attacker to remotely cause the "named" process to exit using a specially crafted packet. This defect affects both recursive and authoritative servers. The code location of the defect makes it impossible to protect BIND using ACLs configured

9

DsrR, a Novel IscA-Like Protein Lacking Iron- and Fe-S-Binding Functions, Involved in the Regulation of Sulfur Oxidation in Allochromatium vinosum  

Science Journals Connector (OSTI)

...sequence. IscA-like proteins without bound iron...DsrR and IscA-like proteins. This disordered region corresponds...site in IscA-like proteins. Several residues...convergence in the NMR ensemble, probably reflecting...

Frauke Grimm; John R. Cort; Christiane Dahl

2010-01-08T23:59:59.000Z

10

U-224: ISC DHCP Multiple Denial of Service Vulnerabilities | Department of  

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

4: ISC DHCP Multiple Denial of Service Vulnerabilities 4: ISC DHCP Multiple Denial of Service Vulnerabilities U-224: ISC DHCP Multiple Denial of Service Vulnerabilities July 31, 2012 - 7:00am Addthis PROBLEM: ISC DHCP Multiple Denial of Service Vulnerabilities PLATFORM: ISC DHCP before versions DHCP 4.1-ESV-R6 or DHCP 4.2.4-P1 ABSTRACT: ISC DHCP is prone to multiple denial-of-service vulnerabilities. reference LINKS: BIND and DHCP Security Updates Released Bugtraq ID: 54665 Secunia Advisory SA50018 CVE-2012-3571 CVE-2012-3570 CVE-2012-3954 IMPACT ASSESSMENT: Medium Discussion: Multiple vulnerabilities have been reported in ISC DHCP, which can be exploited by malicious people to cause a DoS (Denial of Service). 1) An error when handling client identifiers can be exploited to trigger an endless loop and prevent the server from processing further client requests

11

Institute for Sustainable Communities (ISC) | Open Energy Information  

Open Energy Info (EERE)

Sustainable Communities (ISC) Address: 535 Stone Cutters Way Montpelier, Vermont 05602 USA Place: Montpelier, Vermont Zip: 05602 Website: http:www.iscvt.org References: http:...

12

ISC-Reducing Congestion through Smart Parking Management | Open Energy  

Open Energy Info (EERE)

ISC-Reducing Congestion through Smart Parking Management ISC-Reducing Congestion through Smart Parking Management Jump to: navigation, search Tool Summary LAUNCH TOOL Name: ISC-Reducing Congestion through Smart Parking Management Agency/Company /Organization: Institute for Sustainable Communities (ISC) Sector: Climate, Energy Focus Area: Transportation Resource Type: Case studies/examples, Lessons learned/best practices Website: www.iscvt.org/resources/documents/san_francisco_sfpark.pdf Locality: San Francisco, California Cost: Free Language: English ISC-Reducing Congestion through Smart Parking Management Screenshot References: Reducing Congestion through Smart Parking Management[1] "The transit study concluded that congestion is a primary factor reducing the reliability and speed of onroad transit, which in turn is exacerbated

13

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

14

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

Office of Science (SC) Website

IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Freedom of Information Act (FOIA) ISC Conventional...

15

T-617: BIND RPZ Processing Flaw Lets Remote Users Deny Service | Department  

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

7: BIND RPZ Processing Flaw Lets Remote Users Deny Service 7: BIND RPZ Processing Flaw Lets Remote Users Deny Service T-617: BIND RPZ Processing Flaw Lets Remote Users Deny Service May 6, 2011 - 7:00am Addthis PROBLEM: A vulnerability has been reported in BIND, which can be exploited by malicious people to cause a DoS (Denial of Service). PLATFORM: ISC BIND version 9.8.0. ABSTRACT: When a name server is configured with a response policy zone (RPZ), queries for type RRSIG can trigger a server crash. REFERENCE LINKS: ISC Advisory: CVE-2011-1907 Secunia Advisory: SA44416 Vulnerability Report: ISC BIND CVE-2011-1907 SecurityTracker Alert ID: 1025503 IMPACT ASSESSMENT: High Discussion: This advisory only affects BIND users who are using the RPZ feature configured for RRset replacement. BIND 9.8.0 introduced Response Policy Zones (RPZ), a mechanism for modifying DNS responses returned by a

16

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

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

Home Home Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Integrated Support Center The Office of Science Integrated Support Center proudly facilitates work across the ten Office of Science laboratories and site offices. Caption: The Hall D tagger area of the Continuous Electron Beam Accelerator Facility at Thomas Jefferson Laboratory. Hall D tagger area 1 of 2 Print Text Size: A A A RSS Feeds FeedbackShare Page The Office of Science's (SC) Integrated Support Center (ISC) provides

17

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

18

U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service...  

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

service to legitimate users. This issue may also be exploited to disclose certain memory information to clients. Solution: The vendor has issued a fix. Addthis Related...

19

U-038: BIND 9 Resolver crashes after logging an error in query.c |  

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

8: BIND 9 Resolver crashes after logging an error in query.c 8: BIND 9 Resolver crashes after logging an error in query.c U-038: BIND 9 Resolver crashes after logging an error in query.c November 16, 2011 - 8:37am Addthis PROBLEM: BIND 9 Resolver crashes after logging an error in query.c. PLATFORM: Multiple version of BIND 9. Specific versions under investigation ABSTRACT: A remote server can cause the target connected client to crash. Organizations across the Internet are reporting crashes interrupting service on BIND 9 nameservers performing recursive queries. Affected servers crash after logging an error in query.c with the following message: "INSIST(! dns_rdataset_isassociated(sigrdataset))" Multiple versions are reported as being affected, including all currently supported release versions of ISC BIND 9. ISC is actively investigating the root cause and

20

Microsoft Word - ORO ISC Functional Analysis and Inventory 3-6-07 FINAL.doc  

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

Table of Contents Page Introduction 1 Mission 1 Distinctive Characteristics 2 Assumptions 3 Staffing and Trends 4 Critical Skills Inventory 6 Significant Successes 7 Strategic Goals and Objectives 9 Conclusions 10 Appendix A: Functional Descriptions 11 Appendix B: SC ISC Staffing Levels by Occupational Groupings 16 Appendix C: Organizational Metrics 21 F U N C T I O N A L A N A L Y S I S A N D I N V E N T O R Y Introduction The Manager, Oak Ridge Office (ORO), has requested this Functional Analysis and Inventory to identify and present quantifiable performance metrics for various matrix support activities performed by ORO. This analysis will be used to describe the ORO operating model as a component of the Office of Science (SC) Integrated

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

isc golf, that is. The 4,560-foot course winds throughout the woods behind East Campus  

E-Print Network [OSTI]

D isc golf, that is. The 4,560-foot course winds throughout the woods behind East Campus Saturday 6:45 a.m. Spinning Spinning Spinning Noon Boot Camp R.I.P.P.E.D Power Yoga Yoga Pilates Total Body Toning R.I.P.P.E.D. Power Yoga Yoga Pilates Total Body Toning Power Yoga R.I.P.P.E.D. 4:30 p.m. Vinyasa

Suzuki, Masatsugu

22

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

23

V-204: A specially crafted query can cause BIND to terminate abnormally |  

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

V-204: A specially crafted query can cause BIND to terminate V-204: A specially crafted query can cause BIND to terminate abnormally V-204: A specially crafted query can cause BIND to terminate abnormally July 27, 2013 - 4:35am Addthis PROBLEM: A specially crafted query that includes malformed rdata can cause named to terminate with an assertion failure while rejecting the malformed query. PLATFORM: BIND 9.7 ABSTRACT: A specially crafted query sent to a BIND nameserver can cause it to crash (terminate abnormally). REFERENCE LINKS: ISC Knowledge Base CVE-2013-4854 IMPACT ASSESSMENT: High DISCUSSION: BIND is an implementation of the Domain Name System (DNS) protocols. Authoritative and recursive servers are equally vulnerable. Intentional exploitation of this condition can cause a denial of service in all nameservers running affected versions of BIND 9. Access Control Lists do

24

ISC2005v2.ppt  

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

1989 The argument against massive parallelism (ca. 1988) From a presentation by Jim Hack at DOE Salishan High Speed Computing, 1988 Theoretical papers such as this "proved"...

25

ISCED: International Standard Classification of Education ISCED Fields of Education and Training (2013)  

E-Print Network [OSTI]

ERA-Code 022 Humanities (except languages) 0223 Philosophy and ethics [Medizin/Ethik] 031 Social design and administration 0613 Software and applications development and analysis 0618 Inter Informationssystemtechnik [Communications Technology] [Energy Science & Technology] 524 523 06.0 | 06.2 | 06.5 091 Health

Pfeifer, Holger

26

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

27

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

28

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

29

Erythropoietin binding protein from mammalian serum  

DOE Patents [OSTI]

Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described. 11 figs.

Clemons, G.K.

1997-04-29T23:59:59.000Z

30

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

31

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

32

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

33

Atomic-binding-energy oscillations  

Science Journals Connector (OSTI)

We investigate the oscillatory supplement to the statistical nonrelativistic binding-energy formula for neutral atoms. The semiclassical approach proves capable of deriving these oscillations. It turns out that their amplitude is proportional to Z4/3 (Z is the number of electrons), and that their period is determined by the maximum angular momentum available in Thomas-Fermi atoms, i.e., 0.928Z1/3. Our calculation also provides an understanding of the peculiar shape of the oscillations, which show sharp minima and wide, structured maxima.

Berthold-Georg Englert and Julian Schwinger

1985-07-01T23:59:59.000Z

34

The hidden ties that bind | EMSL  

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

hidden ties that bind EMSL advancements open new possibilities for characterizing nanoparticle interactions EMSL's sum-frequency generation vibrational spectrometer The Science...

35

Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules  

Science Journals Connector (OSTI)

......of hydrogen bonding in the interaction between a xylan binding module and xylan. Biochemistry (2001) 40:5700-5707. Yang...predicted ligand-binding residues residing on the surface in the hypothetical structures were verified to......

Wei-Yao Chou; Wei-I Chou; Tun-Wen Pai; Shu-Chuan Lin; Ting-Ying Jiang; Chuan-Yi Tang; Margaret Dah-Tsyr Chang

2010-04-15T23:59:59.000Z

36

Binding (or Cohesive) Energy Denition and Constraints  

E-Print Network [OSTI]

Binding (or Cohesive) Energy Denition and Constraints The binding or cohesive energy cof a substance (either liquid or solid) is the energy required to break all the bonds associated with one of its constituent molecules. It is, therefore a measure of the inter-molecular energy for a substance. We spend time

Nimmo, Francis

37

predictive information, multi-information, and binding  

E-Print Network [OSTI]

predictive information, multi-information, and binding information Samer Abdallah and Mark Plumbley.1 ­ December 9, 2010 Abstract We introduce an information theoretic measure of dependency between multiple random variables, called `binding information' and compare it with several previously proposed measures

Plumbley, Mark

38

Facile Dimer Synthesis for DNA-Binding Polyamide Ligands  

Science Journals Connector (OSTI)

Pyrrole-imidazole polyamide ligands are highly sequence specific synthetic DNA-binding ligands that bind with high affinity. ... Regulation of gene expression by synthetic DNA-binding ligands ...

Modi Wetzler; David E. Wemmer

2010-07-13T23:59:59.000Z

39

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

40

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...

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

Coordinatively unsaturated Al3+ centers as binding sites for...  

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

Coordinatively unsaturated Al3+ centers as binding sites for active catalyst phases on ?-Al2O3. Coordinatively unsaturated Al3+ centers as binding sites for active catalyst...

42

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

43

Metal-binding polymesr as chelating agents  

E-Print Network [OSTI]

Abstract Metal chelating polymers are functional polymers that bear specified chemical groups capable of selectively binding metals. Heavy metal contamination is considered a serious problem because these metals, even at ...

Mohammadi, Zahra

2011-04-11T23:59:59.000Z

44

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.

45

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

46

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

47

Structural Study of Lipid-binding Proteins  

E-Print Network [OSTI]

show stronger inhibition than the known inhibitor triclosan. The triclosan-like analogs with modification at the 5-position revealed a new binding site in PfENR that has great potential for improving the potency of inhibition. We found that two...

Tsai, Han-Chun

2013-08-09T23:59:59.000Z

48

Regulation of Gene Expression by Synthetic DNA-Binding Ligands  

E-Print Network [OSTI]

Regulation of Gene Expression by Synthetic DNA-Binding Ligands Peter B. Dervan ( ) · Adam T. Poulin

Dervan, Peter B.

49

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

50

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

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

retinol-binding protein 1; IRBP--interphotoreceptor retinoid-binding protein; LCA... Da protein; RBP--retinol-binding protein; RDH--retinol dehydrogenase Keywords:...

51

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

52

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

53

CCAAT/enhancer binding protein gene promoter: binding of nuclear factors during differentiation of 3T3-L1 preadipocytes.  

Science Journals Connector (OSTI)

...gene promoter: binding of nuclear factors during differentiation...these differentially expressed nuclear factors. The factor present...that play a central role in energy metabolism, particularly in...the differentiation- induced nuclear factor that binds specifically...

R J Christy; K H Kaestner; D E Geiman; M D Lane

1991-01-01T23:59:59.000Z

54

Synthetic DNA minor groove-binding drugs  

Science Journals Connector (OSTI)

In this review, both cationic and neutral synthetic ligands that bind in the minor groove of DNA are discussed. Certain bis-distamycins and related lexitropsins show activities against human immunodeficiency virus (HIV)-1 and HIV-2 at low nanomolar concentrations. DAPI binds strongly to AT-containing polymers and is located in the minor groove of DNA. DAPI intercalates in DNA sequences that do not contain at least three consecutive AT bp. Berenil can also exhibit intercalative, as well as minor groove binding, properties depending on sequence. Furan-containing analogues of berenil play an important role in their activities against Pneumocystis carinii and Cryptosporidium parvuam infections in vivo. Pt(II)-berenil conjugates show a good activity profile against HL60 and U-937 human leukemic cells. Pt-pentamidine shows higher antiproliferative activity against small cell lung, non-small cell lung, and melanoma cancer cell lines compared with many other tumor cell lines. trans-Butenamidine shows good anti-P. carinii activity in rats. Pentamidine is used against P. carinii pneumonia in individuals infected with HIV who are at high risk from this infection. A comparison of the cytotoxic potencies of adozelesin, bizelesin, carzelesin, cisplatin, and doxorubicin indicates that adozelesin is a potent analog of CC-1065. Naturally occurring pyrrolo[2,1-c][1,4]benzodiazepines such as anthramycin have a 2- to 3-bp sequence specificity, but a synthetic PBD dimer spans 6 bp, actively recognizing a central 5?-GATC sequence. The crosslinking efficiency of PBD dimers is much greater than that of other major groove crosslinkers, such as cisplatin, melphalan, etc. Neothramycin is used clinically for the treatment of superficial carcinoma of the bladder.

B.S.Praveen Reddy; S.Murari Sondhi; J.William Lown

1999-01-01T23:59:59.000Z

55

JC3 Bulletin Archive | Department of Energy  

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

June 7, 2013 V-173: Plesk 0-Day Vulnerability The vulnerability is caused due to PHP misconfiguration in the affected application June 6, 2013 V-172: ISC BIND RUNTIMECHECK...

56

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

57

Specific binding of gibberellic acid by Cytokinin-Specific Binding Proteins: a new aspect of plant hormone-binding proteins with the PR-10 fold  

Science Journals Connector (OSTI)

Two plant cytokinin-specific binding proteins were crystallized in complex with gibberellic acid (GA3), which is an entirely different plant hormone. The crystal structures, determined at high resolution, reveal a highly specific mode of GA3 binding, calling for a revision of the hormone specificity of plant proteins with the PR-10 fold.

Ruszkowski, M.

2014-06-29T23:59:59.000Z

58

Functionalized Polymers For Binding To Solutes In Aqueous Solutions  

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

Functionalized Polymers For Binding To Solutes In Aqueous Solutions Functionalized Polymers For Binding To Solutes In Aqueous Solutions Functionalized Polymers For Binding To Solutes In Aqueous Solutions A functionalized polymer for binding a dissolved molecule in an aqueous solution is presented. Available for thumbnail of Feynman Center (505) 665-9090 Email Functionalized Polymers For Binding To Solutes In Aqueous Solutions A functionalized polymer for binding a dissolved molecule in an aqueous solution is presented. The polymer has a backbone polymer to which one or more functional groups are covalently linked. The backbone polymer can be such polymers as polyethylenimine, polyvinylamine, polyallylamine, and polypropylamine. These polymers are generally water-soluble, but can be insoluble when cross-linked. The functional group can be for example diol

59

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

60

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....

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

Binding and Diffusion of Lithium in Graphite: Quantum Monte Carlo...  

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

Binding and Diffusion of Lithium in Graphite: Quantum Monte Carlo Benchmarks and Validation of van der Waals Density Functional Methods P. Ganesh,* , Jeongnim Kim, Changwon...

62

Dissociative Binding of Carboxylic Acid Ligand on Nanoceria Surface...  

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

Abstract: Carboxylic acid is a common ligand anchoring group to functionalize nanoparticle surfaces. Its binding structures and mechanisms as a function of the oxidation...

63

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

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

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

64

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

65

Designing artificial metal binding peptides | Center for Bio...  

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

Designing artificial metal binding peptides 24 Oct 2012 Dong Wang is a graduate student in the Department of Chemistry and Biochemistry at Arizona State University. He is working...

66

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

67

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

68

Architecture of a Fur Binding Site: a Comparative Analysis  

Science Journals Connector (OSTI)

...configuration). Although Fur can bind synthetic DNA sequences containing the F-F-F...the ability of Fur to recognize synthetic DNA sequences containing two to four...The ability of Fur to bind synthetic DNA fragments containing one to five...

Jennifer L. Lavrrar; Mark A. McIntosh

2003-04-01T23:59:59.000Z

69

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

70

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.

71

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

72

Synthesis and Characterization of Polyamine Bicycles for Anion Binding  

E-Print Network [OSTI]

. Binding studies and crystal structures are discussed within. Structural aspects of the binding of halides in the p-xylyl octaaza cryptand [1,4,11,14,17,24,29,36-octa-azapentacyclo [12.12.12.26,9.219,22.231,34]-tetratetraconta-6 (43), 7,9(44), 19(41), 20...

Morehouse, Paula Kay

2007-10-09T23:59:59.000Z

73

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 ....

74

BPA FINAL Binding Arbitration policy | Department of Energy  

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

BPA FINAL Binding Arbitration policy BPA FINAL Binding Arbitration policy BPA FINAL Binding Arbitration policy Alternative dispute resolution (ADR) encompasses a variety of methods that parties may use to resolve disputes without litigation. Arbitration is a private, less formal process in which parties agree to submit a dispute to one or more impartial arbitrators who then render a decision or award. In non-binding arbitration a party is not required to accept the arbitrator's decision. In contrast, a decision or award in binding arbitration is final and subject to only very limited rights of appeal. See Federal Arbitration Act, 9 U.S.C. §§ 1-16 (FAA). Both types of arbitration can provide benefits to BPA, its customers, and other stakeholders including the public, such as greater flexibility, limited

75

Disordered binding of small molecules to A12-28 DISORDERED BINDING OF SMALL MOLECULES TO A12-28  

E-Print Network [OSTI]

.vitalis@bioc.uzh.ch. Keywords: Alzheimer's disease; intrinsically disordered proteins; molecular dynamics; protein aggregation of Alzheimer's amyloid- protein in subtle but complex fashion. Conclusion: Intrinsic disorder of diseaseDisordered binding of small molecules to A12-28 DISORDERED BINDING OF SMALL MOLECULES TO A12

Caflisch, Amedeo

76

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

77

A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain  

E-Print Network [OSTI]

A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa IIb xylan-binding domain 1 (XBD1) from Cellulomonas fimi xylanase D is shown to bind xylan of two four-stranded sheets that form a twisted ` sandwich'. The xylan-binding site is a groove made

Williamson, Mike P.

78

Product Binding Varies Dramatically between Processive and Nonprocessive Cellulase Enzymes  

SciTech Connect (OSTI)

Cellulases hydrolyze {beta}-1,4 glycosidic linkages in cellulose, which are among the most prevalent and stable bonds in Nature. Cellulases comprise many glycoside hydrolase families and exist as processive or nonprocessive enzymes. Product inhibition negatively impacts cellulase action, but experimental measurements of product-binding constants vary significantly, and there is little consensus on the importance of this phenomenon. To provide molecular level insights into cellulase product inhibition, we examine the impact of product binding on processive and nonprocessive cellulases by calculating the binding free energy of cellobiose to the product sites of catalytic domains of processive and nonprocessive enzymes from glycoside hydrolase families 6 and 7. The results suggest that cellobiose binds to processive cellulases much more strongly than nonprocessive cellulases. We also predict that the presence of a cellodextrin bound in the reactant site of the catalytic domain, which is present during enzymatic catalysis, has no effect on product binding in nonprocessive cellulases, whereas it significantly increases product binding to processive cellulases. This difference in product binding correlates with hydrogen bonding between the substrate-side ligand and the cellobiose product in processive cellulase tunnels and the additional stabilization from the longer tunnel-forming loops. The hydrogen bonds between the substrate- and product-side ligands are disrupted by water in nonprocessive cellulase clefts, and the lack of long tunnel-forming loops results in lower affinity of the product ligand. These findings provide new insights into the large discrepancies reported for binding constants for cellulases and suggest that product inhibition will vary significantly based on the amount of productive binding for processive cellulases on cellulose.

Bu, L.; Nimlos, M. R.; Shirts, M. R.; Stahlberg, J.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T.

2012-07-13T23:59:59.000Z

79

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

80

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...

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

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

82

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

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

2011 Summer Research Program Summary: configuration. The annealing of the two primer binding site regions may: 1) Provide greater stability... of the primer binding sites...

83

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...

84

E-Print Network 3.0 - antithrombin iii binding Sample Search...  

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

binding studies with low-affinity heparin... and a heparin tetrasaccharide suggest that PAA binds antithrombin in both the pentasaccharide- and the extended... weight; nd ) not...

85

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...

86

Regulation of Gene Expression by Synthetic DNA-Binding Ligands  

Science Journals Connector (OSTI)

During the past 20 years, polyamides have evolved from the natural product distamycin to a new class of programmable heterocyclic oligomers that bind a broad repertoire of DNA sequences with high affinity and ...

Peter B. Dervan; Adam T. Poulin-Kerstien

2005-01-01T23:59:59.000Z

87

Visually Relating Gene Expression and in vivo DNA Binding Data  

SciTech Connect (OSTI)

Gene expression and in vivo DNA binding data provide important information for understanding gene regulatory networks: in vivo DNA binding data indicate genomic regions where transcription factors are bound, and expression data show the output resulting from this binding. Thus, there must be functional relationships between these two types of data. While visualization and data analysis tools exist for each data type alone, there is a lack of tools that can easily explore the relationship between them. We propose an approach that uses the average expression driven by multiple of ciscontrol regions to visually relate gene expression and in vivo DNA binding data. We demonstrate the utility of this tool with examples from the network controlling early Drosophila development. The results obtained support the idea that the level of occupancy of a transcription factor on DNA strongly determines the degree to which the factor regulates a target gene, and in some cases also controls whether the regulation is positive or negative.

Huang, Min-Yu; Mackey, Lester; Ker?; nen, Soile V. E.; Weber, Gunther H.; Jordan, Michael I.; Knowles, David W.; Biggin, Mark D.; Hamann, Bernd

2011-09-20T23:59:59.000Z

88

Synthesis Dependent Core Level Binding Energy Shift in the Oxidation...  

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

Energy Shift in the Oxidation State ofPlatinum Coated on CeriaTitania and its Synthesis Dependent Core Level Binding Energy Shift in the Oxidation State ofPlatinum Coated...

89

Lighting Up Individual DNA Binding Proteins with Quantum Dots  

Science Journals Connector (OSTI)

Lighting Up Individual DNA Binding Proteins with Quantum Dots ... Department of Chemistry and Biochemistry, DOE Institute for Genomics and Proteomics, and Department of Physiology, Geffen Medical School, UCLA, Los Angeles, California 90095 ...

Yuval Ebenstein; Natalie Gassman; Soohong Kim; Josh Antelman; Younggyu Kim; Sam Ho; Robin Samuel; Xavier Michalet; Shimon Weiss

2009-03-16T23:59:59.000Z

90

Binding Graphene Sheets Together Using Silicon: Graphene/Silicon Superlattice  

Science Journals Connector (OSTI)

We propose a superlattice consisting of graphene and monolayer thick Si sheets and investigate ... not only strengthen the interlayer binding between the graphene sheets compared to that in graphite, but also inj...

Yong Zhang; Raphael Tsu

2010-05-01T23:59:59.000Z

91

Disordered binding regions of Ewings sarcoma fusion proteins  

Science Journals Connector (OSTI)

A relationship was found between the amino acid (AA) composition, intrinsic protein disorder (IPD) and protein binding regions (PBRs) of the functional regions of Ewings sarcoma protein (EWS) and oncogenic EWS f...

R. Todorova

2014-01-01T23:59:59.000Z

92

A binding energy in light hyperfragments (A?16)  

Science Journals Connector (OSTI)

? binding energy values of 103 uniquely identified mesonic hyperfragments, produced by the interactions of K?-mesons at rest and at momentum 1.5 GeV/c with emulsion nuclei, are presented. One of the events is a ...

B. Bhowmik; T. Chand; D. V. Chopra

1969-02-01T23:59:59.000Z

93

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

94

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

95

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.

96

Triclosan-Loaded Tooth-Binding Micelles for Prevention and Treatment of Dental Biofilm  

Science Journals Connector (OSTI)

To develop tooth-binding micelle formulations of triclosan for the prevention and treatment of dental...

Fu Chen; Kelly C. Rice; Xin-Ming Liu; Richard A. Reinhardt

2010-11-01T23:59:59.000Z

97

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.

98

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

99

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

E-Print Network [OSTI]

The goal of this research project was to determine if atmospheric sources have the potential of contributing significantly to the sulfur content of grazed forage. Sulfur deposition resulting from sulfur dioxide emissions from coal- fired power...

Lopez, Jose Ignacio

2012-06-07T23:59:59.000Z

100

Characterization of salivary alpha-amylase binding to Streptococcus sanguis  

SciTech Connect (OSTI)

The purpose of this study was to identify the major salivary components which interact with oral bacteria and to determine the mechanism(s) responsible for their binding to the bacterial surface. Strains of Streptococcus sanguis, Streptococcus mitis, Streptococcus mutans, and Actinomyces viscosus were incubated for 2 h in freshly collected human submandibular-sublingual saliva (HSMSL) or parotid saliva (HPS), and bound salivary components were eluted with 2% sodium dodecyl sulfate. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western transfer, alpha-amylase was the prominent salivary component eluted from S. sanguis. Studies with {sup 125}I-labeled HSMSL or {sup 125}I-labeled HPS also demonstrated a component with an electrophoretic mobility identical to that of alpha-amylase which bound to S. sanguis. Purified alpha-amylase from human parotid saliva was radiolabeled and found to bind to strains of S. sanguis genotypes 1 and 3 and S. mitis genotype 2, but not to strains of other species of oral bacteria. Binding of ({sup 125}I)alpha-amylase to streptococci was saturable, calcium independent, and inhibitable by excess unlabeled alpha-amylases from a variety of sources, but not by secretory immunoglobulin A and the proline-rich glycoprotein from HPS. Reduced and alkylated alpha-amylase lost enzymatic and bacterial binding activities. Binding was inhibited by incubation with maltotriose, maltooligosaccharides, limit dextrins, and starch.

Scannapieco, F.A.; Bergey, E.J.; Reddy, M.S.; Levine, M.J. (State Univ. of New York, Buffalo (USA))

1989-09-01T23:59:59.000Z

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.


101

BPA GUIDANCE ON THE USE OF BINDING ARBITRATION  

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

BONNEVILLE POWER ADMINISTRATION'S BONNEVILLE POWER ADMINISTRATION'S GUIDANCE ON THE USE OF BINDING ARBITRATION FOR BPA CONTRACTS Introduction Alternative dispute resolution (ADR) encompasses a variety of methods that parties may use to resolve disputes without litigation. Arbitration is a private, less formal process in which parties agree to submit a dispute to one or more impartial arbitrators who then render a decision or award. In non-binding arbitration a party is not required to accept the arbitrator's decision. In contrast, a decision or award in binding arbitration is final and subject to only very limited rights of appeal. See Federal Arbitration Act, 9 U.S.C. §§ 1-16 (FAA). Both types of arbitration can provide benefits to BPA, its customers, and other stakeholders including the public, such as greater flexibility, limited discovery, a

102

BPA GUIDANCE ON THE USE OF BINDING ARBITRATION  

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

BONNEVILLE POWER ADMINISTRATION'S BONNEVILLE POWER ADMINISTRATION'S GUIDANCE ON THE USE OF BINDING ARBITRATION FOR BPA CONTRACTS Introduction Alternative dispute resolution (ADR) encompasses a variety of methods that parties may use to resolve disputes without litigation. Arbitration is a private, less formal process in which parties agree to submit a dispute to one or more impartial arbitrators who then render a decision or award. In non-binding arbitration a party is not required to accept the arbitrator's decision. In contrast, a decision or award in binding arbitration is final and subject to only very limited rights of appeal. See Federal Arbitration Act, 9 U.S.C. §§ 1-16 (FAA). Both types of arbitration can provide benefits to BPA, its customers, and other stakeholders including the public, such as greater flexibility, limited discovery, a

103

T-cadherin structures reveal a novel adhesive binding mechanism  

SciTech Connect (OSTI)

Vertebrate genomes encode 19 classical cadherins and about 100 nonclassical cadherins. Adhesion by classical cadherins depends on binding interactions in their N-terminal EC1 domains, which swap N-terminal {beta}-strands between partner molecules from apposing cells. However, strand-swapping sequence signatures are absent from nonclassical cadherins, raising the question of how these proteins function in adhesion. Here, we show that T-cadherin, a glycosylphosphatidylinositol (GPI)-anchored cadherin, forms dimers through an alternative nonswapped interface near the EC1-EC2 calcium-binding sites. Mutations within this interface ablate the adhesive capacity of T-cadherin. These nonadhesive T-cadherin mutants also lose the ability to regulate neurite outgrowth from T-cadherin-expressing neurons. Our findings reveal the likely molecular architecture of the T-cadherin homophilic interface and its requirement for axon outgrowth regulation. The adhesive binding mode used by T-cadherin may also be used by other nonclassical cadherins

Ciatto, Carlo; Bahna, Fabiana; Zampieri, Niccol; VanSteenhouse, Harper C.; Katsamba, Phini S; Ahlsen, Goran; Harrison, Oliver J.; Brasch, Julia; Jin, Xiangshu; Posy, Shoshana; Vendome, Jeremie; Ranscht, Barbara; Jessell, Thomas M.; Honig, Barry; Shapiro, Lawrence (Columbia); (Burnham)

2010-03-30T23:59:59.000Z

104

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

105

Orientation-dependent binding energy of graphene on palladium  

SciTech Connect (OSTI)

Using density functional theory calculations, we show that the binding strength of a graphene monolayer on Pd(111) can vary between physisorption and chemisorption depending on its orientation. By studying the interfacial charge transfer, we have identified a specific four-atom carbon cluster that is responsible for the local bonding of graphene to Pd(111). The areal density of such clusters varies with the in-plane orientation of graphene, causing the binding energy to change accordingly. Similar investigations can also apply to other metal substrates and suggests that physical, chemical, and mechanical properties of graphene may be controlled by changing its orientation.

Kappes, Branden B.; Ebnonnasir, Abbas; Ciobanu, Cristian V. [Department of Mechanical Engineering and Materials Science Program, Colorado School of Mines, Golden, Colorado 80401 (United States)] [Department of Mechanical Engineering and Materials Science Program, Colorado School of Mines, Golden, Colorado 80401 (United States); Kodambaka, Suneel [Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095 (United States)] [Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095 (United States)

2013-02-04T23:59:59.000Z

106

Binding Energy of a ? Particle in Nuclear Matter  

Science Journals Connector (OSTI)

The binding energy of a ? particle in nuclear matter, B?(?), is calculated using a ?-nucleon two-body potential with a hard core, which reproduces the binding energies of light hypernuclei and the ?-nucleon scattering at intermediate energies. The simplified version of the Brueckner theory used in previous calculations is applied. The effective mass of the ? particle, M?*, is estimated to be about 0.9M?. The rearrangement energy is included in the calculation. The result obtained, B?(?)?31 MeV, is in good agreement with the measured value.

Janusz Dabrowski and H. S. Khler

1964-10-12T23:59:59.000Z

107

Invisibility in non-Hermitian tight-binding lattices  

E-Print Network [OSTI]

Reflectionless defects in Hermitian tight-binding lattices, synthesized by the intertwining operator technique of supersymmetric quantum mechanics, are generally not invisible and time-of-flight measurements could reveal the existence of the defects. Here it is shown that, in a certain class of non-Hermitian tight-binding lattices with complex hopping amplitudes, defects in the lattice can appear fully invisible to an outside observer. The synthesized non-Hermitian lattices with invisible defects possess a real-valued energy spectrum, however they lack of parity-time (PT) symmetry, which does not play any role in the present work.

Stefano Longhi

2010-08-31T23:59:59.000Z

108

Identification of peptides that bind to irradiated pancreatic tumor cells  

SciTech Connect (OSTI)

Purpose: Peptides targeting tumor vascular cells or tumor cells themselves have the potential to be used as vectors for delivering either DNA in gene therapy or antitumor agents in chemotherapy. We wished to determine if peptides identified by phage display could be used to target irradiated pancreatic cancer cells. Methods and Materials: Irradiated Capan-2 cells were incubated with 5 x 10{sup 12} plaque-forming units of a phage display library. Internalized phage were recovered and absorbed against unirradiated cells. After five such cycles of enrichment, the recovered phage were subjected to DNA sequencing analysis and synthetic peptides made. The binding of both phage and synthetic peptides was evaluated by fluorescence staining and flow cytometry in vitro and in vivo. Results: We identified one 12-mer peptide (PA1) that binds to irradiated Capan-2 pancreatic adenocarcinoma cells but not to unirradiated cells. The binding of peptide was significant after 48 h incubation with cells. In vivo experiments with Capan-2 xenografts in nude mice demonstrated that these small peptides are able to penetrate tumor tissue after intravenous injections and bind specifically to irradiated tumor cells. Conclusion: These data suggest that peptides can be identified that target tumors with radiation-induced cell markers and may be clinically useful.

Huang Canhui [Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States); Liu, Xiang Y. [Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States); Rehemtulla, Alnawaz [Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States); Lawrence, Theodore S. [Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States)]. E-mail: tsl@med.umich.edu

2005-08-01T23:59:59.000Z

109

Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis  

SciTech Connect (OSTI)

The annotation of protein function is almost completely performed by in silico approaches. However, computational prediction of protein function is frequently incomplete and error prone. In Mycobacterium tuberculosis (Mtb), ~25% of all genes have no predicted function and are annotated as hypothetical proteins. This lack of functional information severely limits our understanding of Mtb pathogenicity. Current tools for experimental functional annotation are limited and often do not scale to entire protein families. Here, we report a generally applicable chemical biology platform to functionally annotate bacterial proteins by combining activity-based protein profiling (ABPP) and quantitative LC-MS-based proteomics. As an example of this approach for high-throughput protein functional validation and discovery, we experimentally annotate the families of ATP-binding proteins in Mtb. Our data experimentally validate prior in silico predictions of >250 ATPases and adenosine nucleotide-binding proteins, and reveal 73 hypothetical proteins as novel ATP-binding proteins. We identify adenosine cofactor interactions with many hypothetical proteins containing a diversity of unrelated sequences, providing a new and expanded view of adenosine nucleotide binding in Mtb. Furthermore, many of these hypothetical proteins are both unique to Mycobacteria and essential for infection, suggesting specialized functions in mycobacterial physiology and pathogenicity. Thus, we provide a generally applicable approach for high throughput protein function discovery and validation, and highlight several ways in which application of activity-based proteomics data can improve the quality of functional annotations to facilitate novel biological insights.

Ansong, Charles; Ortega, Corrie; Payne, Samuel H.; Haft, Daniel H.; Chauvigne-Hines, Lacie M.; Lewis, Michael P.; Ollodart, Anja R.; Purvine, Samuel O.; Shukla, Anil K.; Fortuin, Suereta; Smith, Richard D.; Adkins, Joshua N.; Grundner, Christoph; Wright, Aaron T.

2013-01-24T23:59:59.000Z

110

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

111

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

112

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

113

Functional implications of multistage copper binding to the prion protein  

Science Journals Connector (OSTI)

...and Wells et al. (26). These workers proposed similar models of Cu 2+ binding...previous work (23) as well as by other workers (24). Using insights from these studies, we now analyze the...Center for Computational Sciences at Oak Ridge National Laboratory. The authors...

Miroslav Hodak; Robin Chisnell; Wenchang Lu; J. Bernholc

2009-01-01T23:59:59.000Z

114

Nanoparticle amplification via photothermal unveiling of cryptic collagen binding sites  

E-Print Network [OSTI]

Nanoparticle amplification via photothermal unveiling of cryptic collagen binding sites Justin H Ruoslahtifg and Sangeeta N. Bhatia*ah The success of nanoparticle-based cancer therapies ultimately depends on their ability to selectively and efficiently accumulate in regions of disease. Outfitting nanoparticles

Bhatia, Sangeeta

115

DNA-Binding Mechanism in Prokaryotic Partition Complex Formation  

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

DNA-Binding Mechanism in DNA-Binding Mechanism in Prokaryotic Partition Complex Formation DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print Wednesday, 29 March 2006 00:00 The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of prokaryotic partition is the Escherichia coli P1 plasmid par system, which consists of a centromere site (parS) on the plasmid DNA and two proteins, ParA and ParB. The initial formation of the so-called partition complex between ParB and the centromere is a critical step in partition. To understand the DNA-binding mechanism utilized by ParB, Schumacher and Funnell determined crystal structures of the C-terminal region of ParB, known as ParB(142-333), bound to centromere sites.

116

Specificity of O-glycosylation in enhancing the stability and cellulose binding affinity of Family 1 carbohydrate-binding modules  

Science Journals Connector (OSTI)

...lignocellulosic biomass to fuels and chemicals . Annu...investigation of glycosylation effects on a family 1 carbohydrate-binding...1357 1360 . 28 Price JL ( 2010 ) Context-dependent...The spectra are the average of 4 scans with an averaged...each CBM analog are the average of the results of the...

Liqun Chen; Matthew R. Drake; Michael G. Resch; Eric R. Greene; Michael E. Himmel; Patrick K. Chaffey; Gregg T. Beckham; Zhongping Tan

2014-01-01T23:59:59.000Z

117

T-677: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of...  

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

77: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of Service Vulnerability T-677: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of Service Vulnerability July 27, 2011 -...

118

T-633: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets...  

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

33: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users Deny Service T-633: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users Deny Service May 31,...

119

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...

120

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...

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

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...

122

Preferential binding of fisetin to the native state of bovine serum albumin: spectroscopic and docking studies  

Science Journals Connector (OSTI)

We have investigated the binding of the biologically important flavonoid fisetin with the carrier protein bovine serum albumin...4M?1...and the number of binding sites was determined as one. MALDI-TOF analyses s...

Atanu Singha Roy; Nitin Kumar Pandey; Swagata Dasgupta

2013-04-01T23:59:59.000Z

123

ANCHOR: web server for predicting protein binding regions in disordered proteins  

Science Journals Connector (OSTI)

......involved in protein-protein interactions. Disordered binding regions...segments differ from protein interaction sites of globular proteins due to their distinct...flexible structural ensemble in isolation and...indicative of disordered binding regions......

Zsuzsanna Dosztnyi; Blint Mszros; Istvn Simon

2009-10-15T23:59:59.000Z

124

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...

125

E-Print Network 3.0 - allosteric modulator binding Sample Search...  

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

by Force Distribution Analysis Summary: bind distal to the active site 2,3. A fundamental question is how the allosteric perturbation... .g., the binding of a cofactor, from...

126

Characterization of the FNR Protein of Escherichid coli, an Iron-Binding Transcriptional Regulator  

Science Journals Connector (OSTI)

...coli, an Iron-Binding Transcriptional Regulator Jeffrey Green Martin Trageser Stephan...John R. Guest FNR is a transcriptional regulator mediating the activation or repression...coli, an iron-binding transcriptional regulator. | FNR is a transcriptional regulator...

1991-01-01T23:59:59.000Z

127

E-Print Network 3.0 - antidepressant binding site Sample Search...  

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

423 J. Biosci. 31(3), September 2006 Summary: the composition of the transcription factors that bind to the CRE sites prior and post-training for learned... binding sites, is...

128

Metal binding in an aluminum based metal-organic framework for...  

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

Metal binding in an aluminum based metal-organic framework for carbon dioxide capture Link to article...

129

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...

130

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...

131

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...

132

Nucleotide-binding flexibility in ultrahigh-resolution structures of the SRP GTPase Ffh  

Science Journals Connector (OSTI)

Crystal structures of the Ffh NG GTPase domain at < 1.24 resolution reveal multiple overlapping nucleotide binding modes.

Ramirez, U.D.

2008-09-19T23:59:59.000Z

133

Yukawa potential approach to the nuclear binding energy formula  

Science Journals Connector (OSTI)

The volume and surface contributions to the nuclear binding energy of a nucleus are calculated from first principles. Yukawas mesontheory of the nucleonnucleon interaction is used to show that the potential energy contains a volume term that is linear in the nucleon number A and asurface term that varies as A 2 / 3 for A sufficiently large. The kinetic energy contribution is accounted for in the usual way. The results are used to estimate the strong force coupling constant. The present approach could be used to discuss the binding energy of a nucleus in terms that are more fundamental than the customary analogy with the case of a drop of liquid.

N. Gauthier

1990-01-01T23:59:59.000Z

134

Improved value for the silicon free exciton binding energy  

SciTech Connect (OSTI)

The free exciton binding energy is a key parameter in silicon material and device physics. In particular, it provides the necessary link between the energy threshold for valence to conduction band optical absorption and the bandgap determining electronic properties. The long accepted low temperature binding energy value of 14.7 0.4 meV is reassessed taking advantage of developments subsequent to its original determination, leading to the conclusion that this value is definitely an underestimate. Using three largely independent experimental data sets, an improved low temperature value of 15.01 0.06 meV is deduced, in good agreement with the most comprehensive theoretical calculations to date.

Green, Martin A., E-mail: m.green@unsw.edu.au [Australian Centre for Advanced Photovoltaics, School of Photovoltaic and Renewable Energy Engineering, University of New South Wales, Sydney, Australia 2052 (Australia)

2013-11-15T23:59:59.000Z

135

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

136

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

137

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.

138

Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to -cyclodextrin  

E-Print Network [OSTI]

starch strands apart thus increasing the hydrolyzable surface, or alternatively it may localize to the catalytic domain is attached is flexible, allowing the catalytic site to access a large surface area Cellulomonas fimi has two noncatalytic binding domains that clearly bind to different ligands; xylan binds only

Williamson, Mike P.

139

Solution Structure of the CBM10 Cellulose Binding Module from Pseudomonas Xylanase A,  

E-Print Network [OSTI]

residues (Tyr8, Trp22, and Trp24), which are exposed and form a flat surface on one face, in a classical). Although there are domains that bind specifically to xylan (denoted xylan-binding modules or XBMs) (4), many xylanases contain domains that bind specifically to cellulose rather than xylan (5). It has been

Williamson, Mike P.

140

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

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

Stereoselective Binding of Ruthenium Complexes to Cytochrome c  

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

Site-Dependent Stereoselective Binding of Ruthenium Aquobipyridine Site-Dependent Stereoselective Binding of Ruthenium Aquobipyridine Complexes to Histidine Side Chains in Horse Heart Cytochrome c Jian Luo, James F. Wishart, and Stephan S. Isied J. Am. Chem. Soc. 120, 12970-12971 (1998) [Find paper at ACS Publications] Abstract: Stereoselective covalent binding of the ruthenium complexes cis-[Ru(bpy)2(H2O)2]2+ (bpy = 2,2'-bipyridine) and cis-[Ru(dmbpy)2(H2O)2]2+ (dmbpy = 4,4'-dimethyl-2,2'-bipyridine) to the surface His 33 residue and the more buried His 26 residues of Horse heart cytochrome c (Hh cyt c) to form large enantiomeric excess of D-[Ru(dmbpy)2(H2O)]-His 26-cyt c (38%), but little or no excess of D-[Ru(bpy)2(H2O)]-His 26-cyt c (6%). At the surface exposed His 33 site, equal entiomeric excess of L-[Ru(dmbpy)2(H2O)]-His 33-cyt c and L-[Ru(bpy)2(H2O)]-His 33-cyt c (34%)

142

Bounds to binding energies from the concavity of thermodynamical functions  

E-Print Network [OSTI]

Sequences of experimental ground-state energies are mapped onto concave patterns cured from convexities due to pairing and/or shell effects. The same patterns, completed by a list of excitation energies, can be used to give numerical estimates of the grand potential $\\Omega(\\beta,\\mu)$ for a mixture of nuclei at low or moderate temperatures $T=\\beta^{-1}$ and at many chemical potentials $\\mu.$ The average nucleon number $(\\beta,\\mu)$ then becomes a continuous variable, allowing extrapolations towards nuclear masses closer to drip lines. We study the possible concavity of several thermodynamical functions, such as the free energy and the average energy, as functions of $.$ Concavity, when present in such functions, allows trivial interpolations and extrapolations providing upper and lower bounds, respectively, to binding energies. Such bounds define an error bar for the prediction of binding energies. An extrapolation scheme for such concave functions is tested. We conclude with numerical estimates of the binding energies of a few nuclei closer to drip lines.

B. K. Jennings; B. R. Barrett; B. G. Giraud

2007-08-22T23:59:59.000Z

143

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

144

Structures of the spectrin-ankyrin interaction binding domains  

SciTech Connect (OSTI)

As key components of the erythrocyte membrane skeleton, spectrin and ankyrin specifically interact to tether the spectrin cytoskeleton to the cell membrane. The structure of the spectrin binding domain of ankyrin and the ankyrin binding domain of spectrin have been solved to elucidate the structural basis for ankyrin-spectrin recognition. The structure of repeats 14 and 15 of spectrin shows that these repeats are similar to all other spectrin repeats. One feature that could account for the preference of ankyrin for these repeats is the presence of a conserved, negatively charged patch on one side of repeat 14. The structure of the ankyrin ZU5 domain shows a novel structure containing a {beta} core. The structure reveals that the canonical ZU5 consensus sequence is likely to be missing an important region that codes for a {beta} strand that forms part of the core of the domain. In addition, a positively charged region is suggestive of a binding surface for the negatively charged spectrin repeat 14. Previously reported mutants of ankyrin that map to this region lie mostly on the surface of the protein, although at least one is likely to be part of the core.

Ipsaro, Jonathan J.; Huang, Lei; Mondragn, Alfonso; (NWU)

2010-01-07T23:59:59.000Z

145

Thermodynamics and Kinetics of Carbon Dioxide Binding to Two Stereoisomers  

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

Binding to Stereoisomers of a Cobalt(I) Macrocycle Binding to Stereoisomers of a Cobalt(I) Macrocycle Carol Creutz, Harold A. Schwarz, James F. Wishart, Etsuko Fujita and Norman Sutin J. Am. Chem. Soc. 113, 3361-3371 (1991) Abstract: The thermodynamics and kinetics of binding of CO2, CO, and H+ to N-racemic and N-meso stereoisomers of the cobalt(I) macrocycle CoL+ (L=5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradeca-4,11-diene) have been determined in aqueous media with use of the pulse radiolysis technique and transient ultraviolet-visible spectroscopy. N-rac or N-meso-CoL+ was produced by the hydrated electron reduction of N-rac or N-meso-CoL2+, with tert-butyl alcohol generally added to scavenge hydroxyl radicals. Reactions of both N-rac- and N-meso CoL+ are readily followed by the disappearance of intense ([epsilon] 1 x 104 M-1 cm-1) absorption bands

146

Page not found | Department of Energy  

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

81 - 25790 of 28,904 results. 81 - 25790 of 28,904 results. Article V-079: ISC BIND AAAA Record Lookup Handling Assertion Failure Vulnerability ISC has learned of the potential for an error condition to occur in BIND 9 http://energy.gov/cio/articles/v-079-isc-bind-aaaa-record-lookup-handling-assertion-failure-vulnerability Article EM Helps Military Families in Need LAS VEGAS - Six families from Nellis Air Force Base in Las Vegas recently received nearly $4,000 in donations - funds that helped provide a welcome relief during the holidays. http://energy.gov/em/articles/em-helps-military-families-need Download CX-009224: Categorical Exclusion Determination Project L-718, Electrical Utilities Transformer Management Support Facility CX(s) Applied: B1.15 Date: 09/04/2012 Location(s): Washington

147

Clostridium thermocellum Xyn10B Carbohydrate-Binding Module 22-2: The Role of Conserved Amino Acids in Ligand Binding,  

E-Print Network [OSTI]

study [Charnock, S. J., et al. (2000) Biochemistry 39, 5013-5021] and revealed a surface cleft which studies have shown that CBMs appended to xylanase catalytic modules often bind prefer- entially to xylan (4-11). CBM families whose members bind xylan include CBM2b, CBM4, CBM6, CBM13, and CBM22

Williamson, Mike P.

148

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

149

Tight-binding model for hydrogen-silicon interactions  

SciTech Connect (OSTI)

We have developed an empirical tight-binding model for use in molecular-dynamics simulations to study hydrogen-silicon systems. The hydrogen-silicon interaction is constructed to reproduce the electronic energy levels and vibration frequencies of silane (SiH{sub 4}). Further use of the model in the studies of disilane (Si{sub 2}H{sub 6}) and of hydrogen on the Si(111) surface also yields results in good agreement with first-principles calculations and experiments.

Min, B.J.; Lee, Y.H.; Wang, C.Z.; Chan, C.T.; Ho, K.M. (Microelectronics Research Center, Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States) Department of Physics and Astronomy, Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States))

1992-03-15T23:59:59.000Z

150

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

151

Defining How Botulinum Toxin Binds to the Synaptotagmin Receptor and  

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

Defining How Botulinum Toxin Binds to Defining How Botulinum Toxin Binds to the Synaptotagmin Receptor and Creating Improved Therapeutics to Block Toxicity Botulinum neurotoxin (BoNT), the most potent toxin known, induces a potentially fatal paralytic condition known as "botulism". Botulism can occur when toxin-producing bacteria infect wounds (wound botulism) or the intestinal tract (infant/intestinal botulism), or following the ingestion of contaminated food in which toxin has been produced (food-borne botulism). In the USA, infant botulism represents the most common manifestation of the disease, where its prevalence has led to speculation of a link to sudden infant death syndrome. BoNTs are subdivided into seven distinct serotypes (types A through G), and an increasingly large number of subtypes continue to be identified within each serotype, highlighting the need to produce broad-spectrum therapeutics. BoNT variants are an important biochemical set of tools for understanding nerve function, and important therapeutic agents in current clinical use to provide relief to patients with a wide spectrum of neurological disorders.

152

Contrasting binding of fisetin and daidzein in ?-cyclodextrin nanocavity  

Science Journals Connector (OSTI)

Steady state and time resolved fluorescence along with anisotropy and induced circular dichroism (ICD) spectroscopy provide useful tools to observe and understand the behavior of the therapeutically important plant flavonoids fisetin and daidzein in ?-cyclodextrin (?-CDx) nanocavity. BenesiHildebrand plots indicated 1:1 stoichiometry for both the supramolecular complexes. However, the mode of the binding of fisetin significantly differs from daidzein in ?-CDx, as is observed from ICD spectra which is further confirmed by docking studies. The interaction with ?-CDx proceeds mainly by the phenyl ring and partly by the chromone ring of fisetin whereas only the phenyl ring takes part for daidzein. A linear increase in the aqueous solubility of the flavonoids is assessed from the increase in the binding of the flavonoids with the ?-CDx cavity, which are determined by the gradual increase in the ICD signal, fluorescence emission as well as increase in fluorescence anisotropy with increasing (?-CDx). This confirms ?-CDx as a nanovehicle for the flavonoids fisetin and daidzein in improving their bioavailability.

Biswapathik Pahari; Bidisha Sengupta; Sandipan Chakraborty; Briannica Thomas; Dyffreyon McGowan; Pradeep K. Sengupta

2013-01-01T23:59:59.000Z

153

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

154

Phosphorylation of the DNA-binding domain of nonhistone high-mobility group I protein by cdc2 kinase: Reduction of binding affinity  

SciTech Connect (OSTI)

Mammalian high-mobility group I nonhistone protein (HMG-I) is a DNA-binding chromatin protein that has been demonstrated both in vitro and in vivo to be localized to the A + T-rich sequenced of DNA. Recently an unusual binding domain peptide, the A{center dot}T-hook motif, that mediates specific interaction of HMG-I with the minor groove of DNA in vitro has been described. Inspection of the A{center dot}T-hook region of the binding domain showed that it matches the consensus sequence for phosphorylation by cdc2 kinase. Here the authors demonstrate that HMG-I is a substrate for phosphorylation by purified mammalian cdc2 kinase in vitro. The site of phosphorylation by this enzyme is a threonine residue at the amino-terminal end of the principal binding-domain region of the protein. Labeling of mitotically blocked mouse cells with ({sup 32}P)phosphate demonstrates that this same threonine residue in HMG-I is also preferentially phosphorylated in vivo. These finding indicate that cdc2 phosphorylation may significantly alter the DNA-binding properties of the HMG-I proteins. Becuase many cdc2 substrated are DNA-binding proteins, these results further suggest that alteration of the DNA-binding affinity of a variety of proteins is an important general component of the mechanism by which cdc2 kinase regulates cell cycle progression.

Reeves, R.; Nissen, M.S. (Washington State Univ., Pullman (United States)); Langan, T.A. (Univ. of Colorado, Denver (United States))

1991-03-01T23:59:59.000Z

155

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

156

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

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

lectin binding sites in river biofilms. Neu... systems. At present the most prom- ising ... Source: Hitchcock, Adam P. - Department of Chemistry, McMaster University...

157

E-Print Network 3.0 - a1 binding site Sample Search Results  

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

Materials Science 4 Stochastic evolution of transcription factor binding sites Johannes Berg and Michael Lassig Summary: . There is typically one particular nucleotide a i...

158

E-Print Network 3.0 - alpha -bungarotoxin binding Sample Search...  

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

Limited Keywords: binding sites; protein structure; geometry; alpha... CPA, 4CPA, 5CPA, alpha-amylase 6TAA) their ... Source: Engelman, Donald M.- Department of Molecular...

159

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

160

E-Print Network 3.0 - acid-binding protein predicts Sample Search...  

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

Summary: and nucleic-acid binding proteins from eukaryotic cell lysates 12;2 Qproteome Nuclear Protein Handbook 07... Preparation of the cytosolic fraction 8 Preparation 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.


161

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,...

162

Reversible CO Binding Enables Tunable CO/H2 and CO/N2 Separations...  

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

2,5-dioxido-1,4-benzenedicarboxylate) structure type are demonstrated to bind carbon monoxide reversibly and at high capacity. Infrared spectra indicate that, upon coordination of...

163

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...

164

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...

165

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,...

166

E-Print Network 3.0 - abrogates son binding Sample Search Results  

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

at San Diego Collection: Biology and Medicine 68 Selective Small Molecules Blocking HIV-1 Tat and Coactivator PCAF Association Summary: in binding (9 vs 5). Surprisingly,...

167

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)...

168

E-Print Network 3.0 - aptamer binding inducing Sample Search...  

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

while... , formamidopyrimidine with an RNA aptamer whose binding to ... Source: Beal, Peter A. - Department of Chemistry, University of Utah Collection: Chemistry 32...

169

Tight-Binding Models of Amorphous Systems: Liquid Metals  

Science Journals Connector (OSTI)

A tight-binding approach to the electronic structure of disordered systems is developed for a simple one-orbital model of a liquid metal. An equation is derived for a one-electron continuum Green's function from which the electronic density of states can be obtained. Utilizing an analogy between this Green's function and the T matrix of multiple-scattering theory, results are obtained corresponding to the quasicrystalline approximation (QCA) of Lax and the self-consistent approximation (SCA) of Schwartz and Ehrenreich. Moments of the spectral function are also analyzed. Calculations were made using random and hard-sphere pair distribution functions. The QCA in this model is quite inadequate, and the SCA, while a considerable improvement, proves to involve a questionable approximation to the three-body distribution function.

Laura M. Roth

1973-05-15T23:59:59.000Z

170

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

171

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

172

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

173

Characterization of Selective Binding of Alkali Cations with Carboxylate  

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

Characterization of Selective Characterization of Selective Binding of Alkali Cations with Carboxylate Characterization of Selective Binding of Alkali Cations with Carboxylate Print Wednesday, 24 September 2008 00:00 During its lifetime, a cell spends a considerable fraction of its energy pumping sodium and calcium out and potassium in. This balancing process is similar to that found in the coils of the DNA double helix, where specific ions nestle and help stabilize this macromolecule. These are only two examples of selective ion interactions in biology; there are many others also vital to life. The existence of these interactions has been known since the early 20th century, when Franz Hofmeister observed that some salts (ionic compounds) aided the solution of proteins in egg, some caused proteins to destabilize and precipitate, and others ranged in activity between the two extremes. Hofmeister then ranked "salt-out" (destabilizing) ions versus "salt-in" (stabilizing) ions according to the magnitude of their effects (the "Hofmeister effects"). However, despite enormous effort, why certain interactions are preferred over others is not completely understood. Recently, a team of researchers from UC Berkeley used the model systems of acetate and formate (two simple carboxylic acids) with a series of cations to test predictions made in the literature for preferential interactions. Near-edge x-ray absorption fine structure (NEXAFS) spectroscopy was used as this technique is highly sensitive to the chemical environments around a molecule. Experiments at ALS Beamline 8.0.1 confirmed strengthening of the interaction between the cations and the carboxylate group in the following order: potassium, sodium, and lithium.

174

Isolation and characterizations of oxalate-binding proteins in the kidney  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer The first large-scale characterizations of oxalate-binding kidney proteins. Black-Right-Pointing-Pointer The recently developed oxalate-conjugated EAH Sepharose 4B beads were applied. Black-Right-Pointing-Pointer 38 forms of 26 unique oxalate-binding kidney proteins were identified. Black-Right-Pointing-Pointer 25/26 (96%) of identified proteins had 'L-x(3,5)-R-x(2)-[AGILPV]' domain. -- Abstract: Oxalate-binding proteins are thought to serve as potential modulators of kidney stone formation. However, only few oxalate-binding proteins have been identified from previous studies. Our present study, therefore, aimed for large-scale identification of oxalate-binding proteins in porcine kidney using an oxalate-affinity column containing oxalate-conjugated EAH Sepharose 4B beads for purification followed by two-dimensional gel electrophoresis (2-DE) to resolve the recovered proteins. Comparing with those obtained from the controlled column containing uncoupled EAH-Sepharose 4B (to subtract the background of non-specific bindings), a total of 38 protein spots were defined as oxalate-binding proteins. These protein spots were successfully identified by quadrupole time-of-flight mass spectrometry (MS) and/or tandem MS (MS/MS) as 26 unique proteins, including several nuclear proteins, mitochondrial proteins, oxidative stress regulatory proteins, metabolic enzymes and others. Identification of oxalate-binding domain using the PRATT tool revealed 'L-x(3,5)-R-x(2)-[AGILPV]' as a functional domain responsible for oxalate-binding in 25 of 26 (96%) unique identified proteins. We report herein, for the first time, large-scale identification and characterizations of oxalate-binding proteins in the kidney. The presence of positively charged arginine residue in the middle of this functional domain suggested its significance for binding to the negatively charged oxalate. These data will enhance future stone research, particularly on stone modulators.

Roop-ngam, Piyachat; Chaiyarit, Sakdithep; Pongsakul, Nutkridta [Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, and Center for Research in Complex Systems Science, Mahidol University, Bangkok (Thailand)] [Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, and Center for Research in Complex Systems Science, Mahidol University, Bangkok (Thailand); Thongboonkerd, Visith, E-mail: vthongbo@yahoo.com [Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, and Center for Research in Complex Systems Science, Mahidol University, Bangkok (Thailand)] [Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, and Center for Research in Complex Systems Science, Mahidol University, Bangkok (Thailand)

2012-08-03T23:59:59.000Z

175

NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse  

Science Journals Connector (OSTI)

......experimental and predicted nuclear receptor binding...experiments. All datasets are processed using...derived from different datasets are comparable...edu 1 INTRODUCTION Nuclear receptors (NRs...experimental and predicted nuclear receptor binding...experiments. All datasets are processed using......

Yaping Fang; Hui-Xin Liu; Ning Zhang; Grace L. Guo; Yu-Jui Yvonne Wan; Jianwen Fang

2013-01-15T23:59:59.000Z

176

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.

177

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

178

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

179

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

180

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

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

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

182

Regulation of Single Stranded DNA Binding by the C-termini of E. coli SSB protein.  

E-Print Network [OSTI]

Regulation of Single Stranded DNA Binding by the C-termini of E. coli SSB protein. Alexander G@biochem.wustl.edu The homotetrameric E. coli single stranded DNA binding (SSB) protein plays a central role in DNA replication, repair domain (5). The E. coli SSB protein is the prototypical example of the homotetrameric class of SSB

Lohman, Timothy M.

183

Membrane binding of SRP pathway components in the halophilic archaea Haloferax volcanii  

E-Print Network [OSTI]

Membrane binding of SRP pathway components in the halophilic archaea Haloferax volcanii Tovit LichiY, the prokaryal signal recognition particle receptor, and SRP54, a central component of the signal recognition par-terminal GTP-binding domain (NG domain) or SRP54, were com- bined separately or in different combinations

Eichler, Jerry

184

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.

185

A Calmodulin Binding Protein from Arabidopsis Is Induced by Ethylene and Contains  

E-Print Network [OSTI]

A Calmodulin Binding Protein from Arabidopsis Is Induced by Ethylene and Contains a DNA- acting with other proteins. To isolate CaM binding proteins involved in ethylene signal transduction, we screened an expression library prepared from ethylene-treated Arabidopsis seedlings with 35 S- labeled Ca

Reddy, A.S.N

186

-Arm flexibility of HU from Staphylococcus aureus dictates the DNA-binding and recognition mechanism  

Science Journals Connector (OSTI)

Structural analysis of apo and DNA-bound HU from S. aureus (SHU) revealed that conformational changes occur in both the protein and DNA upon DNA binding. Base-readout and shape-readout mechanisms are involved in DNA binding and recognition by SHU, in which -arm flexibility is a major determinant.

Kim, D.-H.

2014-11-28T23:59:59.000Z

187

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

188

Binding of a high-energy substrate conformer in antibody catalysis  

Science Journals Connector (OSTI)

...Utilization of binding energy to orient a substrate molecule...4 kcal*mol-1 higher in energy than the pseudodiequatorial...is able to exploit binding energy to preor- ganize its flexible...S. H., Nared, K. D. & Auditor, M.-T. M. (1988) Proc...

A P Campbell; T M Tarasow; W Massefski; P E Wright; D Hilvert

1993-01-01T23:59:59.000Z

189

Cellular/Molecular An Arginine Involved in GABA Binding and Unbinding But  

E-Print Network [OSTI]

on the two interrelated processes of binding (the interaction of re- ceptor and ligand) and gating measures that depend on the interplay of many processes and cannot resolve individualmicroscopictransitions microscopic processes of ligand binding­ unbinding, channel opening­closing, and desensitization

Kemnitz, Joseph

190

Cable-Piliated Burkholderia cepaciaBinds to Cytokeratin 13 of Epithelial Cells  

Science Journals Connector (OSTI)

...ARTICLE MOLECULAR AND CELLULAR PATHOGENESIS Cable-Piliated Burkholderia cepacia Binds to...Canada. This strain expresses surface cable (Cbl) pili and is thought to be the major...epithelial cell (BEC) protein that binds cable pilus-positive B. cepacia. N-terminal...

Umadevi S. Sajjan; Francisco A. Sylvester; Janet F. Forstner

2000-04-01T23:59:59.000Z

191

Sorption of proteins to charged microgels: characterizing binding isotherms and driving forces  

E-Print Network [OSTI]

We present a set of Langmuir binding models in which electrostatic cooperativity effects to protein sorption is incorporated in the spirit of Guoy-Chapman-Stern models, where the global substrate (microgel) charge state is modified by bound reactants (charged proteins). Application of this approach to lysozyme sorption to oppositely charged core-shell microgels allows us to extract the intrinsic, binding affinity of the protein to the gel, which is salt-concentration independent and mostly hydrophobic in nature. The total binding affinity is found to be mainly electrostatic in nature, changes many orders of magnitude during the sorption process, and is significantly influenced by osmotic deswelling effects. The intrinsic binding affinity is determined to be about 7 kBT for our system. We additionally show that Langmuir binding models and those based on excludedvolume interactions are formally equivalent for low to moderate protein packing, if the nature of the bound state is consistently defined. Having appre...

Yigit, Cemil; Ballauff, Matthias; Dzubiella, Joachim

2012-01-01T23:59:59.000Z

192

Paul D. Boyer, Adenosine Triphosphate (ATP), and the Binding Change  

Office of Scientific and Technical Information (OSTI)

Paul D. Boyer, Adenosine Triphosphate (ATP), and the Binding Change Mechanism Resources with Additional Information Paul D. Boyer Courtesy of UCLA 'For Paul Boyer, the Nobel Prize was "an unexpected pleasure." It had been 20 years since he formulated a hypothesis to describe what he calls "the most prominent chemical reaction in the whole world." It is the process by which molecules produce ATP (adenosine triphosphate), thereby transmuting light, air, water and food into the energy required for both plant and animal life. Boyer had been greeted with disbelief when he theorized that the previously mysterious process is the work of a "beautiful little machine" that operates within enzymes on the molecular level. ... Boyer experienced "one of the warmest moments of my life" when he learned that British biochemist John Walker had worked out the methodology required to demonstrate whether Boyer had been right or wrong. ... Using Walker's methodology, one of Boyer's former graduate students "did some elegant chemical work to demonstrate that the molecular rotation actually occurred." Boyer's hypothesis, finally, had been proven correct. For work that so enriched understanding of the life process itself, he and Walker were jointly awarded the Nobel prize [in Chemistry] in 1997.'

193

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

194

Conformational changes in polyelectrolytes and the effect on metal binding  

SciTech Connect (OSTI)

There has been considerable interest in the complexation of metals and other cations by natural humic and fulvic acids, as well as synthetic polyelectrolytes. In order to explain the binding observed for metals, and other species by organic polyelectrolytes, steric effects have been proposed. In this work, the effects of pH changes in aqueous solution on two synthetic polyelectrolytes, polymaleic acid (PMA) and polyacrylic acid (PAA), have been examined by laser Raman spectroscopy and turbidity measurements. These results are compared to Fourier-transform infrared (FTIR) and (/sup 13/C) nuclear magnetic resonance (NMR) spectra for solid samples of PMA, PAA, and fulvic and humic acids. Two types of carboxylic acid groups were detected for PMA in aqueous solution. Crystallization of PMA in a narrow pH range was observed. These data are consistent with strong intramolecular hydrogen bonding occurring in PMA at a pH of approximately 4. This implication of these results on the use of these compounds as models for fulvic and humic acids is discussed. 27 refs., 3 figs., 1 tab.

Marley, N.A.; Gaffney, J.S.; Minai, Y.; Choppin, G.R.

1988-09-01T23:59:59.000Z

195

Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects  

Science Journals Connector (OSTI)

...is to bind soluble xylans and xylooligosaccharides on the surface of the endogenous...2009 ) Enzymatic treatments reveal differential capacities for xylan recognition and degradation...Receptors, Cell Surface 0 Xylans 0 saccharide-binding...

Ccile Herv; Artur Rogowski; Anthony W. Blake; Susan E. Marcus; Harry J. Gilbert; J. Paul Knox

2010-01-01T23:59:59.000Z

196

Rhizobial and Fungal Symbioses Show Different Requirements for Calmodulin Binding to Calcium Calmodulin??Dependent Protein Kinase in Lotus japonicus  

Science Journals Connector (OSTI)

...in binding buffer at room temperature for 1 h. Binding of biotinylated...leghaemoglobin synthesis in snake beans. Biochem. J. 125...regulating symbiotic nodule development. Nature 417 : 962-966...for cortical endosymbiotic development. Plant Cell 22 : 2509-2526...

Yoshikazu Shimoda; Lu Han; Toshimasa Yamazaki; Rintaro Suzuki; Makoto Hayashi; Haruko Imaizumi-Anraku

2012-01-17T23:59:59.000Z

197

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

198

Ebolavirus VP35 uses a bimodal strategy to bind dsRNA for innate immune suppression  

SciTech Connect (OSTI)

Ebolavirus causes a severe hemorrhagic fever and is divided into five distinct species, of which Reston ebolavirus is uniquely nonpathogenic to humans. Disease caused by ebolavirus is marked by early immunosuppression of innate immune signaling events, involving silencing and sequestration of double-stranded RNA (dsRNA) by the viral protein VP35. Here we present unbound and dsRNA-bound crystal structures of the dsRNA-binding domain of Reston ebolavirus VP35. The structures show that VP35 forms an unusual, asymmetric dimer on dsRNA binding, with each of the monomers binding dsRNA in a different way: one binds the backbone whereas the other caps the terminus. Additional SAXS, DXMS, and dsRNA-binding experiments presented here support a model of cooperative dsRNA recognition in which binding of the first monomer assists binding of the next monomer of the oligomeric VP35 protein. This work illustrates how ebolavirus VP35 could mask key recognition sites of molecules such as RIG-I, MDA-5, and Dicer to silence viral dsRNA in infection.

Kimberlin, Christopher R.; Bornholdt, Zachary A.; Li, Sheng; Woods, Jr., Virgil L.; MacRae, Ian J.; Saphire, Erica Ollmann (Scripps); (UCSD)

2010-03-12T23:59:59.000Z

199

Assessing Energetic Contributions to Binding from a Disordered Region in a Protein-Protein Interaction  

SciTech Connect (OSTI)

Many functional proteins are at least partially disordered prior to binding. Although the structural transitions upon binding of disordered protein regions can influence the affinity and specificity of protein complexes, their precise energetic contributions to binding are unknown. Here, we use a model protein-protein interaction system in which a locally disordered region has been modified by directed evolution to quantitatively assess the thermodynamic and structural contributions to binding of disorder-to-order transitions. Through X-ray structure determination of the protein binding partners before and after complex formation and isothermal titration calorimetry of the interactions, we observe a correlation between protein ordering and binding affinity for complexes along this affinity maturation pathway. Additionally, we show that discrepancies between observed and calculated heat capacities based on buried surface area changes in the protein complexes can be explained largely by heat capacity changes that would result solely from folding the locally disordered region. Previously developed algorithms for predicting binding energies of protein-protein interactions, however, are unable to correctly model the energetic contributions of the structural transitions in our model system. While this highlights the shortcomings of current computational methods in modeling conformational flexibility, it suggests that the experimental methods used here could provide training sets of molecular interactions for improving these algorithms and further rationalizing molecular recognition in protein-protein interactions.

S Cho; C Swaminathan; D Bonsor; M Kerzic; R Guan; J Yang; C Kieke; P Anderson; D Kranz; et al.

2011-12-31T23:59:59.000Z

200

Two Cooperating Helices Constitute the Lipid-binding Domain of the Bacterial SRP Receptor  

Science Journals Connector (OSTI)

Protein targeting by the bacterial signal recognition particle requires the specific interaction of the signal recognition particle (SRP)ribosomenascent chain complex with FtsY, the bacterial SRP receptor. Although FtsY in Escherichia coli lacks a transmembrane domain, the membrane-bound FtsY displays many features of an integral membrane protein. Our data reveal that it is the cooperative action of two lipid-binding helices that allows this unusually strong membrane contact. Helix I comprises the first 14 amino acids of FtsY and the second is located at the interface between the A- and the N-domain of FtsY. We show by site-directed cross-linking and binding assays that both helices bind to negatively charged phospholipids, with a preference for phosphatidyl glycerol. Despite the strong lipid binding, helix I does not seem to be completely inserted into the lipid phase, but appears to be oriented parallel with the membrane surface. The two helices together with the connecting linker constitute an independently folded domain, which maintains its lipid binding even in the absence of the conserved NG-core of FtsY. In summary, our data reveal that the two consecutive lipid-binding helices of FtsY can provide a membrane contact that does not differ significantly in stability from that provided by a transmembrane domain. This explains why the bacterial SRP receptor does not require an integral ?-subunit for membrane binding.

David Braig; Constance Br; Jrg-Oliver Thumfart; Hans-Georg Koch

2009-01-01T23:59:59.000Z

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.


201

Identification of Small Molecule Binding Molecules by Affinity Purification Using a Specific Ligand Immobilized on PEGA Resin  

Science Journals Connector (OSTI)

A synthetic ligand for FK506-binding protein 12 (SLF) was immobilized on various resins, and the binding assays between the SLF-immobilized resins and FK506-binding protein 12 (FKBP12) were performed. ... This matrix enabled the isolation of FKBP12 from a cell lysate, and the identification of SLF-binding peptides from a phage cDNA library. ... We confirmed the interaction between SLF and these peptides using a cuvette type quartz crystal microbalance (QCM) apparatus. ...

Kouji Kuramochi; Yuka Miyano; Yoshihiro Enomoto; Ryo Takeuchi; Kazutomo Ishi; Yoichi Takakusagi; Takeki Saitoh; Keishi Fukudome; Daisuke Manita; Yoshifumi Takeda; Susumu Kobayashi; Kengo Sakaguchi; Fumio Sugawara

2008-11-26T23:59:59.000Z

202

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

203

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.

204

Contribution of a Xylan-Binding Module to the Degradation of a Complex Cellulosic Substrate by Designer Cellulosomes  

Science Journals Connector (OSTI)

...ENGINEERING Contribution of a Xylan-Binding Module to the Degradation...The intrinsic cellulose/xylan-binding module (XBM) of...adaptor protein and a cell-surface anchoring protein. J. Bacteriol...121-124. Contribution of a xylan-binding module to the degradation...

Sarah Moras; Yoav Barak; Jonathan Caspi; Yitzhak Hadar; Raphael Lamed; Yuval Shoham; David B. Wilson; Edward A. Bayer

2010-04-16T23:59:59.000Z

205

Roles of the Tetrahymena thermophila type I element binding factor, TIF1, in DNA replication and genome stability  

E-Print Network [OSTI]

element that is essential for replication initiation, fork progression and promoter activation. TIF1 is a non-ORC single strand-binding protein that binds the type I element in vivo. TIF1 binds opposing strands at the origin and promoter regions indicating...

Morrison, Tara Laine

2005-11-01T23:59:59.000Z

206

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

207

Positron binding to atoms and apolar molecules: A convergence of theory and experiment  

Science Journals Connector (OSTI)

The problem of the bound states of a positron with atoms and apolar molecules is studied with a regularized polarization potential V=Vrc??r?42, where Vrc is a repulsive hard-core potential. A continuous relation between the core radius and the target polarizability is identified for alkanes, leading to the observed linear relation between their experimental binding energies and polarizabilities. New values for the binding energies for I and Pt atoms are suggested. Some predictions for related molecules are made, suggesting positron binding to GeH4 and, possibly, to C2F6.

Paulo H. R. Amaral and Jos R. Mohallem

2012-10-25T23:59:59.000Z

208

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

209

V-058: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets  

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

8: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw 8: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote Users Execute Arbitrary Code V-058: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote Users Execute Arbitrary Code December 31, 2012 - 6:58am Addthis PROBLEM: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote Users Execute Arbitrary Code PLATFORM: Version(s): 6, 7, 8 ABSTRACT: A vulnerability was reported in Microsoft Internet Explorer. A remote user can cause arbitrary code to be executed on the target user's system. REFERENCE LINKS: SecurityTracker Alert ID: 1027930 Secunia Advisory SA51695 CVE-2012-4792 IMPACT ASSESSMENT: High DISCUSSION: A remote user can create specially crafted HTML that, when loaded by the target user, will trigger a memory corruption error and execute arbitrary

210

CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application  

Science Journals Connector (OSTI)

Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of proteinligand complexes. However, these methods rely on several sophisticated command scripts ...

Sunhwan Jo; Wei Jiang; Hui Sun Lee; Beno??t Roux; Wonpil Im

2012-12-04T23:59:59.000Z

211

E-Print Network 3.0 - alpha 1-adrenoceptor binding Sample Search...  

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

of alpha-methyl d-glucopyranoside. Biochem J 109... binding site in hog pancreatic alpha-amylase. Biochemistry 15, 1987-93. 57 Sevilla, N., Steer, M. L... ., Helmreich, E....

212

The neutron binding energy in the neutron-rich nucleus93Sr  

Science Journals Connector (OSTI)

The neutron binding energy in93Sr has been determined to (52306) keV from energy correspondences between levels defined by ?-ray transitions and ?-delayed neutron emission.

K. -L. Kratz; H. Ohm

1980-01-01T23:59:59.000Z

213

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....

214

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,...

215

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...

216

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....

217

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...

218

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...

219

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,...

220

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....

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

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...

222

E-Print Network 3.0 - amino-terminal dna binding Sample Search...  

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

Nucleic Acid Copying using 2-amino-2, 3- Summary: -labeled-2-amino-terminated DNA primer, 0.5M template (5- GGGUp Up Up -3-primer binding site), 100mM MES... Figure S1. Acid...

223

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

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

2009 http:www.cstl.nist.govbiotechstrbaseNISTpub.htm 1 Summary: dropout* *Due to primer binding site mutation All allele calls with MiniFiler for CSF1PO, D7S820, D13S317... ....

224

Purification and Properties of a Xylan-Binding Endoxylanase from Alkaliphilic Bacillus sp. Strain K-1  

Science Journals Connector (OSTI)

...rates that varied with their xylan content and structural complexity. The xylan-binding region, which exhibits high affinity to insoluble xylan, appears to be a potential...the xylanase directly to the surface of the insoluble hemicellulose-containing...

Khanok Ratanakhanokchai; Khin Lay Kyu; Morakot Tanticharoen

1999-02-01T23:59:59.000Z

225

Binding Kinetics of Triclosan (Irgasan) to Alloplastic Vascular Grafts: An In Vitro Study  

Science Journals Connector (OSTI)

The aim of this study was to investigate the binding kinetics of triclosan (Irgasan) to alloplastic vascular grafts and ... . Grafts were incubated in 10 g/L triclosan (Irgasan), dried, sterilized, and incubated...

T. Hernndez-Richter; H.M. Schardey; F. Lhlein

2000-07-01T23:59:59.000Z

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

A redox-regulated chloroplast protein phosphatase binds to starch diurnally and functions in its accumulation  

Science Journals Connector (OSTI)

...linear and branched glucans (amylose and amylopectin) that determine the properties of...the activity and binding of {alpha}-glucan, water dikinase...possibly the activity of {beta}-amylase (21). However, to our knowledge...

Lubomir N. Sokolov; Jose R. Dominguez-Solis; Anne-Laure Allary; Bob B. Buchanan; Sheng Luan

2006-01-01T23:59:59.000Z

228

E-Print Network 3.0 - albumin impaired drug-binding Sample Search...  

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

acid concentrations and variants on Summary: such as quinidine to ORM1 S and* 5 * ORM1 F1 ( , ). drug-binding studies are warranted to determine the possible... . Drug Metab...

229

PDB-wide collection of binding data: current status of the PDBbind database  

Science Journals Connector (OSTI)

......characteristic interaction patterns on protein-protein binding interfaces. J. Chem...SA on true conformational ensembles of protein-ligand complexes. J. Chem...quantitative theory of intrinsically disordered proteins and their function......

Zhihai Liu; Yan Li; Li Han; Jie Li; Jie Liu; Zhixiong Zhao; Wei Nie; Yuchen Liu; Renxiao Wang

2014-10-01T23:59:59.000Z

230

Binding to Cellular Macromolecules as a Possible Mechanism for the Cytotoxicity of Misonidazole  

Science Journals Connector (OSTI)

...Varghese G. F. Whitmore Physics Division, Ontario Cancer Institute...Varghese and G. F. Whitmore Physics Division. Ontario Cancer Institute...derivative of misonida zole does not bind to DNA.3 Hence...R. Gillette (eds.), Handbook of Experimental Pharmacology...

A. J. Varghese and G. F. Whitmore

1980-07-01T23:59:59.000Z

231

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...

232

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

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

Sciences and Ecology 30 Biochemistry 1988, 27, 1205-1212 1205 Ogata, R. T., & Gilbert, W. (1979) J. Mol. Biol. 132, 709. Summary: . The effect of ATP binding to recA...

233

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

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

Physics ; Biology and Medicine 27 Biochemistry 1988, 27, 1205-1212 1205 Ogata, R. T., & Gilbert, W. (1979) J. Mol. Biol. 132, 709. Summary: . The effect of ATP binding to recA...

234

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

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

Chemistry ; Biology and Medicine 37 Biochemistry 1988, 27, 1205-1212 1205 Ogata, R. T., & Gilbert, W. (1979) J. Mol. Biol. 132, 709. Summary: DNA binding affinity by nucleotide...

235

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

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

Collection: Biology and Medicine 5 Biochemistry 1988, 27, 1205-1212 1205 Ogata, R. T., & Gilbert, W. (1979) J. Mol. Biol. 132, 709. Summary: . The effect of ATP binding to recA...

236

Specific binding of a fungal glucan phytoalexin elicitor to membrane fractions from soybean Glycine max  

Science Journals Connector (OSTI)

...arabinogalactan from larch wood, chitosan from crab shells, glucan...cerevisiae), dextran, chitosan, xylan, arabinogalactan...and xylan from larch wood, chitosan from crab shells, glucan...binding assay of the competitive inhibitor of f3-glucosidase, 1...

Walter E. Schmidt; Jrgen Ebel

1987-01-01T23:59:59.000Z

237

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

238

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

239

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

240

Molecular Binding in Post-KohnSham Orbital-Free DFT  

Science Journals Connector (OSTI)

Alex Borgoo *, James A. Green , and David J. Tozer * ... Molecular binding in post-KohnSham orbital-free DFT is investigated, using noninteracting kinetic energy functionals that satisfy the uniform electron gas condition and which are inhomogeneous under density scaling. ... A parameter is introduced that quantifies binding, and a series of functionals are determined from fits to near-exact effective homogeneities and/or KohnSham noninteracting kinetic energies. ...

Alex Borgoo; James A. Green; David J. Tozer

2014-10-30T23:59:59.000Z

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.


241

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

242

Modeling the chemical shift of lanthanide 4f electron binding energies  

Science Journals Connector (OSTI)

Lanthanides in compounds can adopt the tetravalent [Xe]4fn?1 (like Ce4+, Pr4+, Tb4+), the trivalent [Xe]4fn (all lanthanides), or the divalent [Xe]4fn+1 configuration (like Eu2+, Yb2+, Sm2+, Tm2+). The 4f-electron binding energy depends on the charge Q of the lanthanide ion and its chemical environment A. Experimental data on three environments (i.e., the bare lanthanide ions where A=vacuum, the pure lanthanide metals, and the lanthanides in aqueous solutions) are employed to determine the 4f-electron binding energies in all divalent and trivalent lanthanides. The action of the chemical environment on the 4f-electron binding energy will be represented by an effective ambient charge QA=?Q at an effective distance from the lanthanide. This forms the basis of a model that relates the chemical shift of the 4f-electron binding energy in the divalent lanthanide with that in the trivalent one. Eu will be used as the lanthanide of reference, and special attention is devoted to the 4f-electron binding energy difference between Eu2+ and Eu3+. When that difference is known, the model provides the 4f-electron binding energies of all divalent and all trivalent lanthanide ions relative to the vacuum energy.

Pieter Dorenbos

2012-04-06T23:59:59.000Z

243

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

244

Sorption of proteins to charged microgels: characterizing binding isotherms and driving forces  

E-Print Network [OSTI]

We present a set of Langmuir binding models in which electrostatic cooperativity effects to protein sorption is incorporated in the spirit of Guoy-Chapman-Stern models, where the global substrate (microgel) charge state is modified by bound reactants (charged proteins). Application of this approach to lysozyme sorption to oppositely charged core-shell microgels allows us to extract the intrinsic, binding affinity of the protein to the gel, which is salt-concentration independent and mostly hydrophobic in nature. The total binding affinity is found to be mainly electrostatic in nature, changes many orders of magnitude during the sorption process, and is significantly influenced by osmotic deswelling effects. The intrinsic binding affinity is determined to be about 7 kBT for our system. We additionally show that Langmuir binding models and those based on excludedvolume interactions are formally equivalent for low to moderate protein packing, if the nature of the bound state is consistently defined. Having appreciated this, a more quantitative interpretation of binding isotherms in terms of separate physical interactions is possible in future for a wide variety of experimental approaches.

Cemil Yigit; Nicole Welsch; Matthias Ballauff; Joachim Dzubiella

2012-09-13T23:59:59.000Z

245

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

E-Print Network [OSTI]

From opportunistic protist Cryptosporidium parvum we identified and functionally assayed a fatty acyl-CoA-binding protein (ACBP) gene. The CpACBP1 gene encodes a protein of 268 aa that is three times larger than typical ~10 KD ACBPs of humans...

Zeng, Bin

2009-05-15T23:59:59.000Z

246

Site-Specific Characterization of the Association of Xylooligosaccharides with the CBM13 Lectin-like Xylan Binding Domain from Streptomyces liVidans Xylanase  

E-Print Network [OSTI]

-like Xylan Binding Domain from Streptomyces liVidans Xylanase 10A by NMR Spectroscopy Manuela Scha binding sites (R, , and ) for a variety of small sugars, xylooligosaccharides, and xylan polymers surfaces, type B CBMs bind to polysaccharides, and type C CBMs bind to mono- and disaccharides (3). Within

McIntosh, Lawrence P.

247

T-633: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users  

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

3: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets 3: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users Deny Service T-633: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users Deny Service May 31, 2011 - 3:35pm Addthis PROBLEM: A vulnerability was reported in BIND. A remote user can cause denial of service conditions. PLATFORM: BIND Version(s): 9.4-ESV-R3 and later, 9.6-ESV-R2 and later, 9.6.3, 9.7.1 and later, 9.8.0 and later; prior to 9.4-ESV-R4-P1, 9.6-ESV-R4-P1, 9.7.3-P1, 9.8.0-P2 ABSTRACT: A remote DNS server can supply very large RRSIG RRsets in a negative response to trigger an off-by-one error in a buffer size check and cause the target requesting named process to crash. A remote user can cause named to crash. reference LINKS: SecurityTracker Alert ID: 1025575 SecurityTracker Alert ID: 1025572

248

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

249

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

250

A model for the hypolipidemic effect of chitosan : in vitro binding of bile acids and mixed micelles  

E-Print Network [OSTI]

lipids in the micelles or microemulsions are then incapable of being absorbed by the intestines. The proposal was tested in vitro by binding pure bile salts, mixed micelles, and model microemulsions to chitosan. The free lipids were separated from... the chitosan-lipid complex by rapid ultrafiltration and analyzed by either a colorimetric determina- tion or radioactive labeling. Chitosan was found to be an excellent binding agent for pure bile salts, binding up to 5 mg of bile salt per mg chitosan...

Nauss, Jeffrey Lynn

2012-06-07T23:59:59.000Z

251

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

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

1: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding 1: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding Use-After-Free Vulnerability U-101: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding Use-After-Free Vulnerability February 13, 2012 - 7:00am Addthis PROBLEM: A vulnerability has been reported in multiple Mozilla products. PLATFORM: Mozilla Firefox 10.x Mozilla SeaMonkey 2.x Mozilla Thunderbird 10.x ABSTRACT: A vulnerability has been reported in multiple Mozilla products, which can be exploited by malicious people to compromise a user's system. reference LINKS: Vendor Advisory Secunia Advisory SA48008 CVE-2012-0452 IMPACT ASSESSMENT: High Discussion: A remote user can create HTML that, when loaded by the target user, will execute arbitrary code on the target user's system. The vulnerability is caused due to a use-after-free error in the

252

The Unique Binding Mode of Cellulosomal CBM4 from Clostridium thermocellum Cellobiohydrolase A  

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

Unique Unique Binding Mode of Cellulosomal CBM4 from Clostridium thermocellum Cellobiohydrolase A Markus Alahuhta, Qi Xu, Yannick J. Bomble, Roman Brunecky, William S. Adney, Shi-You Ding, Michael E. Himmel and Vladimir V. Lunin⁎ National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401, USA Received 26 April 2010; received in revised form 12 July 2010; accepted 14 July 2010 Available online 21 July 2010 The crystal structure of the carbohydrate-binding module (CBM) 4 Ig fused domain from the cellulosomal cellulase cellobiohydrolase A (CbhA) of Clostridium thermocellum was solved in complex with cellobiose at 2.11 Å resolution. This is the first cellulosomal CBM4 crystal structure reported to date. It is similar to the previously solved noncellulosomal soluble oligosaccharide-binding CBM4 structures. However, this new structure possesses a significant

253

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

254

Structural Plasticity Underpins Promiscuous Binding of the Prosurvival Protein A1  

SciTech Connect (OSTI)

Apoptotic pathways are regulated by protein-protein interactions. Interaction of the BH3 domains of proapoptotic Bcl-2 family proteins with the hydrophobic groove of prosurvival proteins is critical. Whereas some BH3 domains bind in a promiscuous manner, others exhibit considerable selectivity and the sequence characteristics that distinguish these activities are unclear. In this study, crystal structures of complexes between the prosurvival protein A1 and the BH3 domains from Puma, Bmf, Bak, and Bid have been solved. The structure of A1 is similar to that of other prosurvival proteins, although features, such as an acidic patch in the binding groove, may allow specific therapeutic modulation of apoptosis. Significant conformational plasticity was observed in the intermolecular interactions and these differences explain some of the variation in affinity. This study, in combination with published data, suggests that interactions between conserved residues demarcate optimal binding.

Smits,C.; Czabotar, P.; Hinds, M.; Day, C.

2008-01-01T23:59:59.000Z

255

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

256

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

257

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

258

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

259

Ethylene oxides as hydrogen storage material with pockets in the electronic binding energy distribution  

Science Journals Connector (OSTI)

Using ab initio calculations, we have found that the oxygen atoms in oligomers of ethylene oxide have optimal binding with hydrogen molecules for hydrogen storage. Our theoretical model and molecular-dynamics simulations predict that adsorption-desorption process for such a candidate material occurs under unprecedented ambient conditions, T?300?K and P=113?atm, achieving gravimetric storage capacity of hydrogen up to 6.2?wt?%. We have also uncovered the special binding mechanism between a hydrogen molecule and an oxygen-embedded material which is enhanced by electron donation and back-donation.

Sungjong Woo and Young-Kyun Kwon

2009-02-02T23:59:59.000Z

260

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

E-Print Network [OSTI]

. , Texas A&M University Chairman of Advisory Committee: Walter Michael Kemp (Ph. D. ) An indirect assay was used to detect binding of Fc associated specific anti-schistosome antibody (homospec1fic antibody) to adult male schistosomes. Binding... of this homospecific antibody could be demonstrated by utilizing freeze thaw antigen, anti-schistosome ~ ntihody a d iiuoresceinated ~Sta h iococcus au eus tnBI which h d to the Fc reg1on of the second antibody. Control experiments w1th reconstitution of eluted...

Rasmussen, Kathleen Ruth

2012-06-07T23:59:59.000Z

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

Importance of the Doppler Effect to the Determination of the Deuteron Binding Energy  

E-Print Network [OSTI]

The deuteron binding energy extracted from the reaction ${}^1H(n,\\gamma){}^2H$ is reviewed with the exact relativistic formula, where the initial kinetic energy and the Doppler effect are taken into account. We find that the negligible initial kinetic energy of the neutron could cause a significant uncertainty which is beyond the errors available up to now. Therefore, we suggest an experiment which should include the detailed informations about the initial kinetic energy and the detection angle. It could reduce discrepancies among the recently reported values about the deuteron binding energy and pin down the uncertainty due to the Doppler broadening of $\\gamma$ ray.

Yongkyu Ko; Myung Ki Cheoun; Il-Tong Cheon

1999-04-01T23:59:59.000Z

262

New Mathematical Method Reveals Where Proteins Bind with DNA to Switch  

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

Mathematical Mathematical Method Reveals Where Genes Switch On or Off New Mathematical Method Reveals Where Genes Switch On or Off "Compressed sensing" determines atomic-level energy potentials with accuracy approaching experimental measurement February 22, 2012 | Tags: Biological and Environmental Research (BER), Carver, Chemistry, Life Sciences, Math & Computer Science, NISE John Hules, JAHules@lbl.gov, +1 510 486 6008 Figure 1. Helix-turn-helix (HTH) proteins are the most widely distributed family of DNA-binding proteins, occurring in all biological kingdoms. This image shows a lambda repressor HTH transcription factor (green) binding to a lambda operator DNA sequence (blue and red) of the virus bacteriophage lambda. Image: Richard Wheeler, Wikipedia

263

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.

264

A beta 3 integrin mutation abolishes ligand binding and alters divalent cation-dependent conformation  

Science Journals Connector (OSTI)

...Dean, L. Kincla, H. R. Sykes, A. R. Lehmann, I. A. Wise, Exp. Cell Res. 183, 473 (1989)]. 15. S. J. Baker...JOSEPH C. LOFTUS,* TIMOTHY E. O'TOOLE, EDWARD F. PLOW, ALISON GLASs, ANDREW L. FRELINGER III, MARK H. GINSBERG The ligand-binding...

JC Loftus; TE O'Toole; EF Plow; A Glass; AL Frelinger 3rd; MH Ginsberg

1990-08-24T23:59:59.000Z

265

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

266

Influenza Virus Neuraminidases with Reduced Enzymatic Activity That Avidly Bind Sialic Acid Receptors  

Science Journals Connector (OSTI)

...reaction, the catalytic efficiency (k cat/Km ) is...enhancement of the catalytic efficiency of avian NAs by binding...the governments of Egypt and the United States...S. Department of Energy (DOE) Office of Basic Energy Sciences. The Stanford...

Xueyong Zhu; Ryan McBride; Corwin M. Nycholat; Wenli Yu; James C. Paulson; Ian A. Wilson

2012-09-26T23:59:59.000Z

267

Pax-2 is a DNA-binding protein expressed in embryonic kidney and Wilms tumor  

Science Journals Connector (OSTI)

...ingly, the Zn finger-containing gene WTI (34, 35) is expressed during kidney development...capsule (38). In the mouse expression of WTI peaks at about 3 days postpartum and decreases...tectable levels in the adult (39). The WTI gene can bind DNA specifically, indicative...

G R Dressler; E C Douglass

1992-01-01T23:59:59.000Z

268

Poly(C)-binding proteins as transcriptional regulators of gene expression  

SciTech Connect (OSTI)

Poly(C)-binding proteins (PCBPs) are generally known as RNA-binding proteins that interact in a sequence-specific fashion with single-stranded poly(C). They can be divided into two groups: hnRNP K and PCBP1-4. These proteins are involved mainly in various posttranscriptional regulations (e.g., mRNA stabilization or translational activation/silencing). In this review, we summarize and discuss how PCBPs act as transcriptional regulators by binding to specific elements in gene promoters that interact with the RNA polymerase II transcription machinery. Transcriptional regulation of PCBPs might itself be regulated by their localization within the cell. For example, activation by p21-activated kinase 1 induces increased nuclear retention of PCBP1, as well as increased promoter activity. PCBPs can function as a signal-dependent and coordinated regulator of transcription in eukaryotic cells. We address the molecular mechanisms by which PCBPs binding to single- and double-stranded DNA mediates gene expression.

Choi, Hack Sun [Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455 (United States)], E-mail: choix074@umn.edu; Hwang, Cheol Kyu; Song, Kyu Young; Law, P.-Y.; Wei, L.-N.; Loh, Horace H. [Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455 (United States)

2009-03-13T23:59:59.000Z

269

Nuclear Physics A 611 ( 1996) 484-513 Mesonic and binding contributions to the EMC  

E-Print Network [OSTI]

NUCLEAR PHYSICS A Nuclear Physics A 611 ( 1996) 484-513 Mesonic and binding contributions November 1995; revised 30 July 1996 Abstract We revise the conventional nuclear effects of Fermi motion for an interacting Fermi sea and the local density approximation to translate results from nuclear matter to finite

Fernández de Córdoba, Pedro

270

The Structural Basis for the Ligand Specificity of Family 2 Carbohydrate-binding Modules*  

E-Print Network [OSTI]

of proteins with polysaccharides play a key role in the microbial hydrolysis of cellulose and xylan, the most family, CBM2, contains members that bind cellu- lose (CBM2a) and xylan (CBM2b), respectively. A possi- ble explanation for the different ligand specificity of CBM2b is that one of the surface tryptophans

Williamson, Mike P.

271

Increased enzyme binding to substrate is not necessary for more efficient cellulose hydrolysis  

Science Journals Connector (OSTI)

...desorption, despite high xylan solubilization, which...inactive enzymes from the surface of cellulose is competitive...the increased fibril surface hydrophilicity as confirmed...enzyme binding, cellulose surface chain extraction, and...substrates and chemical treatment methods used are provided in SI...

Dahai Gao; Shishir P. S. Chundawat; Anurag Sethi; Venkatesh Balan; S. Gnanakaran; Bruce E. Dale

2013-01-01T23:59:59.000Z

272

Comparison between the many-body perturbative and Green's-function approaches for calculating electron binding  

E-Print Network [OSTI]

electron binding energies and affinities: Brueckner and Dyson orbitals Ingvar Lindgren November 30, 2003 exact. The former approach leads to Brueckner orbitals and the latter to Dyson orbitals, and it is shown's-function technique, Brueckner orbital, Dyson equation, Dyson orbital, self energy, electron affinity Table

Lindgren, Ingvar

273

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.

274

ATP-binding cassette transporters are required for efficient RNA interference in Caenorhabditis elegans  

E-Print Network [OSTI]

that facilitate RNAi have been identified, current descriptions of RNAi and interrelated mechanisms are far from complete. Here, we report that the Caenorhabditis elegans gene haf-6 is required for efficient RNAi. HAF-6 is a member of the ATP-binding cassette (ABC...

Timmons, Lisa; Hull, Dawn; Han, Wang; Echalier, B.; Sundaram, P.

2006-08-01T23:59:59.000Z

275

A blue-light-activated GTP-binding protein in the plasma membranes of etiolated peas.  

Science Journals Connector (OSTI)

...GTP-binding protein in the plasma membranes of etiolated peas KATHERINE M. F. WARPEHA*, HEIDI E. HAMMt, MARK M. RASENICKt...Acad. Sci. USA 85, 3066-3070. 20. Rasenick, M. M., Wheeler, G. L., Bitensky, M. W., Kosack, C. & Stein, P...

K M Warpeha; H E Hamm; M M Rasenick; L S Kaufman

1991-01-01T23:59:59.000Z

276

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

277

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

278

Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea  

Science Journals Connector (OSTI)

We have addressed the distribution and abundance of 75 transcription factor (TF) families in complete genomes from 90 different bacterial and archaeal species. We found that the proportion of TFs increases with genome size. The deficit of TFs in some ... Keywords: Genome size, Helix-turn-helix DNA-binding motif, Protein families, Transcription factors

Ernesto Prez-Rueda; Julio Collado-Vides; Lorenzo Segovia

2004-12-01T23:59:59.000Z

279

Monoclonal antibodies to the human insulin receptor block insulin binding and inhibit insulin action  

Science Journals Connector (OSTI)

...This 10-fold difference in the relative affinitv ; c 60 A God of the antibody for the receptors from different tissues may...IGF-I binding to its receptor in both IM-9 cells and placenta particles. However, 500-fold higher antibody concen- , ;, E 40 1...

R A Roth; D J Cassell; K Y Wong; B A Maddux; I D Goldfine

1982-01-01T23:59:59.000Z

280

Membrane Binding of Ribosomes Occurs at SecYE-based Sites in the Archaea Haloferax volcanii  

E-Print Network [OSTI]

by the signal recognition particle (SRP).10 SRP binding subsequently slows or pre- vents the continuation of further protein synthe- sis.11 The ternary complex of ribosome­nascent polypeptide chain­SRP then interacts with the ER membrane via the affinities of SRP for the mem- brane-associated SRP receptor,12

Eichler, Jerry

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

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

282

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

283

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

E-Print Network [OSTI]

Strip, Bind, and Search: A Method for Identifying Abnormal Energy Consumption in Buildings Romain usage that leads to energy waste. The av- erage waste uncovered is as high as 2500 kWh per device; Energy Consumption; Anomaly Detection 1. INTRODUCTION Buildings are one of the prime targets to reduce

California at Berkeley, University of

284

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

285

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

286

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

287

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

288

RESEARCH Open Access HIV-1 Tat protein binds to TLR4-MD2 and signals  

E-Print Network [OSTI]

RESEARCH Open Access HIV-1 Tat protein binds to TLR4-MD2 and signals to induce TNF- and IL-10 Nawal in a TLR4 dependent manner. Conclusions: Collectively, our data showed for the first time that, HIV-1 Tat progression. Keywords: HIV-1, TLR4, Tat, IL-10, TNF- Background HIV-1 infects numerous cells of the immune

Boyer, Edmond

289

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.

290

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

291

Single-molecule binding experiments on long time scales Mark P. Elenko,1  

E-Print Network [OSTI]

Single-molecule binding experiments on long time scales Mark P. Elenko,1 Jack W. Szostak,2; accepted 11 July 2010; published online 27 August 2010 We describe an approach for performing single-molecule than have been previously investigated by single-molecule techniques. Total internal reflection

Heller, Eric

292

Ammonium PerchlorateBinding Poly(allylamine hydrochloride) Hydrogels for Wastewater Remediation  

E-Print Network [OSTI]

(allylamine hydrochloride) (PAA HCl) polymeric hydrogel. The pH-sensitive PAA HCl hydrogels were synthesized by chemically crosslinking a solu- tion of linear PAA HCl chains with epichlorohydrin (EPI). The perchlorate-binding capacity opportunities to recover and reuse the hydrogel over multiple regeneration cycles. The PAA HCl hydrogels

Kofinas, Peter

293

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

294

Structural and Functional Analysis of Coxsackievirus A9 Integrin ?v?6 Binding and Uncoating  

Science Journals Connector (OSTI)

...which binds to the bent alpha2beta1 integrin...D Stuart. 1999. The crystal structure of coxsackievirus...integrins by conversion from bent to extended conformations...and MA Arnaout. 2002. Crystal structure of the extracellular...method for identifying spherical particles in electron...

Shabih Shakeel; Jani J. T. Seitsonen; Tommi Kajander; Pasi Laurinmki; Timo Hyypi; Petri Susi; Sarah J. Butcher

2013-01-30T23:59:59.000Z

295

JOURNAL OF CELLULAR PHYSIOLOGY 198:188196 (2004) Geldanamycin, a Heat Shock Protein 90-Binding Agent,  

E-Print Network [OSTI]

JOURNAL OF CELLULAR PHYSIOLOGY 198:188­196 (2004) Geldanamycin, a Heat Shock Protein 90-Binding and Feramisco, 1982). It has been reported that Hsp90 plays a critical role in regulating signal transduc- tion of proteins including nuclear hormone receptors, protein kinases, and transcription factors (Pratt, 1998

Tian, Weidong

296

Distribution of binding energies of a water molecule in the water liquid-vapor interface  

SciTech Connect (OSTI)

Distributions of binding energies of a water molecule in the water liquid-vapor interface are obtained on the basis of molecular simulation with the SPC/E model of water. These binding energies together with the observed interfacial density profile are used to test a minimally conditioned Gaussian quasi-chemical statistical thermodynamic theory. Binding energy distributions for water molecules in that interfacial region clearly exhibit a composite structure. A minimally conditioned Gaussian quasi-chemical model that is accurate for the free energy of bulk liquid water breaks down for water molecules in the liquid-vapor interfacial region. This breakdown is associated with the fact that this minimally conditioned Gaussian model would be inaccurate for the statistical thermodynamics of a dilute gas. Aggressive conditioning greatly improves the performance of that Gaussian quasi-chemical model. The analogy between the Gaussian quasi-chemical model and dielectric models of hydration free energies suggests that naive dielectric models without the conditioning features of quasi-chemical theory will be unreliable for these interfacial problems. Multi-Gaussian models that address the composite nature of the binding energy distributions observed in the interfacial region might provide a mechanism for correcting dielectric models for practical applications.

Chempath, Shaji [Los Alamos National Laboratory; Pratt, Lawrence R [TULANE UNIV

2008-01-01T23:59:59.000Z

297

Structural Plasticity of Malaria Dihydroorotate Dehydrogenase Allows Selective Binding of Diverse Chemical Scaffolds  

SciTech Connect (OSTI)

Malaria remains a major global health burden and current drug therapies are compromised by resistance. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) was validated as a new drug target through the identification of potent and selective triazolopyrimidine-based DHODH inhibitors with anti-malarial activity in vivo. Here we report x-ray structure determination of PfDHODH bound to three inhibitors from this series, representing the first of the enzyme bound to malaria specific inhibitors. We demonstrate that conformational flexibility results in an unexpected binding mode identifying a new hydrophobic pocket on the enzyme. Importantly this plasticity allows PfDHODH to bind inhibitors from different chemical classes and to accommodate inhibitor modifications during lead optimization, increasing the value of PfDHODH as a drug target. A second discovery, based on small molecule crystallography, is that the triazolopyrimidines populate a resonance form that promotes charge separation. These intrinsic dipoles allow formation of energetically favorable H-bond interactions with the enzyme. The importance of delocalization to binding affinity was supported by site-directed mutagenesis and the demonstration that triazolopyrimidine analogs that lack this intrinsic dipole are inactive. Finally, the PfDHODH-triazolopyrimidine bound structures provide considerable new insight into species-selective inhibitor binding in this enzyme family. Together, these studies will directly impact efforts to exploit PfDHODH for the development of anti-malarial chemotherapy.

Deng, Xiaoyi; Gujjar, Ramesh; El Mazouni, Farah; Kaminsky, Werner; Malmquist, Nicholas A.; Goldsmith, Elizabeth J.; Rathod, Pradipsinh K.; Phillips, Margaret A.; (UWASH); (UTSMC)

2010-01-20T23:59:59.000Z

298

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

299

Effect of pH on the Binding of -Lactoglobulin to Sodium Polystyrenesulfonate R. K. Hallberg and P. L. Dubin*  

E-Print Network [OSTI]

or for pentalysine/DNA data. The current results suggest that the free energy of binding of a protein to a synthetic, Indianapolis, Indiana 46202-3274 ReceiVed: June 23, 1998 The binding of -lactoglobulin to the synthetic. Introduction Proteins interact strongly with both natural polyelectrolytes and synthetic polyelectrolytes

Dubin, Paul D.

300

Binding energies and electronic structures of adsorbed titanium chains on carbon nanotubes Chih-Kai Yang,1  

E-Print Network [OSTI]

Binding energies and electronic structures of adsorbed titanium chains on carbon nanotubes Chih studied the binding energies and electronic structures of metal Ti, Al, Au chains adsorbed on single in nanoscale materials and devices. A nanotube with adsorbed materials may also significantly changes its physi

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

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.

302

Biochem. J. (2000) 345, 5360 (Printed in Great Britain) 53 Carbohydrate-binding modules from a thermostable Rhodothermus marinus  

E-Print Network [OSTI]

binding to insoluble xylan and to phosphoric-acid- swollen cellulose but not to Avicel or crystalline occurred with different xylans and -glucan. CBM4-2 displayed a somewhat higher binding affinity than CBM4 in the effective enzyme concentration on the substrate surface that is caused by the attachment of the CBM [14

Williamson, Mike P.

303

A Secondary Xylan-binding Site Enhances the Catalytic Activity of a Single-domain Family 11  

E-Print Network [OSTI]

A Secondary Xylan-binding Site Enhances the Catalytic Activity of a Single-domain Family 11 surface region. Chemical shift perturbation mapping and affinity electrophoresis, combined with mutational studies, identified the xylan-specific secondary binding site (SBS) as a shallow groove lined by Asn, Ser

McIntosh, Lawrence P.

304

LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures  

Science Journals Connector (OSTI)

......ligand-binding sites than inspection of sequence conservation alone. Indeed, binding sites with a...Press 2002 LigBase themselves; however, water molecules are not retained in the database...integration will also dramatically increase the pool of available structures for the study......

Ashley C. Stuart; Valentin A. Ilyin; Andrej Sali

2002-01-01T23:59:59.000Z

305

A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome  

E-Print Network [OSTI]

the human genome; 1,654 proteins are predicted to have DNA-binding function. Comparison with existing Gene) A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome. PLo have been released, and about 5,000 active genome sequencing projects are on the way [6

Skolnick, Jeff

306

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.

307

Measurement of the Binding Energy for Di-C2H4/Pt{111}: Does a Radical Intermediate Form  

E-Print Network [OSTI]

Measurement of the Binding Energy for Di- C2H4/Pt{111}: Does a Radical Intermediate Form During energy surface. This well depth, or binding energy, is determined by measuring the threshold that temperature-programmed desorption involves a nonequilibrium measurement; thus, the activation energy

Levis, Robert J.

308

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

309

Inhibition of Both HIV-1 Reverse Transcription and Gene Expression by a Cyclic Peptide that Binds the Tat-  

E-Print Network [OSTI]

Inhibition of Both HIV-1 Reverse Transcription and Gene Expression by a Cyclic Peptide that Binds the Tat- Transactivating Response Element (TAR) RNA Matthew S. Lalonde1" , Michael A. Lobritz2" , Annette The RNA response element TAR plays a critical role in HIV replication by providing a binding site

Levin, Judith G.

310

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

311

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0  

Science Journals Connector (OSTI)

......Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0 Xiaolei Zhu 1 Yi Xiong 1 Daisuke Kihara...Results: We present a computational method named Patch-Surfer2.0, which predicts binding ligands for......

Xiaolei Zhu; Yi Xiong; Daisuke Kihara

2014-10-01T23:59:59.000Z

312

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

313

Cable Pili and the 22-Kilodalton Adhesin Are Required for Burkholderia cenocepacia Binding to and Transmigration across the Squamous Epithelium  

Science Journals Connector (OSTI)

...PATHOGEN-HOST CELL MOLECULAR INTERACTIONS Cable Pili and the 22-Kilodalton Adhesin Are...Burkholderia cenocepacia strains expressing both cable (Cbl) pili and the 22-kDa adhesin bind...binding (0 to 8%). Mutants lacking either cable pili or the adhesin were compromised in...

Teresa A. Urban; Joanna B. Goldberg; Janet F. Forstner; Umadevi S. Sajjan

2005-09-01T23:59:59.000Z

314

Specific Fluorine Labeling of the HyHEL10 Antibody Affects Antigen Binding and Dynamics  

SciTech Connect (OSTI)

To more fully understand the molecular mechanisms responsible for variations in binding affinity with antibody maturation, we explored the use of site specific fluorine labeling and {sup 19}F nuclear magnetic resonance (NMR). Several single-chain (scFv) antibodies, derived from an affinity-matured series of anti-hen egg white lysozyme (HEL) mouse IgG1, were constructed with either complete or individual replacement of tryptophan residues with 5-fluorotryptophan ({sup 5F}W). An array of biophysical techniques was used to gain insight into the impact of fluorine substitution on the overall protein structure and antigen binding. SPR measurements indicated that {sup 5F}W incorporation lowered binding affinity for the HEL antigen. The degree of analogue impact was residue-dependent, and the greatest decrease in affinity was observed when {sup 5F}W was substituted for residues near the binding interface. In contrast, corresponding crystal structures in complex with HEL were essentially indistinguishable from the unsubstituted antibody. {sup 19}F NMR analysis showed severe overlap of signals in the free fluorinated protein that was resolved upon binding to antigen, suggesting very distinct chemical environments for each {sup 5F}W in the complex. Preliminary relaxation analysis suggested the presence of chemical exchange in the antibody-antigen complex that could not be observed by X-ray crystallography. These data demonstrate that fluorine NMR can be an extremely useful tool for discerning structural changes in scFv antibody-antigen complexes with altered function that may not be discernible by other biophysical techniques.

Acchione, Mauro; Lee, Yi-Chien; DeSantis, Morgan E.; Lipschultz, Claudia A.; Wlodawer, Alexander; Li, Mi; Shanmuganathan, Aranganathan; Walter, Richard L.; Smith-Gill, Sandra; Barchi, Jr., Joseph J. (SAIC); (NCI)

2012-10-16T23:59:59.000Z

315

Aldosterone binding in isolated tubules. IV. Autoradiography along the nephron of the spontaneously hypertensive rat  

SciTech Connect (OSTI)

The binding of aldosterone was studied in tubular segments isolated by microdissection from kidneys of spontaneously hypertensive (SHR, n = 8), Kyoto normotensive (KWR, n = 8), and normal Wistar (NWR, n = 6) rats with an autoradiographic technique on dry film. All animals had been previously adrenalectomized. Kidney pyramids were incubated in vitro before microdissection with collagenase and 2 X 10(-9) M (/sup 3/H)aldosterone in the presence or absence of an excess of unlabeled aldosterone. In addition, the displacement of the binding by 10 times excess dexamethasone or aldosterone was examined in the cortical and medullary collecting tubule of SHR and KWR to assess the specificity of binding sites. In the three groups, no specific nuclear labeling was detectable in the proximal tubule. The highest specific nuclear labeling was found in the distal portions of the nephron, and intermediate values were present along the loop of Henle. In the cortical collecting tubule, the most specific mineralocorticoid segment, the specific nuclear binding, expressed in silver grains per unit surface, was significantly elevated in SHR (16.1 +/- 1.5) and KWR (13.7 +/- 1.5) as compared with NWR (10.2 +/- 0.8, P less than 0.001 and less than 0.05, respectively). The difference between SHR and KWR did not reach statistical significance. In the medullary collecting tubule, binding was higher in SHR (14.3 +/- 1.6) than in both KWR (8.7 +/- 1.0, P less than 0.005) and NWR (10.1 +/- 0.9, P less than 0.025).

Farman, N.; Bonvalet, J.P.

1985-07-01T23:59:59.000Z

316

Calculation of the binding affinity of the anticancer drug daunomycin to DNA by a statistical mechanics approach  

Science Journals Connector (OSTI)

Equilibrium binding constants of the anticancer drug daunomycin, bound to several GC containing polymeric DNAs (G represent guanine and C cytosine), are calculated by means of a microscopic statistical mechanics approach and based on observed x-ray crystal structures. Our calculation shows base sequence specificity of daunomycin in agreement with the observations. We find the drug binding constant to be sensitive to the base composition of the host sequence. The binding stability decreases in the order of CGTACG, CGATCG, and CGGCCG, which is consistent with observations (T represents thymine and A adenine). This binding specificity arises from sequence specific hydrogen bond and nonbonded interactions between the drug and a host DNA. These interactions are affected by sequence specific structural features exhibited from x-ray crystallography. The agreement between our calculations and experiments shows that our method is of practical application in analyzing sequence specific binding stability of anticancer drugs.

Y. Z. Chen and Yong-Li Zhang

1997-06-01T23:59:59.000Z

317

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

318

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

319

Structural Basis of Low-Affinity Nickel Binding to the Nickel-Responsive Transcription Factor NikR from Escherichia coli  

E-Print Network [OSTI]

Escherichia coli NikR regulates cellular nickel uptake by binding to the nik operon in the presence of nickel and blocking transcription of genes encoding the nickel uptake transporter. NikR has two binding affinities for ...

Phillips, Christine M.

320

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.

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

Prediction of HLA-DRB1*0401 binding peptides using support vector machine  

Science Journals Connector (OSTI)

In recent years, many machine learning methods have been developed to predict HLA binding peptides. However, because only limited types of descriptors characterising the protein features are included in these approaches, these methods have poor prediction accuracy. In this study, we applied support vector machine methods to predict the peptides that bind to the major histocompatibility complexes Class II molecule HLA-DRB1*0401 using six sets of molecular descriptors characterising the primary structures of the peptides. We found that some feature groups provided good prediction accuracies and the overall accuracies were greater than 95% and some feature groups had poor accuracies of only 50%. The performance was improved significantly by additional feature selection and the overall accuracies from each group or combination of descriptors were greater than 90%. Of note, the inclusion of necessary informative and discriminative descriptors improved the prediction accuracies.

Wenli Huang; Guobing Yang; Xiaojun Zhao; Zerong Li

2014-01-01T23:59:59.000Z

322

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

323

Mutations in FMN Binding Pocket Diminish Chromate Reduction Rates for Gh-ChrR Isolated from Gluconacetobacter hansenii  

SciTech Connect (OSTI)

A putative chromate ion binding site was identified proximal to a rigidly bound FMN from electron densities in the crystal structure of the quinone reductase from Gluconacetobacter hansenii (Gh-ChrR) (3s2y.pdb). To clarify the location of the chromate binding site, and to understand the role of FMN in the NADPH-dependent reduction of chromate, we have expressed and purified four mutant enzymes involving the site-specific substitution of individual side chains within the FMN binding pocket that form non-covalent bonds with the ribityl phosphate (i.e., S15A and R17A in loop 1 between ?1 sheet and ?1 helix) or the isoalloxanzine ring (E83A or Y84A in loop 4 between the ?3 sheet and ?4 helix). Mutations that selectively disrupt hydrogen bonds between either the N3 nitrogen on the isoalloxanzine ring (i.e., E83) or the ribitylphos- phoate (i.e., S15) respectively result in 50% or 70% reductions in catalytic rates of chromate reduction. In comparison, mutations that disrupt ?-? ring stacking interactions with the isoal-loxanzine ring (i.e., Y84) or a salt bridge with the ribityl phosphate result in 87% and 97% inhibittion. In all cases there are minimal alterations in chromate binding affinities. Collectively, these results support the hypothesis that chromate binds proximal to FMN, and implicate a structural role for FMN positioning for optimal chromate reduction rates. As side chains proximal to the ?3/?4 FMN binding loop 4 contribute to both NADH and metal ion binding, we propose a model in which structural changes around the FMN binding pocket couples to both chromate and NADH binding sites.

Khaleel, Janin A.; Gong, Chunhong; Zhang, Yanfeng; Tan, Ruimin; Squier, Thomas C.; Jin, Hongjun

2013-06-01T23:59:59.000Z

324

Membrane binding mode of intrinsically disordered cytoplasmic domains of T cell receptor signaling subunits depends on lipid composition  

SciTech Connect (OSTI)

Intrinsically disordered cytoplasmic domains of T cell receptor (TCR) signaling subunits including {zeta}{sub cyt} and CD3{epsilon}{sub cyt} all contain one or more copies of an immunoreceptor tyrosine-based activation motif (ITAM), tyrosine residues of which are phosphorylated upon receptor triggering. Membrane binding-induced helical folding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} ITAMs is thought to control TCR activation. However, the question whether or not lipid binding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} is necessarily accompanied by a folding transition of ITAMs remains open. In this study, we investigate whether the membrane binding mechanisms of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} depend on the membrane model used. Circular dichroic and fluorescence data indicate that binding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} to detergent micelles and unstable vesicles is accompanied by a disorder-to-order transition, whereas upon binding to stable vesicles these proteins remain unfolded. Using electron microscopy and dynamic light scattering, we show that upon protein binding, unstable vesicles fuse and rupture. In contrast, stable vesicles remain intact under these conditions. This suggests different membrane binding modes for {zeta}{sub cyt} and CD3{epsilon}{sub cyt} depending on the bilayer stability: (1) coupled binding and folding, and (2) binding without folding. These findings explain the long-standing puzzle in the literature and highlight the importance of the choice of an appropriate membrane model for protein-lipid interactions studies.

Sigalov, Alexander B., E-mail: Alexander.sigalov@umassmed.edu [University of Massachusetts Medical School, Worcester, MA 01655 (United States); Hendricks, Gregory M. [University of Massachusetts Medical School, Worcester, MA 01655 (United States)] [University of Massachusetts Medical School, Worcester, MA 01655 (United States)

2009-11-13T23:59:59.000Z

325

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

326

The use of binding arbitration for Arizona's public works disputes as viewed from the contractor's perspective  

E-Print Network [OSTI]

contract disputes in Arizona. The research was based upon a survey of Arizona contractors holding Class A ? General Engineering Contracting licenses. The research included an examination of the existing statutory requirements used in Arizona... for resolving public works contract disputes in addition to a comprehensive review of public works arbitration statutes in other states. Four conclusions were drawn from the research: 1) Most contractors prefer binding arbitration to litigation of public...

Bluff, Michael Robert

2012-06-07T23:59:59.000Z

327

Binding of the Inhibitor Protein IF1 to Bovine F1-ATPase  

Science Journals Connector (OSTI)

In the structure of bovine F1-ATPase inhibited with residues 160 of the bovine inhibitor protein IF1, the ?-helical inhibitor interacts with five of the nine subunits of F1-ATPase. In order to understand the contributions of individual amino acid residues to this complex binding mode, N-terminal deletions and point mutations have been introduced, and the binding properties of each mutant inhibitor protein have been examined. The N-terminal region of IF1 destabilizes the interaction of the inhibitor with F1-ATPase and may assist in removing the inhibitor from its binding site when F1Fo-ATPase is making ATP. Binding energy is provided by hydrophobic interactions between residues in the long ?-helix of IF1 and the C-terminal domains of the ?DP-subunit and ?TP-subunit and a salt bridge between residue E30 in the inhibitor and residue R408 in the C-terminal domain of the ?DP-subunit. Several conserved charged amino acids in the long ?-helix of IF1 are also required for establishing inhibitory activity, but in the final inhibited state, they are not in contact with F1-ATPase and occupy aqueous cavities in F1-ATPase. They probably participate in the pathway from the initial interaction of the inhibitor and the enzyme to the final inhibited complex observed in the structure, in which two molecules of ATP are hydrolysed and the rotor of the enzyme turns through two 120 steps. These findings contribute to the fundamental understanding of how the inhibitor functions and to the design of new inhibitors for the systematic analysis of the catalytic cycle of the enzyme.

John V. Bason; Michael J. Runswick; Ian M. Fearnley; John E. Walker

2011-01-01T23:59:59.000Z

328

Biochem. J. (1987) 246, 227-232 (Printed in Great Britain) The binding of the cyclic AMP receptor protein to synthetic DNA  

E-Print Network [OSTI]

protein to synthetic DNA sites containing permutations in the consensus sequence TGTGA Claudia JANSEN synthetic DNA-binding sites was investigated with a gel-retardation assay. A set of ten different sequences of synthetic-DNA binding sites. First, we show that a completely symmetric site binds better to CRP than

Clore, G. Marius

329

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

330

Biochemical and Domain Analyses of FSUAxe6B, a Modular Acetyl Xylan Esterase, Identify a Unique Carbohydrate Binding Module in Fibrobacter succinogenes S85  

Science Journals Connector (OSTI)

...insoluble b-1,4-xylan. The F. succinogenes...A CBMs are defined as surface binding, and they bind...FPm-1 preferred insoluble xylan, harboring heterogeneous...Lamed. 2008. Cell surface enzyme attachment is...modules and the presence of xylan-binding domains in...

Shosuke Yoshida; Roderick I. Mackie; Isaac K. O. Cann

2009-11-06T23:59:59.000Z

331

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

332

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

333

T-677: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of Service  

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

7: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of 7: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of Service Vulnerability T-677: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of Service Vulnerability July 27, 2011 - 3:58pm Addthis PROBLEM: F5 has acknowledged a vulnerability in BIG-IP, which can be exploited by malicious people to cause a DoS (Denial of Service). PLATFORM: The vulnerability is reported in the following products and versions: BIG-IP LTM versions 9.0.0 through 9.4.8, 10.0.0 through 10.1.0, and 10.2.0 through 10.2.2 BIG-IP GTM versions 9.0.0 through 9.4.8, 10.0.0 through 10.1.0, and 10.2.0 through 10.2.2 BIG-IP ASM versions 9.0.0 through 9.4.8, 10.0.0 through 10.1.0, and 10.2.0 through 10.2.2 BIG-IP Link Controller versions 9.0.0 through 9.4.8, 10.0.0 through 10.1.0, and 10.2.0 through 10.2.2

334

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

335

Three-Dimensional Structures Reveal Multiple ADP/ATP Binding Modes  

SciTech Connect (OSTI)

The creation of synthetic enzymes with predefined functions represents a major challenge in future synthetic biology applications. Here, we describe six structures of de novo proteins that have been determined using protein crystallography to address how simple enzymes perform catalysis. Three structures are of a protein, DX, selected for its stability and ability to tightly bind ATP. Despite the addition of ATP to the crystallization conditions, the presence of a bound but distorted ATP was found only under excess ATP conditions, with ADP being present under equimolar conditions or when crystallized for a prolonged period of time. A bound ADP cofactor was evident when Asp was substituted for Val at residue 65, but ATP in a linear configuration is present when Phe was substituted for Tyr at residue 43. These new structures complement previously determined structures of DX and the protein with the Phe 43 to Tyr substitution [Simmons, C. R., et al. (2009) ACS Chem. Biol. 4, 649-658] and together demonstrate the multiple ADP/ATP binding modes from which a model emerges in which the DX protein binds ATP in a configuration that represents a transitional state for the catalysis of ATP to ADP through a slow, metal-free reaction capable of multiple turnovers. This unusual observation suggests that design-free methods can be used to generate novel protein scaffolds that are tailor-made for catalysis.

C Simmons; C Magee; D Smith; L Lauman; J Chaput; J Allen

2011-12-31T23:59:59.000Z

336

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

337

Molecular docking and NMR binding studies to identify novel inhibitors of human phosphomevalonate kinase  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer Natural and synthetic inhibitors of human phosphomevalonate kinase identified. Black-Right-Pointing-Pointer Virtual screening yielded a hit rate of 15%, with inhibitor K{sub d}'s of 10-60 {mu}M. Black-Right-Pointing-Pointer NMR studies indicate significant protein conformational changes upon binding. -- Abstract: Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using autodock. Promising hits were verified and their affinity measured using NMR-based {sup 1}H-{sup 15}N heteronuclear single quantum coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored, plotted, and fitted to obtain dissociation constants (K{sub d}). Tight binding compounds with K{sub d}'s ranging from 6-60 {mu}M were identified. These compounds tended to have significant polarity and negative charge, similar to the natural substrates (M5P and ATP). HSQC cross peak changes suggest that binding induces a global conformational change, such as domain closure. Compounds identified in this study serve as chemical genetic probes of human PMK, to explore pharmacology of the mevalonate pathway, as well as starting points for further drug development.

Boonsri, Pornthip [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States) [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Neumann, Terrence S.; Olson, Andrew L.; Cai, Sheng [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States)] [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Herdendorf, Timothy J.; Miziorko, Henry M. [Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110 (United States)] [Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110 (United States); Hannongbua, Supa [Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand)] [Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Sem, Daniel S., E-mail: daniel.sem@cuw.edu [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States)

2013-01-04T23:59:59.000Z

338

Intermolecular versus intramolecular interactions of the vinculin binding site 33 of talin  

SciTech Connect (OSTI)

The cytoskeletal proteins talin and vinculin are localized at cell-matrix junctions and are key regulators of cell signaling, adhesion, and migration. Talin couples integrins via its FERM domain to F-actin and is an important regulator of integrin activation and clustering. The 220 kDa talin rod domain comprises several four- and five-helix bundles that harbor amphipathic {alpha}-helical vinculin binding sites (VBSs). In its inactive state, the hydrophobic VBS residues involved in binding to vinculin are buried within these helix bundles, and the mechanical force emanating from bound integrin receptors is thought necessary for their release and binding to vinculin. The crystal structure of a four-helix bundle of talin that harbors one of these VBSs, coined VBS33, was recently determined. Here we report the crystal structure of VBS33 in complex with vinculin at 2 {angstrom} resolution. Notably, comparison of the apo and vinculin bound structures shows that intermolecular interactions of the VBS33 {alpha}-helix with vinculin are more extensive than the intramolecular interactions of the VBS33 within the talin four-helix bundle.

Yogesha, S.D.; SHarff, A.; Bricogne, G.; Izard, .T. (Globel Phasing); (Scripps)

2012-03-13T23:59:59.000Z

339

The nucleotide-binding domain of NLRC5 is critical for nuclear import and transactivation activity  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer NLRC5 requires an intact NLS for its function as MHC class I transactivator. Black-Right-Pointing-Pointer Nuclear presence of NLRC5 is required for MHC class I induction. Black-Right-Pointing-Pointer Nucleotide-binding controls nuclear import and transactivation activity of NLRC5. -- Abstract: Major histocompatibility complex (MHC) class I and class II are crucial for the function of the human adaptive immune system. A member of the NLR (nucleotide-binding domain, leucine-rich repeat) protein family, NLRC5, has recently been identified as a transcriptional regulator of MHC class I and related genes. While a 'master regulator' of MHC class II genes, CIITA, has long been known, NLRC5 specifically associates with and transactivates the proximal promoters of MHC class I genes. In this study, we analyzed the molecular requirements of NLRC5 nuclear import and transactivation activity. We show that NLRC5-mediated MHC class I gene induction requires an intact nuclear localization signal and nuclear distribution of NLRC5. In addition, we find that the nucleotide-binding domain (NBD) of NLRC5 is critical not only for nuclear translocation but also for the transactivation of MHC class I genes. Changing the cellular localization of NLRC5 is likely to immediately impact MHC class I expression as well as MHC class I-mediated antigen presentation. NLRC5 may thus provide a promising target for the modulation of MHC class I antigen presentation, especially in the setting of transplant medicine.

Meissner, Torsten B. [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States) [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States); Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02215 (United States); Li, Amy; Liu, Yuen-Joyce [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States)] [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States); Gagnon, Etienne [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States) [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States); Institut de Recherche en Immunologie et Cancerologie, Departement de Microbiologie et Immunologie, Universite de Montreal, Montreal, Canada H3T1J4 (Canada); Kobayashi, Koichi S., E-mail: Koichi_Kobayashi@dfci.harvard.edu [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States); Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02215 (United States)

2012-02-24T23:59:59.000Z

340

Precision Measurement of the 29Si, 33S, and 36Cl Binding Energies  

E-Print Network [OSTI]

The binding energies of 29Si, 33S, and 36Cl have been measured with a relative uncertainty $measurements are 1) nearly perfect crystals whose lattice spacing is known in meters, 2) a highly precise angle scale that is derived from first principles, and 3) a gamma-ray measurement facility that is coupled to a high flux reactor with near-core source capability. The binding energy is obtained by measuring all gamma-rays in a cascade scheme connecting the capture and ground states. The measurements require the extension of precision flat-crystal diffraction techniques to the 5 to 6 MeV energy region, a significant precision measurement challenge. The binding energies determined from these gamma-ray measurements are consistent with recent highly accurate atomic mass measurements within a relative uncertainty of $4.3 \\times 10^{-7}$. The gamma-ray measurement uncertainties are the dominant contributors to the uncertainty of this consistency test. The measured gamma-ray energies are in agreement with earlier precision gamma-ray measurements.

M. S. Dewey; E. G. Kessler Jr; R. D. Deslattes; H. G. Borner; M. Jentschel; C. Doll; P. Mutti

2005-07-06T23:59:59.000Z

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.


341

Investigation of metal binding sites on soil fulvic acid using Eu(III) luminescence spectroscopy  

SciTech Connect (OSTI)

The [sup 7]F[sub 0] [yields] [sup 5]D[sub 0] excitation spectra of Eu(III) complexed with soil fulvic acid (FA) were acquired over a range of solution pH (2.9-7.8) and FA concentrations (800-3200 mg L[sup [minus]1]) using a pulsed tunable dye laser system. The broad asymmetric excitation spectra were well-fitted to a sum of two conventional Lorentzian-shaped curves, revealing the existence of two types of carboxylate moieties for the binding of metal ions on FA which formed 1:1 (EuL[sup 2+]; L = carboxylate) and 1:2 complexes (EuL[sub 2][sup +]). The weaker binding species, EuL[sup 2+], seemed to be quite abundant and showed a rapid increase as the pH was raised from 2.9 to 6.3, but it was susceptible to hydrolysis at pH higher than 7 while the stronger binding species, EuL[sub 2][sup +], showed only a modest growth with an increase in pH. By contrast, on a more flexible synthetic linear polymer, poly(acrylic acid) (PAA) and poly(vinylbenzoic acid) (PVBA) as model polymers, EuL[sub 2][sup +] was seen as the dominant species except in acidic media. 28 refs., 10 figs., 3 tabs.

Yoon, T.H.; Moon, H. (Korea Advanced Inst. of Science and Technology, Taejun (Korea, Democratic People's Republic of)); Park, Y.J.; Park, K.K. (Korea Atomic Energy Research Inst., Taejun (Korea, Democratic People's Republic of))

1994-11-01T23:59:59.000Z

342

Binding of Uridine 5-Diphosphate in the Basic Patch of the Zinc Deacetylase LpxC and Implications for Substrate Binding  

SciTech Connect (OSTI)

LpxC is a zinc metalloenzyme that catalyzes the first committed step in the biosynthesis of lipid A, a vital component of the outer membrane of Gram-negative bacteria. Accordingly, the inhibition of LpxC is an attractive strategy for the treatment of Gram-negative bacterial infections. Here, we report the 2.7 {angstrom} resolution X-ray crystal structure of LpxC from Aquifex aeolicus complexed with uridine 5'-diphosphate (UDP), and the 3.1 {angstrom} resolution structure of LpxC complexed with pyrophosphate. The X-ray crystal structure of the LpxC-UDP complex provides the first view of interactions likely to be exploited by the substrate UDP group in the 'basic patch' of the active site. The diphosphate group of UDP makes hydrogen bond interactions with strictly conserved residue K239 as well as solvent molecules. The ribose moiety of UDP interacts with partially conserved residue E197. The UDP uracil group hydrogen bonds with both the backbone NH group and the backbone carbonyl group of E160, and with the backbone NH group of K162 through an intervening water molecule. Finally, the {alpha}-phosphate and uracil groups of UDP interact with R143 and R262 through intervening water molecules. The structure of LpxC complexed with pyrophosphate reveals generally similar intermolecular interactions in the basic patch. Unexpectedly, diphosphate binding in both complexes is accompanied by coordination to an additional zinc ion, resulting in the identification of a new metal-binding site termed the E-site. The structures of the LpxC-UDP and LpxC-pyrophosphate complexes provide new insights with regard to substrate recognition in the basic patch and metal ion coordination in the active site of LpxC.

Gennadios,H.; Christianson, D.

2006-01-01T23:59:59.000Z

343

Whole Genome Analysis of Functional Protein Binding Sites and DNA Methylation: Application to p53 and Low Dose Ionizing Radiation.  

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

Whole Genome Analysis of Functional Protein Binding Sites and DNA Methylation: Whole Genome Analysis of Functional Protein Binding Sites and DNA Methylation: Application to p53 and Low Dose Ionizing Radiation. Krassimira Botcheva, John J. Dunn and Carl W. Anderson Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA The effects of exposure to low doses of ionizing radiation on humans results largely from changes in gene expression mediated by the activation of sequence-specific DNA binding proteins (transcription factors) as well as changes to other chromosomal proteins and perhaps to DNA. To develop a molecular understanding of the consequences of exposures to low doses of ionizing radiation, it will be necessary to understanding where radiation-activated transcription factors bind in whole genomes and how

344

Natural and synthetic double-stranded DNA binding studies of macrocyclic tetraamine zinc(II) complexes appended with polyaromatic groups  

Science Journals Connector (OSTI)

...?The characteristic binding mode of zinc(II) complexes of macrocyclic tetraamines (1,4,7,10-tetraazacyclododecane, cyclen) appended with one or two arylmethyl group(s) [(4-quinolyl)methyl-, 1,7-bis(4-quinolyl)...

Emiko Kikuta; Naomi Katsube; E. Kimura

1999-08-01T23:59:59.000Z

345

Spatial and temporal coupling models for the discovery of binding events in ChIP-Seq data  

E-Print Network [OSTI]

In this thesis, we will present two methods for identifying binding events in ChIP-Seq data. The motivation of this venture is to propose a complete read generating process under a probabilistic graphical model framework ...

Papachristoudis, Georgios

2010-01-01T23:59:59.000Z

346

Purification, crystallization and preliminary X-ray diffraction analysis of water-soluble chlorophyll-binding protein from Chenopodium album  

Science Journals Connector (OSTI)

A water-soluble chlorophyll-binding protein with photoconvertibility from C. album was extracted, purified and crystallized in a darkroom. The crystal diffracted to around 2.0 resolution.

Ohtsuki, T.

2007-08-10T23:59:59.000Z

347

Dangling Bond Defects in a-Si,Ge Alloys: A Theoretical Study Using the Tight-Binding Method  

Science Journals Connector (OSTI)

This paper presents a theoretical study of Si and Ge atom dangling bond defects in a-Si,Ge alloys. We use a tight-binding Hamiltonian, and a structural model based on a cluster Bethe Lattice. The central clust...

S. Y. Lin; G. Lucovsky

1985-01-01T23:59:59.000Z

348

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

349

Methyl p-Hydroxyphenyllactate and Nuclear Type II Binding Sites in Malignant Cells: Metabolic Fate and Mammary Tumor Growth  

Science Journals Connector (OSTI)

...Heterogeneity of estrogen-binding sites and the nuclear matrix. In: G. Maul (ed.). The Nuclear Matrix and the Nuclear Envelope, pp. 259-269. New York...inhibition on mitochondria! ATPase and energy-linked reactions in submitochondrial...

Barry M. Markaverich; Rebecca R. Gregory; MaryAnn Alejandro; Francis S. Kittrell; Daniel Medina; James H. Clark; Manju Varma; and Rajender S. Varma

1990-03-01T23:59:59.000Z

350

A Large-Scale Test of Free-Energy Simulation Estimates of ProteinLigand Binding Affinities  

Science Journals Connector (OSTI)

We have performed a large-scale test of alchemical perturbation calculations with the Bennett acceptance-ratio (BAR) approach to estimate relative affinities for the binding of 107 ligands to 10 different proteins. Employing 20- truncated spherical ...

Paulius Mikulskis; Samuel Genheden; Ulf Ryde

2014-09-29T23:59:59.000Z

351

Abstract 4495: Fisetin, a dietary flavonoid, binds to and disrupts microtubule dynamic instability in prostate cancer cells.  

Science Journals Connector (OSTI)

...2013; Washington, DC Abstract 4495: Fisetin, a dietary flavonoid, binds to and disrupts...urgently needed. We hypothesized that fisetin may offer PCa chemotherapeutic and/or...polymerization assay, we observed that fisetin enhanced tubulin polymerization whose...

Eiman Mukhtar; Vaqar M. Adhami; Deeba N. Syed; Hasan Mukhtar

2013-04-15T23:59:59.000Z

352

Interaction of monoclonal antibodies with the enzymatic domains of penicillin-binding protein 1b of Escherichia coli.  

Science Journals Connector (OSTI)

...transglycosylation reaction. Binding of penicillin by PBP lb. (i) Reaction results of in vitro murein synthesis by m( information about the amount of synthesized ever, the extent that transglycosylation or tr is involved could not be specified...

T den Blaauwen; M Aarsman; N Nanninga

1990-01-01T23:59:59.000Z

353

MFSPSSMpred: identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation  

Science Journals Connector (OSTI)

Molecular recognition features (MoRFs) are short binding regions located in longer intrinsically disordered protein regions. Although these short regions lack a ... in the natural state, they readily undergo disorder

Chun Fang; Tamotsu Noguchi; Daisuke Tominaga; Hayato Yamana

2013-10-01T23:59:59.000Z

354

Evolutionary substitution of two amino acids in chloroplast SRP54 of higher plants cause its inability to bind SRP RNA  

Science Journals Connector (OSTI)

The chloroplast signal recognition particle (cpSRP) consists of a conserved 54kDa subunit (cpSRP54) and a unique 43kDa subunit (cpSRP43) but lacks SRP-RNA, an essential and universally conserved component of cytosolic SRPs. High sequence similarity exists between cpSRP54 and bacterial SRP54 except for a plant-specific C-terminal extension containing the cpSRP43-binding motif. We found that cpSRP54 of higher plants lacks the ability to bind SRP-RNA because of two amino acid substitutions within a region corresponding to the RNA binding domain of cytosolic SRP54, whereas the C-terminal extension does not affect RNA binding. Phylogenetic analysis revealed that these mutations occur in the cpSRP54 homologues of higher plants but not in most algae.

Christine V. Richter; Chantal Trger; Danja Schnemann

2008-01-01T23:59:59.000Z

355

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

356

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

357

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

358

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

359

Carcass characteristics and fatty acid-binding protein activity in tissues of porcine and bovine species fed elevated monounsaturated fats  

E-Print Network [OSTI]

CARCASS CHARACTERISTICS AND FATTY ACID ? BINDING PROTEIN ACTIVITY IN TISSUES OF PORCINE AND BOVINE SPECIES FED ELEVATED MONOUNSATURATED FATS A Thesis LORI CEANNE ST. JOHN Submitted to the Graduate College of Texas A g M University in partial... Thesis LORI CEANNE ST. JOHN Approved as to style and content by: S. B. ith (Chairman) H. R. Cross (Member) L. J. ' ger (Member) G. C. mit (Head of Department) May 1986 ABSTRACT Carcass Characteristics and Fatty Acid-Binding Protein Activity...

St. John, Lori Ceanne

2012-06-07T23:59:59.000Z

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,
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We encourage you to perform a real-time search of NLEBeta
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361

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

362

Structure of an Arrestin2-clathrin Complex Reveals a Novel Clathrin Binding Domain that Modulates Receptor Trafficking  

SciTech Connect (OSTI)

Non-visual arrestins play a pivotal role as adaptor proteins in regulating the signaling and trafficking of multiple classes of receptors. Although arrestin interaction with clathrin, AP-2, and phosphoinositides contributes to receptor trafficking, little is known about the configuration and dynamics of these interactions. Here, we identify a novel interface between arrestin2 and clathrin through x-ray diffraction analysis. The intrinsically disordered clathrin binding box of arrestin2 interacts with a groove between blades 1 and 2 in the clathrin {beta}-propeller domain, whereas an 8-amino acid splice loop found solely in the long isoform of arrestin2 (arrestin2L) interacts with a binding pocket formed by blades 4 and 5 in clathrin. The apposition of the two binding sites in arrestin2L suggests that they are exclusive and may function in higher order macromolecular structures. Biochemical analysis demonstrates direct binding of clathrin to the splice loop in arrestin2L, whereas functional analysis reveals that both binding domains contribute to the receptor-dependent redistribution of arrestin2L to clathrin-coated pits. Mutagenesis studies reveal that the clathrin binding motif in the splice loop is (L/I){sub 2}GXL. Taken together, these data provide a framework for understanding the dynamic interactions between arrestin2 and clathrin and reveal an essential role for this interaction in arrestin-mediated endocytosis.

Kang, D.; Kern, R; Puthenveedu, M; von Zastrow, M; Williams, J; Benovic, J

2009-01-01T23:59:59.000Z

363

Immunological properties of prolactin and studies on a gonadotropin binding inhibitor  

SciTech Connect (OSTI)

The physiological role of prolactin in horses has not yet been well defined. With the availability of highly purified ePRL for inducing antibody formation in rabbits and for radiolabeling with Na/sup 125/I, a very sensitive (0.4-0.6 ng/ml) and highly specific homologous RIA for ePRL was developed. A heterologous RIA using /sup 125/I-labeled ovine PRL and anti-ePRL antiserum was also developed and compared to the homologous RIA for ePRL. Of the two systems, it is concluded that this homologous RIA system is more suitable and more reliable for measuring prolactin concentration in horse serum samples. Until now, biochemical information on PRL has not been available for reptilian species. Sea turtle (Chelonia mydas) prolactin was purified from pituitary extracts by selective precipitation, DEAE-cellulose chromatography and gel filtration. Similar to other species of PRL, sea turtle PRL is a 22,000-24,000 daltons protein and contains a high content of glutamic acid, aspartic acid, serine and leucine, the N-terminal amino acid residue. Gonadotropin (FSH) binding inhibitor was partially purified from sheep testes by ammonium sulfate fractionation and ion exchange chromatography. The FSH-BI (molecular weight: 50,000 daltons, estimated by gel filtration) contains a protein moiety necessary for binding inhibitory activity. The inhibition of the binding of /sup 125/I-labeled ovine FSH to its receptor by the FSH-BI is not competitive. Both in vivo and in vitro biological studies of FSH-BI preparations in rats indicated various effects on FSH and LH activities at the gonadal level. These findings suggest a physiological role for FSH-BI in the regulation of reproduction.

Chang, Y.S.

1985-01-01T23:59:59.000Z

364

Effect of quark antisymmetrization on the binding energy of nuclear matter  

Science Journals Connector (OSTI)

We estimate, to leading order in the nuclear matter density, the effect of antisymmetrizing quarks belonging to different nucleons upon the binding energy per nucleon in nuclear matter. A simple Gaussian model for the nucleon quark wave function, together with a one-gluon-exchange potential between quarks, is assumed. Using a linked cluster expansion developed earlier for nuclear matter, we calculate separately the effect of quark interchanges upon the kinetic, hyperfine, Coulomb, and contact terms in the Hamiltonian. A strong net repulsion is found which grows rapidly with the dimensionless parameter ?=r0kF, where kF is the nuclear Fermi momentum and r0 the nucleon size.

Mohammad Nzar and Pervez Hoodbhoy

1990-10-01T23:59:59.000Z

365

Site-specific measurement of adatom binding energy differences by atom extraction with the STM  

Science Journals Connector (OSTI)

Using a scanning tunneling microscope, single adatoms can be extracted from a Si(111)77 surface by field evaporation, when the sample voltage is pulsed at 4 V or more in either polarity. Statistically, adatoms at the center of the 77 unit cell are more frequently removed than those near the corner holes, by a ratio of 1.6:1. This difference can be explained by assuming that the binding energy of center adatoms is approximately 0.01 eV less than for corner adatoms. The relationship of this result to previous observations of greater chemical reactivity at center adatom sites is discussed.

Hironaga Uchida; Dehuan Huang; Franois Grey; Masakazu Aono

1993-03-29T23:59:59.000Z

366

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

367

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

368

JC3 High Impact Assessment Bulletins | Department of Energy  

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

August 1, 2012 August 1, 2012 U-225: Citrix Access Gateway Plug-in for Windows nsepacom ActiveX Control Vulnerabilities Two vulnerabilities in Citrix Access Gateway Plug-in for Windows can be exploited by malicious people to compromise a user's system. July 30, 2012 U-223: Bugzilla May Disclose Confidential Information to Remote Users Two vulnerabilities were reported in Bugzilla. July 27, 2012 U-222: Apple Safari Bugs Let Remote Users Execute Arbitrary Code, Spoof the URL Address Bar, Conduct Cross-Site Scripting Attacks, and Obtain Potentially Sensitive Information Multiple vulnerabilities were reported in Apple Safari. July 26, 2012 U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability ISC BIND is prone to a denial-of-service vulnerability. July 24, 2012

369

JC3 Medium Impact Assessment Bulletins | Department of Energy  

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

3, 2012 3, 2012 U-227: bind-dyndb-ldap DN Escaping Flaw Lets Remote Users Deny Service A vulnerability has been reported in bind-dyndb-ldap, which can be exploited by malicious people to cause a DoS (Denial of Service). August 2, 2012 U-226: Linux Kernel SFC Driver TCP MSS Option Handling Denial of Service Vulnerability The Linux kernel is prone to a remote denial-of-service vulnerability. July 31, 2012 U-224: ISC DHCP Multiple Denial of Service Vulnerabilities ISC DHCP is prone to multiple denial-of-service vulnerabilities. July 25, 2012 U-220: Google Android DNS Resolver Randomization Flaw Lets Remote Users Poison the DNS Cache A remote user can poison the DNS cache. July 23, 2012 U-218: Cisco Linksys WMB54G TFTP Command Injection Vulnerability System access from local network

370

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

371

Autoradiographic evidence of nuclear binding of spironolactone in rabbit cortical collecting tubule  

SciTech Connect (OSTI)

Previous biochemical studies indicated that the spirolactone-mineralocorticoid receptor complexes are unable to translocate into the nucleus. The present study was designed to reinvestigate the intracellular distribution of spirolactone-binding sites, using autoradiography. For this purpose, rabbit kidney pyramids were incubated at 30 C with tritiated SC9420 or aldosterone. Thereafter, aldosterone-sensitive cortical collecting tubules were microdissected and processed for dry film autoradiography. The concentration was 2 nM for both steroids. Non-specific labeling was determined by incubations with tritiated steroids plus a 100-fold excess of unlabeled steroids. Results show the presence of specific nuclear labeling for both ({sup 3}H) aldosterone and ({sup 3}H)SC9420. Specific cytoplasmic labeling was very low for both ({sup 3}H)aldosterone and ({sup 3}H)SC9420. The nuclear labeling by ({sup 3}H)SC9420 was equally and almost completely displaced by a 100-fold excess of unlabeled aldosterone or SC9420 (91% and 87%, respectively). We conclude that spironolactone-receptor complexes migrate into the nucleus. The difference between these results and those of previous studies with biochemical techniques, which failed to detect specific nuclear binding of spirolactone, may be due to methodological reasons.

Bonvalet, J.P.; Blot-Chabaud, M.; Farman, N. (CEN Saclay, Gif-Yvette (France))

1991-01-01T23:59:59.000Z

372

A single domain thermophilic xylanase can bind insoluble xylan: evidence for surface aromatic clusters  

Science Journals Connector (OSTI)

A clone expressing xylanase activity in Escherichia coli has been selected from a genomic plasmid library of the thermophilic Bacillus strain D3. Subcloning from the 9-kb insert located the xylanase activity to a 2.7-kb HindII/BamHI fragment. The DNA sequence of this clone revealed an ORF of 367 codons encoding a single domain type-F or family 10 enzyme, which was designated as XynA. Purification of the enzyme following over-expression in E. coli produced an enzyme of 42 kDa with a temperature optimum of 75C which can efficiently bind and hydrolyse insoluble xylan. The pH optimum of the enzyme is 6.5, but it is active over a broad pH range. A homology model of the xylanase has been constructed which reveals a series of surface aromatic residues which form hydrophobic clusters. This unusual structural feature is strikingly similar to the situation observed in the structure determined for the type-G xylanase from the Bacillus D3 strain and may constitute a common evolutionary mechanism imposed on different structural frameworks by which these xylanases may bind potential substrates and exhibit thermostability.

Ian Connerton; Nicola Cummings; Gillian W. Harris; Philippe Debeire; Christelle Breton

1999-01-01T23:59:59.000Z

373

Tight-binding study of the electronic structure of amorphous silicon  

Science Journals Connector (OSTI)

We have performed tight-binding calculations on a model of an amorphous silicon sample generated previously by a molecular-dynamics simulation employing the Stillinger-Weber potential. The sample consists of 588 atoms and contains a high density of floating-bond defects. Two tight-binding calculations are presented, one using the widely accepted Chadi parameters, which include only nearest-neighbor interactions, and the other using the parameters recently proposed by Allen, Broughton, and McMahan (ABM) [Phys. Rev. B 34, 859 (1986)] for a nonorthogonal basis set. Comparison of the densities of states shows similar behavior in the valence band, but the electron density near a defect is less localized with the ABM parameters. It is also found that the projected density of states on the fivefold-coordinated atoms is very close to that on the fourfold-coordinated atoms, while the projected density of states on the threefold-coordinated atoms is distinctly different and has more states in the gap.

James L. Mercer; Jr. and M. Y. Chou

1991-03-15T23:59:59.000Z

374

Structural Insights into RNA Recognition by the Alternate-Splicing Regulator CUG-Binding Protein 1  

SciTech Connect (OSTI)

CUG-binding protein 1 (CUGBP1) regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of myotonic dystrophy. CUGBP1 harbors three RRM domains and preferentially targets UGU-rich mRNA elements. We describe crystal structures of CUGBP1 RRM1 and tandem RRM1/2 domains bound to RNAs containing tandem UGU(U/G) elements. Both RRM1 in RRM1-RNA and RRM2 in RRM1/2-RNA complexes use similar principles to target UGU(U/G) elements, with recognition mediated by face-to-edge stacking and water-mediated hydrogen-bonding networks. The UG step adopts a left-handed Z-RNA conformation, with the syn guanine recognized through Hoogsteen edge-protein backbone hydrogen-bonding interactions. NMR studies on the RRM1/2-RNA complex establish that both RRM domains target tandem UGUU motifs in solution, whereas filter-binding assays identify a preference for recognition of GU over AU or GC steps. We discuss the implications of CUGBP1-mediated targeting and sequestration of UGU(U/G) elements on pre-mRNA alternative-splicing regulation, translational regulation, and mRNA decay.

M Teplova; J Song; H Gaw; A Teplov; D Patel

2011-12-31T23:59:59.000Z

375

Ab initio study of dihydrogen binding in metal-decorated polyacetylene for hydrogen storage  

Science Journals Connector (OSTI)

Using first-principles calculations based on the density-functional theory, we perform a detailed study of the dihydrogen (H2) binding in cis- and trans-polyacetylene decorated with transition metal atoms. First, we investigate the origin of metal-dihydrogen bonding and observe the hybridization of eg (t2g) orbitals of the Ti atom with the ? (?*) orbitals of the H2 molecules in octahedral geometries, which is consistent with the Kubas model. Second, using a statistical model parametrized by the results of ab initio calculations and experimental data, the adsorption and desorption of molecular hydrogens are calculated at ambient temperature and pressure. We find that the usable capacity at ambient conditions is dramatically reduced from the maximum capacity, the zero-point energy affects the storage capacity significantly, and the optimal binding energy of H2 molecules under practical conditions is ?0.3eV?H2. Third, we examine the effects of the aggregation and intercalation of the Ti atoms on H2 adsorption.

Hoonkyung Lee; Woon Ih Choi; Manh Cuong Nguyen; Moon-Hyun Cha; Eungook Moon; Jisoon Ihm

2007-11-09T23:59:59.000Z

376

Crystal structure of Plasmodium falciparum phosphoglycerate kinase: Evidence for anion binding in the basic patch  

SciTech Connect (OSTI)

3-Phosphoglycerate kinase (EC 2.7.2.3) is a key enzyme in the glycolytic pathway and catalyzes an important phosphorylation step leading to the production of ATP. The crystal structure of Plasmodium falciparum phosphoglycerate kinase (PfPGK) in the open conformation is presented in two different groups, namely I222 and P6{sub 1}22. The structure in I222 space group is solved using MAD and refined at 3 {angstrom} whereas that in P6{sub 1}22A is solved using MR and refined at 2.7 {angstrom}. I222 form has three monomers in asymmetric unit whereas P6{sub 1}22 form has two monomers in the asymmetric unit. In both crystal forms a sulphate ion is located at the active site where ATP binds, but no Mg{sup 2+} ion is observed. For the first time another sulphate ion is found at the basic patch where the 3-phosphate of 1,3-biphosphoglycerate normally binds. This was found in both chains of P6{sub 1}22 form but only in chain A of I222 form.

Smith, Craig D.; Chattopadhyay, Debasish; Pal, Biswajit (UAB)

2012-11-09T23:59:59.000Z

377

NMr studies of the AMP binding site and mechanism of adenylate kinase  

SciTech Connect (OSTI)

The authors recently located by NMR the MgATP binding site on adenylate kinase correcting the proposed location for this site based on X-ray studies of the binding of salicylate. To determine the conformation and location of the other substrate, they have determined distances from Cr/sup 3 +/ AMPPCP to 6 protons and to the phosphorus atom of AMP on adenylate kinase using the paramagnetic-probe-T/sub 1/ method. They have also used time-dependent NOEs to measure five interproton distances on AMP, permitting evaluation of the conformation of enzyme-bound AMP and its position with respect to metal-ATP. Enzyme-bound AMP exhibits a high-anti glycosyl torsional angle (X = 110/sup 0/), a 3'-endo sugar pucker (delta = 105/sup 0/), and a gauche-trans orientation about the C/sub 4/'-C/sub 5/' bond (..gamma.. = 180/sup 0/). The distance from Cr/sup 3 +/ to the phosphorus of AMP is 6.4 +/- 0.3 A, indicating a reaction coordinate distance of greater than or equal to A which is consistent with an associative SN2 mechanism for the phosphoryl transfer. Ten intermolecular NOEs, from protons of the enzyme to those of AMP were detected. These constraints, together with the conformation of AMP and the X-ray structure of the enzyme, suggest proximity (less than or equal to A) of AMP to leu 116, arg 171, val 173, gln 185, thr 188, and asp 191.

Kuby, S.A.; Fry, D.C.; Mildvan, A.S.

1986-05-01T23:59:59.000Z

378

Binding motifs in bacterial gene promoters modulate transcriptional effects of global regulators CRP and ArcA  

SciTech Connect (OSTI)

Bacterial gene regulation involves transcription factors (TF) that bind to DNA recognition sequences in operon promoters. These recognition sequences, many of which are palindromic, are known as regulatory elements or transcription factor binding sites (TFBS). Some TFs are global regulators that can modulate the expression of hundreds of genes. In this study we examine global regulator half-sites, where a half-site, which we shall call a binding motif (BM), is one half of a palindromic TFBS. We explore the hypothesis that the number of BMs plays an important role in transcriptional regulation, examining empirical data from transcriptional profiling of the CRP and ArcA regulons. We compare the power of BM counts and of full TFBS characteristics to predict induced transcriptional activity. We find that CRP BM counts have a nonlinear effect on CRP-dependent transcriptional activity and predict this activity better than full TFBS quality or location.

Leuze, Mike; Karpinets, Tatiana V.; Syed, Mustafa H.; Beliaev, Alex S.; Uberbacher, Edward

2012-05-30T23:59:59.000Z

379

One-step synthesis of efficient binding-inhibitor for influenza virus through multiple addition of sialyloligosaccharides on chitosan  

Science Journals Connector (OSTI)

We have succeeded in one-step synthesis of an efficient binding-inhibitor for influenza virus, which is composed of only sugar chains. This binding-inhibitor utilizes the carbohydrate recognition of influenza virus, thus it can prevent the virus from infection. We modified chitosan with multiple sialyl saccharides, ?2,6-sialyllactose or free sialyl glycan, using reductive amination reaction. The resulting inhibitors showed sufficient inhibitory activity against influenza virus infection in MDCK cells compared to that of ?2,6-sialyllactose or free sialyl glycan. Unlike the other binding-inhibitors of influenza virus, this virus inhibitor of sugar chains requires only one step in its synthesis. Therefore this inhibitor is suitable for use in products such as filters and masks.

Myco Umemura; Yutaka Makimura; Masae Itoh; Takeshi Yamamoto; Toshiki Mine; Seiji Mitani; Ichiro Simizu; Hisashi Ashida; Kenji Yamamoto

2010-01-01T23:59:59.000Z

380

A van der Waals density functional study of adenine on graphene: Single molecular adsorption and overlayer binding  

SciTech Connect (OSTI)

The adsorption of an adenine molecule on graphene is studied using a first-principles van der Waals functional (vdW-DF) [Dion et al., Phys. Rev. Lett. 92, 246401 (2004)]. The cohesive energy of an ordered adenine overlayer is also estimated. For the adsorption of a single molecule, we determine the optimal binding configuration and adsorption energy by translating and rotating the molecule. The adsorption energy for a single molecule of adenine is found to be 711 meV, which is close to the calculated adsorption energy of the similar-sized naphthalene. Based on the single molecular binding configuration, we estimate the cohesive energy of a two-dimensional ordered overlayer. We find a significantly stronger binding energy for the ordered overlayer than for single-molecule adsorption.

Berland, Kristian [Chalmers University of Technology, Sweden; Cooper, Valentino R [ORNL; Langreth, David C. [Rutgers University; Schroder, Prof. Elsebeth [Chalmers University of Technology, Sweden; Chakarova-Kack, Svetla [Chalmers University of Technology, Sweden

2011-01-01T23:59:59.000Z

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.


381

IQGAP Proteins Reveal an Atypical Phosphoinositide (aPI) Binding Domain with a Pseudo C2 Domain Fold  

SciTech Connect (OSTI)

Class I phosphoinositide (PI) 3-kinases act through effector proteins whose 3-PI selectivity is mediated by a limited repertoire of structurally defined, lipid recognition domains. We describe here the lipid preferences and crystal structure of a new class of PI binding modules exemplified by select IQGAPs (IQ motif containing GTPase-activating proteins) known to coordinate cellular signaling events and cytoskeletal dynamics. This module is defined by a C-terminal 105-107 amino acid region of which IQGAP1 and -2, but not IQGAP3, binds preferentially to phosphatidylinositol 3,4,5-trisphosphate (PtdInsP3). The binding affinity for PtdInsP3, together with other, secondary target-recognition characteristics, are comparable with those of the pleckstrin homology domain of cytohesin-3 (general receptor for phosphoinositides 1), an established PtdInsP3 effector protein. Importantly, the IQGAP1 C-terminal domain and the cytohesin-3 pleckstrin homology domain, each tagged with enhanced green fluorescent protein, were both re-localized from the cytosol to the cell periphery following the activation of PI 3-kinase in Swiss 3T3 fibroblasts, consistent with their common, selective recognition of endogenous 3-PI(s). The crystal structure of the C-terminal IQGAP2 PI binding module reveals unexpected topological similarity to an integral fold of C2 domains, including a putative basic binding pocket. We propose that this module integrates select IQGAP proteins with PI 3-kinase signaling and constitutes a novel, atypical phosphoinositide binding domain that may represent the first of a larger group, each perhaps structurally unique but collectively dissimilar from the known PI recognition modules.

Dixon, Miles J.; Gray, Alexander; Schenning, Martijn; Agacan, Mark; Tempel, Wolfram; Tong, Yufeng; Nedyalkova, Lyudmila; Park, Hee-Won; Leslie, Nicholas R.; van Aalten, Daan M.F.; Downes, C. Peter; Batty, Ian H. (Toronto); (Dundee)

2012-10-16T23:59:59.000Z

382

Interaction of Salivary alpha-Amylase and Amylase-Binding-Protein A (AbpA) ofStreptococcus gordoniiwith Glucosyltransferase ofS. gordoniiandStreptococcus mutans  

Science Journals Connector (OSTI)

Glucosyltransferases (Gtfs), enzymes that produce extracellular glucans from dietary sucrose, contribute to dental plaque formation byStreptococcus gordoniiandStreptococcus mutans. The alpha-amylase-binding prote...

Biswendu Chaudhuri; Jennifer Rojek; M Margaret Vickerman

2007-06-01T23:59:59.000Z

383

Fluorescence-detected assembly of the signal recognition particle: binding of the two SRP protein heterodimers to SRP RNA is noncooperative  

Science Journals Connector (OSTI)

Fluorescence-detected assembly of the signal recognition particle: binding of the two SRP protein heterodimers to SRP RNA is noncooperative ...

Fabiola Janiak; Peter Walter; Arthur E. Johnson

1992-06-01T23:59:59.000Z

384

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

385

Structure of the second RRM domain of Nrd1, a fission yeast MAPK target RNA binding protein, and implication for its RNA recognition and regulation  

SciTech Connect (OSTI)

Highlights: Solution structure of the second RRM of Nrd1 was determined. RNA binding site of the second RRM was estimated. Regulatory mechanism of RNA binding by phosphorylation is discussed. -- Abstract: Negative regulator of differentiation 1 (Nrd1) is known as a negative regulator of sexual differentiation in fission yeast. Recently, it has been revealed that Nrd1 also regulates cytokinesis, in which physical separation of the cell is achieved by a contractile ring comprising many proteins including actin and myosin. Cdc4, a myosin II light chain, is known to be required for cytokinesis. Nrd1 binds and stabilizes Cdc4 mRNA, and thereby suppressing the cytokinesis defects of the cdc4 mutants. Interestingly, Pmk1 MAPK phosphorylates Nrd1, resulting in markedly reduced RNA binding activity. Furthermore, Nrd1 localizes to stress granules in response to various stresses, and Pmk1 phosphorylation enhances the localization. Nrd1 consists of four RRM domains, although the mechanism by which Pmk1 regulates the RNA binding activity of Nrd1 is unknown. In an effort to delineate the relationship between Nrd1 structure and function, we prepared each RNA binding domain of Nrd1 and examined RNA binding to chemically synthesized oligo RNA using NMR. The structure of the second RRM domain of Nrd1 was determined and the RNA binding site on the second RRM domain was mapped by NMR. A plausible mechanism pertaining to the regulation of RNA binding activity by phosphorylation is also discussed.

Kobayashi, Ayaho; Kanaba, Teppei [Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji 192-0397 (Japan)] [Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji 192-0397 (Japan); Satoh, Ryosuke [Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku 141-0021, Tokyo (Japan)] [Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku 141-0021, Tokyo (Japan); Fujiwara, Toshinobu [Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku 141-0021, Tokyo (Japan) [Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku 141-0021, Tokyo (Japan); Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku,Nagoya 467-8603 (Japan); Ito, Yutaka [Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji 192-0397 (Japan)] [Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji 192-0397 (Japan); Sugiura, Reiko [Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka 577-8502 (Japan)] [Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka 577-8502 (Japan); Mishima, Masaki, E-mail: mishima-masaki@tmu.ac.jp [Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji 192-0397 (Japan)] [Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji 192-0397 (Japan)

2013-07-19T23:59:59.000Z

386

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

387

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

388

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

389

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

390

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

391

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

392

Repertoire Selection of Variant Single-Chain Cro:? Toward Directed DNA-Binding Specificity of Helix?Turn?Helix Proteins  

Science Journals Connector (OSTI)

Utilizing phage display-afforded affinity selection, scCro variants have been isolated for binding to synthetic DNA ligands. ... Variant proteins with altered DNA-sequence specificity were identified, which favored binding of targeted synthetic DNA sequences over a consensus operator sequence, bound with high affinity by wild-type Cro. ... The specificities were relatively modest (2?3-fold, as calculated from KD values), which can be attributed to the inherent properties in the design of the selection system; one half-site of the synthetic DNA sequences maintains the consensus operator sequence, and one subunit of the variant single-chain Cro dimers was conserved as wild-type sequence. ...

Mikael T. I. Nilsson; Mikael Widersten

2004-08-28T23:59:59.000Z

393

Dependence of Nuclear Binding Energies on the Cutoff Momentum of Low-Momentum Nucleon-Nucleon Interaction  

E-Print Network [OSTI]

Binding energies of ^{3}H, ^{4}He, and ^{16}O are calculated, using low-momentum nucleon-nucleon interactions (V_{low-k}) for a wide range of the cutoff momentum \\Lambda. In addition, single-particle energies in nuclei around ^{16}O are computed. The dependence of the binding energies and the single-particle energies in these nuclei on the cutoff momentum \\Lambda of the V_{low-k} is examined. Furthermore, the availability of the V_{low-k} in nuclear structure calculations is discussed.

S. Fujii; H. Kamada; R. Okamoto; K. Suzuki

2004-06-30T23:59:59.000Z

394

Structure of Human Toll-like Receptor 3 (TLR3) Ligand-binding Domain  

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

Human Toll-like Receptor Human Toll-like Receptor 3 (TLR3) Ligand-binding Domain Jungwoo Choe1, Matthew S. Kelker1, and Ian A. Wilson1 1Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 Figure 1. Overall structure of human TLR3 ECD. The N-terminal region is colored blue, the 23 canonical LRRs are in yellow and the C-terminal region is in pink. N-linked sugars that are observed in the electron density maps are shown in ball-and-stick. (From Choe et al. 2005). Innate immunity is the front line host defense that acts within minutes of infection to counter invasion by microorganisms. Members of the Toll-like receptor (TLR) family recognize conserved pathogen-associated molecular

395

DNA Nanostructures as Models for Evaluating the Role of Enthalpy and Entropy in Polyvalent Binding  

SciTech Connect (OSTI)

DNA nanotechnology allows the design and construction of nanoscale objects that have finely tuned dimensions, orientation, and structure with remarkable ease and convenience. Synthetic DNA nanostructures can be precisely engineered to model a variety of molecules and systems, providing the opportunity to probe very subtle biophysical phenomena. In this study, several such synthetic DNA nanostructures were designed to serve as models to study the binding behavior of polyvalent molecules and gain insight into how small changes to the ligand/receptor scaffolds, intended to vary their conformational flexibility, will affect their association equilibrium. This approach has yielded a quantitative identification of the roles of enthalpy and entropy in the affinity of polyvalent DNA nanostructure interactions, which exhibit an intriguing compensating effect.

Nangreave, Jeanette; Yan, Hao; Liu, Yan

2011-01-01T23:59:59.000Z

396

Tight-Binding Modeling and Low-Energy Behavior of the Semi-Dirac Point  

Science Journals Connector (OSTI)

We develop a tight-binding model description of semi-Dirac electronic spectra, with highly anisotropic dispersion around point Fermi surfaces, recently discovered in electronic structure calculations of VO2-TiO2 nanoheterostructures. We contrast their spectral properties with the well-known Dirac points on the honeycomb lattice relevant to graphene layers and the spectra of bands touching each other in zero-gap semiconductors. We also consider the lowest order dispersion around one of the semi-Dirac points and calculate the resulting electronic energy levels in an external magnetic field. In spite of apparently similar electronic structures, Dirac and semi-Dirac systems support diverse low-energy physics.

S. Banerjee; R. R. P. Singh; V. Pardo; W. E. Pickett

2009-07-01T23:59:59.000Z

397

CO2-Binding Organic Liquids, an Integrated Acid Gas Capture System  

SciTech Connect (OSTI)

Amine systems are effective for CO2 capture, but they are still inefficient because the solvent regeneration energy is largely defined by the amount of water in the process. Most amines form heat-stable salts with SO2 and COS resulting in parasitic solvent loss and degradation. Stripping the CO2-rich solvent is energy intensive it requires temperatures above 100 ?C due to the high specific heat and heat of vaporization of water. CO2-capture processes could be much more energy efficient in a water free amine process. In addition, if the capture-material is chemically compatible with other acid gases, less solvent would be lost to heat-stable salts and the process economics would be further improved. One such system that can address these concerns is Binding Organic Liquids (BOLs), a class of switchable ionic liquids.

Heldebrant, David J.; Koech, Phillip K.; Rainbolt, James E.; Zheng, Feng

2011-04-01T23:59:59.000Z

398

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

399

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

400

Tight-binding theory of spin-orbit coupling in graphynes  

Science Journals Connector (OSTI)

We investigate the effects of Rashba and intrinsic spin-orbit couplings (SOC) in graphynes. First, we develop a general method to address spin-orbit couplings within the tight-binding theory. Then, we apply this method to ?-, ?-, and ?-graphyne, and determine the SOC parameters in terms of the microscopic hopping and onsite energies. We find that for ?-graphyne, as in graphene, the intrinsic SOC opens a nontrivial gap, whereas the Rashba SOC splits each Dirac cone into four. In ?- and ?-graphyne, the Rashba SOC can lead to a Lifshitz phase transition, thus transforming the zero-gap semiconductor into a gapped system or vice versa, when pairs of Dirac cones annihilate or emerge. The existence of internal (within the benzene ring) and external SOC in these compounds allows us to explore a myriad of phases not available in graphene.

Guido van Miert; Vladimir Juri?i?; Cristiane Morais Smith

2014-11-11T23:59:59.000Z

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

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

402

Trp22, Trp24, and Tyr8 Play a Pivotal Role in the Binding of the Family 10 Cellulose-Binding Module from Pseudomonas Xylanase A to Insoluble Ligands+  

E-Print Network [OSTI]

-bromosuccinimide indicated that Trp22 and Trp24 were on the surface of the protein, while Trp7 was buried. Collectively of five CBMs that bind cellulose and one that interacts with xylan, from five different families, have been solved (3-8). Each protein contains several surface aromatic residues, which site

Williamson, Mike P.

403

Precisely Defined ProteinPolymer Conjugates: Construction of Synthetic DNA Binding Domains on Proteins by Using Multivalent Dendrons  

Science Journals Connector (OSTI)

Precisely Defined ProteinPolymer Conjugates: Construction of Synthetic DNA Binding Domains on Proteins by Using Multivalent Dendrons ... The authors describe the parallel synthesis of a library comprising 146 nanoparticles decorated with different synthetic small mols. ... (a) Newkome, G. R.; Moorefield, C. N.; Vgtle, F. Dendrimers and Dendrons:Concepts, Syntheses, Applications; Wiley-VCH: Weinheim, 2001. ...

Mauri A. Kostiainen; Gza R. Szilvay; Julia Lehtinen; David K. Smith; Markus B. Linder; Arto Urtti; Olli Ikkala

2007-08-25T23:59:59.000Z

404

Highly Sensitive in Vitro Selections for DNA-Linked Synthetic Small Molecules with Protein Binding Affinity and Specificity  

E-Print Network [OSTI]

Highly Sensitive in Vitro Selections for DNA-Linked Synthetic Small Molecules with Protein Binding oligonucleotides to corresponding synthetic molecules, either as a consequence of DNA-templated organic synthesis3 or as a result of conjugating DNA to synthetic molecules, in theory enables synthetic molecules to satisfy

Liu, David R.

405

Single-Molecule Detection of Transcription Factor Binding to DNA in Real Time:? Specificity, Equilibrium, and Kinetic Parameters  

Science Journals Connector (OSTI)

Preparation of Synthetic DNA Duplexes. ... DNA targets for the proteins consisted of short synthetic DNA duplexes formed from oligonucleotides purchased from Integrated DNA Technologies. ... Binding of synthetic DNA duplexes was tested by measuring the ability of duplexes labeled with the quencher dabcyl to quench GFP or BFL emission, because the excitation spectrum of dabcyl overlaps with the emission spectrum of these fluorophores. ...

Eric A. Nalefski; Eugene Nebelitsky; Janice A. Lloyd; Steven R. Gullans

2006-10-31T23:59:59.000Z

406

Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs  

Science Journals Connector (OSTI)

...orange squares, exp, Yun et al.; green diamonds, calculation. Table-1. Binding...Black line, WT; red line, G719S; green line, L858R; navy blue line, T790M...Kollman, and D. A. Case 1998 Continuum solvent studies of the stability of DNA, RNA...

2011-01-01T23:59:59.000Z

407

The Bacteroides fragilis BtgA Mobilization Protein Binds to the oriT Region of pBFTM10  

Science Journals Connector (OSTI)

...conformational change of the nick site. TraK is not required...It binds downstream of the nick site over an approximate 180-nucleotide...inverted repeats, and possible nick site, raises the possibility...Administration Medical Research Service Merit Review grant 001. We thank...

Leonid A. Sitailo; Alexander M. Zagariya; Patrick J. Arnold; Gayatri Vedantam; David W. Hecht

1998-09-01T23:59:59.000Z

408

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data  

Science Journals Connector (OSTI)

......size to the original dataset, selected at random...using TRANSFAC data for nuclear hormone receptor proteins...3 Similarity of the nuclear hormone receptor DNA-binding...of HNF4alpha and each nuclear hormone receptor protein...cross-validation error for each dataset were corrupted with varying......

Kenzie D. MacIsaac; D. Benjamin Gordon; Lena Nekludova; Duncan T. Odom; Joerg Schreiber; David K. Gifford; Richard A. Young; Ernest Fraenkel

2006-02-15T23:59:59.000Z

409

Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein  

Science Journals Connector (OSTI)

A neutron crystallographic study of perdeuterated transthyretin reveals important aspects of the structure relating to its stability and its propensity to form fibrils, as well as evidence of a single water molecule that affects the symmetry of the two binding pockets.

Haupt, M.

2014-10-21T23:59:59.000Z

410

The structure of cytomegalovirus immune modulator UL141 highlights structural Ig-fold versatility for receptor binding  

Science Journals Connector (OSTI)

The crystal structure of Human cytomegalovirus immune modulator UL141 was solved at 3.25 ? resolution. Here, a detailed analysis of its intimate dimerization interface and the biophysical properties of its receptor (TRAIL-R2 and CD155) binding interactions are presented.

Nemcovicov?, I.

2014-02-22T23:59:59.000Z

411

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

412

Cellulose Binding Protein from the Parasitic Nematode Heterodera schachtii Interacts with Arabidopsis Pectin Methylesterase: Cooperative Cell Wall Modification during Parasitism  

Science Journals Connector (OSTI)

...Two-week-old seedlings were inoculated with 250 surface-sterilized J2 Heterodera schachtii or...d, each plant was inoculated with 150 surface-sterilized J2 of H. schachtii, and...recognition of plant cell walls by microbial xylan-specific carbohydrate-binding modules...

Tarek Hewezi; Peter Howe; Tom R. Maier; Richard S. Hussey; Melissa Goellner Mitchum; Eric L. Davis; Thomas J. Baum

2008-11-11T23:59:59.000Z

413

Cellulose Binding Protein from the Parasitic Nematode Heterodera schachtii Interacts with Arabidopsis Pectin Methylesterase: Cooperative Cell Wall Modification during Parasitism  

Science Journals Connector (OSTI)

...seedlings were inoculated with 250 surface-sterilized J2 Heterodera...plant was inoculated with 150 surface-sterilized J2 of H. schachtii...manufacturers instructions. DNase treatment of total RNA was performed...plant cell walls by microbial xylan-specific carbohydrate-binding...

Tarek Hewezi; Peter Howe; Tom R. Maier; Richard S. Hussey; Melissa Goellner Mitchum; Eric L. Davis; Thomas J. Baum

2008-11-11T23:59:59.000Z

414

Mapping of the SecA Signal Peptide Binding Site and Dimeric Interface by Using the Substituted Cysteine Accessibility Method  

Science Journals Connector (OSTI)

...binding induces changes in the oligomeric state and conformation of Sec A in a lipid environment: a small-angle neutron-scattering study. J. Mol. Biol. 332 :23-30. 13. Or E , A Navon, and T Rapoport. 2002. Dissociation of the dimeric...

Meera K. Bhanu; Ping Zhao; Debra A. Kendall

2013-08-09T23:59:59.000Z

415

Heparan Sulfate Glycosaminoglycans Are Receptors Sufficient To Mediate the Initial Binding of Adenovirus Types 2 and 5  

Science Journals Connector (OSTI)

...Therefore, the experiments in CAR-defective CHO K1 il cells grown at low...experiments performed. Ad binding to CAR-defective recombinant CHO cells as a function...density. Ad2 is able to infect CAR-defective CHO K1 il cells in a time-dependent...

M. C. Dechecchi; P. Melotti; A. Bonizzato; M. Santacatterina; M. Chilosi; G. Cabrini

2001-09-01T23:59:59.000Z

416

Use of Cre/loxP recombination to swap cell binding motifs on the adenoviral capsid protein IX  

SciTech Connect (OSTI)

We used Cre/loxP recombination to swap targeting ligands present on the adenoviral capsid protein IX (pIX). A loxP-flanked sequence encoding poly-lysine (pK-binds heparan sulfate proteoglycans) was engineered onto the 3'-terminus of pIX, and the resulting fusion protein allowed for routine virus propagation. Growth of this virus on Cre-expressing cells removed the pK coding sequence, generating virus that could only infect through alternative ligands, such as a tyrosine kinase receptor A (TrkA)-binding motif engineered into the capsid fibre protein for enhanced infection of neuronal cells. We used a similar approach to swap the pK motif on pIX for a sequence encoding a single-domain antibody directed towards CD66c for targeted infection of cancer cells; Cre-mediated removal of the pK-coding sequence simultaneously placed the single-domain antibody coding sequence in frame with pIX. Thus, we have developed a simple method to propagate virus lacking native viral tropism but containing cell-specific binding ligands. - Highlights: > We describe a method to grow virus lacking native tropism but containing novel cell-binding ligands. > Cre/loxP recombination was used to modify the adenovirus genome. > A targeting ligand present on capsid protein IX was removed or replaced using recombination. > Cre-loxP was also used to 'swap' the identity of the targeting ligand present on pIX.

Poulin, Kathy L. [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Tong, Grace; Vorobyova, Olga [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Pool, Madeline [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario (Canada); Kothary, Rashmi [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario (Canada); Department of Medicine, University of Ottawa, Ottawa, Ontario (Canada); Parks, Robin J., E-mail: rparks@ohri.ca [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Department of Medicine, University of Ottawa, Ottawa, Ontario (Canada); Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario (Canada)

2011-11-25T23:59:59.000Z

417

Identification of small-molecule binding pockets in the soluble monomeric form of the A?42 peptide  

Science Journals Connector (OSTI)

The aggregation of intrinsically disordered peptides and proteins is associated with a wide range of highly debilitating neurological and systemic disorders. In this work we explored the potential of a structure-based drug discovery procedure to target one such system the soluble monomeric form of the A?42 peptide. We utilised for this purpose a set of structures of the A?42 peptide selected from clusters of conformations within an ensemble generated by molecular dynamics simulations. Using these structures we carried out fragment mapping calculations to identify binding hot spots on the monomeric form of the A?42 peptide. This procedure provided a set of hot spots with ligand efficiencies comparable to those observed for structured proteins and clustered into binding pockets. Such binding pockets exhibited a propensity to bind small molecules known to interact with the A?42 peptide. Taken together these results provide an initial indication that fragment-based drug discovery may represent a potential therapeutic strategy for diseases associated with the aggregation of intrinsically disordered proteins.

Michele Vendruscolo

2013-01-01T23:59:59.000Z

418

A New Trick for an Old Dog: TraY Binding to a Homopurine-homopyrimidine Run Attenuates  

E-Print Network [OSTI]

progression in E. coli strains carrying FH episomes. The potency of replica- tion stalling increased, or transcription through the repeat. Treatment of E. coli cells with the protein synthesis inhibitor. Overexpression of an individual TraY protein in the F ? E. coli strain con- veyed d(GA)n Ád(TC)n-binding activity

Mirkin, Sergei

419

CELL REGULATION, Vol. 2, 851-859, October 1991 An ATP-binding membrane protein is required for  

E-Print Network [OSTI]

steps: signal sequence recognition by signal recognition particle (SRP), targeting to the ER via the SRP chain (Rapoport, 1990). Both SRP and SRP re- ceptor bind GTP (Connolly and Gilmore, 1989; Miller, GTP hydrolysis by SRP and SRP receptor probably does not contribute to the vectorial movement

Walter, Peter

420

Cell, Vol. 94, 181191, July 24, 1998, Copyright 1998 by Cell Press Crystal Structure of the Signal Sequence Binding  

E-Print Network [OSTI]

with their eukary- otic counterparts, SRP54, SRP RNA, and the SRP re- ceptor. Ffh is essential for viability of the SRP- dependent cotranslational targeting pathway blocks theSchool of Medicine University of California; Valent et al., 1995) and substitutes for the signal se- quence binding activity of SRP54 when

Walter, Peter

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

RNA Interference of Signal Peptide-binding Protein SRP54 Elicits Deleterious Effects and Protein Sorting Defects in Trypanosomes*  

E-Print Network [OSTI]

RNA Interference of Signal Peptide-binding Protein SRP54 Elicits Deleterious Effects and Protein recognition particle (SRP) has a unique composition compared with all known SRP complexes, because it contains the essentiality of the SRP pathway and its role in protein translocation in Trypanosoma brucei. The production

Unger, Ron

422

Translocation of Proteins Across the Endoplasmic Reticulum I . Signal Recognition Protein (SRP) Binds to In-Vitro-  

E-Print Network [OSTI]

Translocation of Proteins Across the Endoplasmic Reticulum I . Signal Recognition Protein (SRP protein, termed signal recognition protein (SRP), has been shown here (a) to inhibit translation-affinity binding as wel l as the selective translation- inhibitory effect were abol ished after modification of SRP

Walter, Peter

423

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

424

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.

425

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

426

Arabidopsis EIN3-binding F-box 1 and 2 form ubiquitin-protein ligases that repress ethylene action  

E-Print Network [OSTI]

Arabidopsis EIN3-binding F-box 1 and 2 form ubiquitin-protein ligases that repress ethylene action-box proteins, EBF1 and -2, that work coordinately in SCF complexes to repress ethylene action. Mutations in either gene cause hypersensitivity to exogenous ethylene and its precursor 1-aminocyclopropane-1

Sheen, Jen

427

Electron microprobe and X-ray microfluorescence analyses of copper binding to active and inactivated cells of Mucor rouxii  

SciTech Connect (OSTI)

Electron microprobe and x-ray microfluorescence spectroscopies have been used to study copper binding to active and inactivated Mucor rouxii copper-sensitive and copper-tolerant cells. A better understanding of metal resistance may help in the application of fungal biomass for the treatment of metal-contaminated water, and also in enrichment or recycling of valuable metals. After repeated culturing in progressively higher concentrations of copper sulfate, a copper-tolerant Mucor rouxii strain was obtained. The copper-tolerant strain differed from the sensitive parental strain in both shape and size. Copper binding studies using a laboratory batch technique revealed that the copper-tolerant strain cultured at higher copper levels bound large amounts of this metal. Electron microprobe and x-ray microfluorescence analyses showed that the copper characteristic x-ray signal on the cell surface of the copper-tolerant strain after copper binding was higher than the copper signal in sensitive cells. The copper signal in cross sections of the copper-tolerant cells also showed a statistically significant correlation with the sulfur signal but no correlation with the phosphorus signal. These results suggest that there are several mechanisms for metal detoxification inside and outside of the Mucor rouxii cells and that copper may be binding to sulfur-containing groups.

Cano-Aguilera, I.; Gardea-Torresdey, J.L.; Pingitore, N.E. Jr.; Webb, R. [Univ. of Texas, El Paso, TX (United States)

1997-12-31T23:59:59.000Z

428

Discovery of New Small Molecules Targeting the Vitronectin-Binding Site of the Urokinase Receptor That Block Cancer Cell Invasion  

Science Journals Connector (OSTI)

...364 compounds) were extracted by the website (31) and prepared using LigPrep software...Protein Data Bank). Before starting the search, the binding site for vitronectin was...Biochem J 2001;358:673-9. 38. Bodary SC , McLean JW.The integrin beta 1 subunit...

Vincenza Elena Anna Rea; Antonio Lavecchia; Carmen Di Giovanni; Francesca Wanda Rossi; Anna Gorrasi; Ada Pesapane; Amato de Paulis; Pia Ragno; and Nunzia Montuori

2013-08-01T23:59:59.000Z

429

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

430

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.

431

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.

432

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

433

Single Molecule Force Spectroscopy of Salt-dependent Bacteriophage T7 Gene 2.5 Protein Binding to  

E-Print Network [OSTI]

Single Molecule Force Spectroscopy of Salt-dependent Bacteriophage T7 Gene 2.5 Protein Binding by single molecule force spectroscopy. T7 gp2.5- 26C, lacking 26 acidic C-terminal residues, also reduces of single DNA molecules by stretch- ing the molecules and measuring the required force for a given extension

Richardson, Charles C.

434

Anion Binding Properties of Reduced and Oxidized Iron-Containing Superoxide Dismutase Reveal No Requirement for Tyrosine 34  

E-Print Network [OSTI]

nuclear magnetic relaxation dispersion (NMRD) results. Thus, we propose that two F- ions can bind magnetic resonance; NMRD, nuclear magnetic relaxation dispersion; OCN- , cyanate; PIPES, piperazine circular dichroism; MES, 2-(N-morpholino) ethane sulfonic acid; MnSOD, Mn-containing SOD; NMR, nuclear

Miller, Anne-Frances

435

Modeling Binding Kinetics at the QA Site in Bacterial Reaction Centers Jennifer Madeo and M. R. Gunner*  

E-Print Network [OSTI]

. Gunner* Physics Department J-419 City College of New York 138th Street and ConVent AVenue, New York, New quinones with similar Kd values take minutes to bind or dissociate. These slow rates are independent). The primary electron donor P, a bacte- riochlorophyll dimer, absorbs a photon obtaining the energy to reduce

Gunner, Marilyn

436

Different adsorbate binding mechanisms of hydrocarbons: Theoretical studies for Cu(111)C2H2 and Cu(111)C2H4  

E-Print Network [OSTI]

Different adsorbate binding mechanisms of hydrocarbons: Theoretical studies for Cu(111)±C2H2 and Cu qualitatively different adsorbate binding mechanisms, depending on the adsorbate and substrate material. Experiments on Cu(111)±C2H2 identify a strongly distorted adsorbate while the adsorption energy is small

437

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.

438

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

439

Intrinsically disordered C-terminal segments of voltage-activated potassium channels: a possible fishing rod-like mechanism for channel binding to scaffold proteins  

Science Journals Connector (OSTI)

Membrane-embedded voltage-activated potassium channels (Kv) bind intracellular scaffold proteins, such as the Post Synaptic Density 95 (PSD-95) protein, using a conserved PDZ-binding motif located at the channels' C-terminal tip. This interaction underlies ...

Elhanan Magidovich; Sarel J. Fleishman; Ofer Yifrach

2006-07-01T23:59:59.000Z

440

Isolation and characterization of a cDNA clone encoding the 19 kDa protein of signal recognition particle (SRP): expression and binding to 7SL RNA  

E-Print Network [OSTI]

particle (SRP): expression and binding to 7SL RNA K.Lingelbach, C.Zwieb+, J.R.Webb, C.Marshallsay, P Signal recognition particle (SRP) consists of a 7SL RNA molecule and 6 protein subunits. We have isolated and characterized cDNA clones from human liver which encode the 19kDa protein subunit (SRP19). This subunit binds

Walter, Peter

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

A New Arabidopsis Gene, FLK, Encodes an RNA Binding Protein with K Homology Motifs and Regulates Flowering Time via FLOWERING LOCUS C  

Science Journals Connector (OSTI)

...It is now evident that a battery of different RNA binding proteins...Motifs A high-throughput thermal asymmetric interlaced PCR method...T-DNA insert junctions by thermal asymmetric interlaced PCR...It is now evident that a battery of different RNA binding proteins...

Mi-Hye Lim; Joonki Kim; Youn-Sung Kim; Kyung-Sook Chung; Yeon-Hee Seo; Ilha Lee; Jungmook Kim; Choo Bong Hong; Hie-Joon Kim; Chung-Mo Park

2004-02-18T23:59:59.000Z

442

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

443

Selective collision-induced desorption: Measurement of the -bonded C2H4 binding energy on Pt^111 precovered with atomic oxygen  

E-Print Network [OSTI]

Selective collision-induced desorption: Measurement of the -bonded C2H4 binding energy on Pt^111 CID is used to selectively probe the well depth of one particular adsorbate­surface potential energy K x-ray photoelectron XP spectra suggests that C(1s) XP binding energy is 283.1 eV for -C2H4

Levis, Robert J.

444

Quantum Monte Carlo calculation of the electronic binding energy in a C60 molecule Fei Lin, Jurij Smakov, Erik S. Srensen, Catherine Kallin, and A. John Berlinsky  

E-Print Network [OSTI]

Quantum Monte Carlo calculation of the electronic binding energy in a C60 molecule Fei Lin, Jurij electrons4­11 and lattice-level calculations based on an effec- tive Hamiltonian in which the intramolecular,5,15­17 This argument was supported by perturbative calculations of the electronic binding energies of the conven

Sørensen, Erik S.

445

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

446

Energy Employees Occupational Illness Compensation Program Act...  

Office of Science (SC) Website

Energy Employees Occupational Illness Compensation Program Act (EEOICPA) Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act...

447

f_Binding-Motifs-in-Bacterial-Gene-Promoters-Modulate-Transcriptional2_4335.pdf  

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

Regulation and Systems Biology 2012:6 93-107 Regulation and Systems Biology 2012:6 93-107 doi: 10.4137/GRSB.S9357 This article is available from http://www.la-press.com. © the author(s), publisher and licensee Libertas Academica Ltd. This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. OPEN ACCESS Full open access to this and thousands of other papers at http://www.la-press.com. Gene Regulation and Systems Biology O R I G I N A L R E S E A R C H Gene Regulation and Systems Biology 2012:6 93 Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA Michael R. Leuze 1, *, Tatiana V. Karpinets 2,3, *, Mustafa H. Syed 2 , Alexander S. Beliaev 4 and Edward C. Uberbacher 2 1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.

448

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

449

'In-Crystallo' Capture of a Michaelis Complex And Product Binding Modes of a Bacterial Phosphotriesterase  

SciTech Connect (OSTI)

The mechanism by which the binuclear metallophosphotriesterases (PTEs, E.C. 3.1.8.1) catalyse substrate hydrolysis has been extensively studied. The {mu}-hydroxo bridge between the metal ions has been proposed to be the initiating nucleophile in the hydrolytic reaction. In contrast, analysis of some biomimetic systems has indicated that {mu}-hydroxo bridges are often not themselves nucleophiles, but act as general bases for freely exchangeable nucleophilic water molecules. Herein, we present crystallographic analyses of a bacterial PTE from Agrobacterium radiobacter, OpdA, capturing the enzyme-substrate complex during hydrolysis. This model of the Michaelis complex suggests the alignment of the substrate will favor attack from a solvent molecule terminally coordinated to the {alpha}-metal ion. The bridging of both metal ions by the product, without disruption of the {mu}-hydroxo bridge, is also consistent with nucleophilic attack occurring from the terminal position. When phosphodiesters are soaked into crystals of OpdA, they coordinate bidentately to the {beta}-metal ion, displacing the {mu}-hydroxo bridge. Thus, alternative product-binding modes exist for the PTEs, and it is the bridging mode that appears to result from phosphotriester hydrolysis. Kinetic analysis of the PTE and promiscuous phosphodiesterase activities confirms that the presence of a {mu}-hydroxo bridge during phosphotriester hydrolysis is correlated with a lower pK{sub a} for the nucleophile, consistent with a general base function during catalysis.

Jackson, C.J.; Foo, J.-L.; Kim, H.-K.; Carr, P.D.; Liu, J.-W.; Salem, G.; Ollis, D.L.

2009-05-18T23:59:59.000Z

450

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

451

Structure of a Blm10 Complex Reveals Common Mechanisms for Proteasome Binding and Gate Opening  

SciTech Connect (OSTI)

The proteasome is an abundant protease that is critically important for numerous cellular pathways. Proteasomes are activated in vitro by three known classes of proteins/complexes, including Blm10/PA200. Here, we report a 3.4 {angstrom} resolution crystal structure of a proteasome-Blm10 complex, which reveals that Blm10 surrounds the proteasome entry pore in the 1.2 MDa complex to form a largely closed dome that is expected to restrict access of potential substrates. This architecture and the observation that Blm10 induces a disordered proteasome gate structure challenge the assumption that Blm10 functions as an activator of proteolysis in vivo. The Blm10 C terminus binds in the same manner as seen for 11S activators and inferred for 19S/PAN activators and indicates a unified model for gate opening. We also demonstrate that Blm10 acts to maintain mitochondrial function. Consistent with the structural data, the C-terminal residues of Blm10 are needed for this activity.

Sadre-Bazzaz, K.; Robinson, H.; Whitby, F. G.; Formosa, T.; Hill, C. P.

2010-03-12T23:59:59.000Z

452

Glutamate 87 is important for menaquinol binding in DmsC of the DMSO reductase (DmsABC) from Escherichia coli  

Science Journals Connector (OSTI)

Escherichia coli dimethylsulfoxide (DMSO) reductase is a trimeric enzyme with a catalytic dimer (DmsAB) and an integral membrane anchor (DmsC). Using site-directed mutagenesis, we examined six residues in the periplasmic loop between helices two and three, potentially involved in menaquinol binding in DmsC. Mutants were characterised for growth, enzyme expression and activity, and 2-n-heptyl-4-hydroxoquinoline N-oxide (HOQNO) inhibitor binding. Mutations of leucine 66, glycine 67, arginine 71, phenylalanine 73 and serine 75 had no effect on menaquinol binding. Only a glutamate residue (E87) located in helix three was important for menaquinol binding. E87 was replaced with lysine, glutamine and aspartate. All three mutants were assembled into the membrane. Neither the lysine nor the glutamine mutant enzymes were able to support anaerobic growth on glycerol/DMSO minimal media or oxidise lapachol. The glutamine mutant bound the inhibitor with lower affinity compared to wild-type, whereas in the lysine mutant, binding was almost abolished. The aspartate mutant behaved as a wild-type enzyme. The data shows that E87 is important for menaquinol binding and oxidation and is likely to act as a proton acceptor in the menaquinol binding site.

Paulina Geijer; Joel H. Weiner

2004-01-01T23:59:59.000Z

453

The R6A-1 peptide binds to switch II of G{alpha}{sub i1} but is not a GDP-dissociation inhibitor  

SciTech Connect (OSTI)

Heterotrimeric G-proteins are molecular switches that convert signals from membrane receptors into changes in intracellular physiology. Recently, several peptides that bind heterotrimeric G-protein {alpha} subunits have been isolated including the novel G{alpha}{sub i1} . GDP binding peptides R6A and KB-752. The R6A peptide and its minimized derivative R6A-1 interact with G{alpha}{sub i1} . GDP. Based on spectroscopic analysis of BODIPYFL-GTP{gamma}S binding to G{alpha}{sub i1}, it has been reported that R6A-1 has guanine nucleotide dissociation inhibitor (GDI) activity against G{alpha}{sub i1} [W.W. Ja, R.W. Roberts, Biochemistry 43 (28) (2004) 9265-9275]. Using radioligand binding, we show that R6A-1 is not a GDI for G{alpha}{sub i1} subunits. Furthermore, we demonstrate that R6A-1 reduces the fluorescence quantum yield of the G{alpha}{sub i1}-BODIPYFL-GTP{gamma}S complex, thus explaining the previously reported GDI activity as a fluorescence artifact. We further show that R6A-1 has significant sequence similarity to the guanine nucleotide exchange factor peptide KB-752 that binds to switch II of G{alpha}{sub i1}. We use competitive binding analysis to show that R6A-1 also binds to switch II of G{alpha} subunits.

Willard, Francis S. [Department of Pharmacology, CB 7365, 1106 Mary Ellen Jones Building, University of North Carolina, Chapel Hill, NC 27599-7365 (United States)]. E-mail: fwillard@med.unc.edu; Siderovski, David P. [Department of Pharmacology, CB 7365, 1106 Mary Ellen Jones Building, University of North Carolina, Chapel Hill, NC 27599-7365 (United States)

2006-01-27T23:59:59.000Z

454

Isotopic dependence of the nuclear charge radii and binding energies in the relativistic Hartree-Fock formalism  

SciTech Connect (OSTI)

Relativistic nonlinear models based on the Hartree and Hartree-Fock approximations, including the {sigma}, {omega}, {pi}, and {rho} mesons, are worked out to explore the behavior of the nuclear charge radii and the binding energies of several isotopic chains. We find a correlation between the magnitude of the anomalous kink effect (KE) in the Pb isotopic family and the compressibility modulus (K) of nuclear matter. The KE appears to be sensitive, in particular, to the mechanisms which control the K value. The influence of the symmetry energy on the Ca isotopic chain is also studied. The behavior of the charge radii of single-particle states for some special cases and its repercussion on the nuclear charge radius is analyzed. The effect of pairing correlations on the models improves considerably the quality of the results in both binding energy and KE.

Niembro, R., E-mail: niembror@unican.es; Marcos, S.; Lopez-Quelle, M. [Universidad de Cantabria (Spain); Savushkin, L. N. [St. Petersburg University for Telecommunications (Russian Federation)

2012-03-15T23:59:59.000Z

455

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

456

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

457

Investigation of metal-ion binding in the four-way junction construct of the hairpin ribozyme  

E-Print Network [OSTI]

??????????????????....... 67 Room-Temperature Mn2+ EPR Binding Isotherms ??. 73 Broadening of the EPR Lineshape of a Mn2+ Ion Bound to the Hairpin Ribozyme?????.???????. 78 Conclusion?...??????????. ??..??... 81 V A LIGAND-TO-METAL CHARGE TRANSFER BAND BETWEEN.....?????????????????.... 90 vii Page Future Work?????????????????.. 93 Low-Temperature EPR Spectroscopy of the Loopless Mutant??????...?..????.. 94 Low-Temperature EPR Microwave Power Saturation Studies???..????????... 94 Probing for Specific Metal...

Buckelew, Aurelie Lina

2005-08-29T23:59:59.000Z

458

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

E-Print Network [OSTI]

IDENTIFICATION OF PROTEIN BINDING BITEB IN TEE PROMOTER REGIONB OF A LIGHT RESPONSIVE GENE FAMILY IN A CYANOEACTERIUM A Thesis by ULRICH WOLFGANG MUELLER Submitted to the Office of Graduate Studies of Texas A&M University in partial f ulf i 1... Regions of a Light-responsive Gene Family in a Cyanobacterium. (December 1991) Ulrich Wolfgang Mueller, B. S. , New Mexico State University Chair of Advisory Committee: Dr. Susan S. Golden The D1 polypeptide of the photosystem II reaction center...

Mueller, Ulrich Wolfgang

1991-01-01T23:59:59.000Z

459

Use of Stabilizing Mutations To Engineer a Charged Group within a Ligand-Binding Hydrophobic Cavity in T4 Lysozyme  

Science Journals Connector (OSTI)

Use of Stabilizing Mutations To Engineer a Charged Group within a Ligand-Binding Hydrophobic Cavity in T4 Lysozyme ... This disrupts the hydrogen-bond network and causes the Glu102 side chain to move away from the ligand by up to 0.8 where it remains buried in a completely nonpolar environment. ... Brenk et al. (36) have explored the use of an engineered cavity of comparable volume in cytochrome c peroxidase that also includes a negative charge (Asp23). ...

Lijun Liu; Walter A. Baase; Miya M. Michael; Brian W. Matthews

2009-08-10T23:59:59.000Z

460

Apoferritin-based nanomedicine platform for drug delivery: equilibrium binding study of daunomycin with DNA  

SciTech Connect (OSTI)

Apoferritin is a nanostructured material with a uniform size and spherical structure, and it has excellent bio-compatibility. In this work, we report the use of apoferritin as a novel and biocompatible carrier for stabilizing enzymes and their activities. We used glucose oxidase (GOx) as a model enzyme. GOx was immobilized on the surface of the apoferritin through a green synthetic approach taking advantage of bioaffinity binding between streptavidin and biotin. As a result, a glucose oxidase-biotin/streptavidin/biotin-apoferritin conjugate (Apo-GOx) was prepared using streptavidin as a bridge. The synthesized Apo-GOx was characterized with transmission electron microscopy, ultraviolet, and fluorescence spectroscopy. The activity and stability of GOx on the surface of the apoferritin were studied in different environments, such as temperature, chemicals, and pH, in comparison with the biotinylated GOx (B-GOx). The results showed that the activity of GOx on the apoferritin surface was significantly enhanced. The thermal and chemical stability of the GOx on the apoferritin was also greatly improved compared to free B-GOx in a solution. It was found that the activity of the GOx on the apoferritin only lost 30% in comparison to a 70% loss of free B-GOx after a 2-hr incubation at 50oC. There was almost no decrease in activity for the GOx on the apoferritin as compared to an 80% activity decrease for free B-GOx after 30 minutes of incubation in a 5 M urea solution. The GOx immobilized apoferritin nanoparticles exhibited high sensitivity for glucose detection with a detection limit of 3 nM glucose. This work offers a novel approach for immobilizing enzymes with enhanced stability and activity, and this method may find a number of applications, such as in catalysis and bioassys/biosensors.

Ma Ham, Aihui; Wu, Hong J.; Wang, Jun; Kang, Xinhuang; Zhang, Youyu; Lin, Yuehe

2011-05-11T23:59:59.000Z

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.


461

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

462

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

463

Identical phosphatase mechanisms achieved through distinct modes of binding phosphoprotein substrate  

SciTech Connect (OSTI)

Two-component signal transduction systems are widespread in prokaryotes and control numerous cellular processes. Extensive investigation of sensor kinase and response regulator proteins from many two-component systems has established conserved sequence, structural, and mechanistic features within each family. In contrast, the phosphatases which catalyze hydrolysis of the response regulator phosphoryl group to terminate signal transduction are poorly understood. Here we present structural and functional characterization of a representative of the CheC/CheX/FliY phosphatase family. The X-ray crystal structure of Borrelia burgdorferi CheX complexed with its CheY3 substrate and the phosphoryl analogue BeF{sub 3}{sup -} reveals a binding orientation between a response regulator and an auxiliary protein different from that shared by every previously characterized example. The surface of CheY3 containing the phosphoryl group interacts directly with a long helix of CheX which bears the conserved (E - X{sub 2} - N) motif. Conserved CheX residues Glu96 and Asn99, separated by a single helical turn, insert into the CheY3 active site. Structural and functional data indicate that CheX Asn99 and CheY3 Thr81 orient a water molecule for hydrolytic attack. The catalytic residues of the CheX-CheY3 complex are virtually superimposable on those of the Escherichia coli CheZ phosphatase complexed with CheY, even though the active site helices of CheX and CheZ are oriented nearly perpendicular to one other. Thus, evolution has found two structural solutions to achieve the same catalytic mechanism through different helical spacing and side chain lengths of the conserved acid/amide residues in CheX and CheZ.

Pazy, Y.; Motaleb, M.A.; Guarnieri, M.T.; Charon, N.W.; Zhao, R.; Silversmith, R.E. (WVU); (UNC); (Colorado); (EC Uni.)

2010-04-05T23:59:59.000Z

464

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

465

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

466

Interaction of an Engineered [3Fe-4S] Cluster with a Menaquinol Binding Site of Escherichia coli DMSO Reductase  

Science Journals Connector (OSTI)

We have identified a residue in DmsC involved in MQH2 oxidation, DmsCH65, and in a double mutant, DmsABC102SCH65R, the DmsC mutation blocks the HOQNO effect on the [3Fe-4S] EPR line shape, suggesting that the DmsCH65R mutation either blocks HOQNO binding or blocks a conformational link between a HOQNO binding site and the DmsBC102S [3Fe-4S] cluster. ... These results suggest that the MQH2 binding site of DmsC is conformationally and functionally linked to the Em,7 = ?50 mV [4Fe-4S] cluster of DmsB. ... DmsABC is a heterotrimer comprising a molybdenum cofactor containing catalytic subunit (DmsA, 87.4 kDa), an [Fe-S] cluster containing electron-transfer subunit (DmsB, 23.1 kDa), and a membrane-intrinsic anchor subunit (DmsC, 30.8 kDa) (Bilous et al., 1988). ...

Richard A. Rothery; Joel H. Weiner

1996-03-12T23:59:59.000Z

467

Distinct Characteristics of Single Starch-Binding Domain SBD1 Derived from Tandem Domains SBD1-SBD2 of Halophilic Kocuria varians Alpha-Amylase  

Science Journals Connector (OSTI)

Kocuria varians alpha-amylase contains tandem starch-binding domains SBD1-SBD2...Escherichia coli. The circular dichroism (CD) spectrum of His-SBD12 was characterized by a positive peak at 233nm...

Rui Yamaguchi; Tsutomu Arakawa; Hiroko Tokunaga; Matsujiro Ishibashi

2012-03-01T23:59:59.000Z

468

Calcium binding in. alpha. -amylases: An X-ray diffraction study at 2. 1- angstrom resolution of two enzymes from Aspergillus  

SciTech Connect (OSTI)

X-ray diffraction analysis (at 2.1-{angstrom} resolution) of an acid alpha-amylase from Aspergillus niger allowed a detailed description of the stereochemistry of the calcium-binding sites. The primary site (which is essential in maintaining proper folding around the active site) contains a tightly bound Ca{sup 2+} with an unusually high number of eight ligands. A secondary binding site was identified at the bottom of the substrate binding cleft; it involves the residues presumed to play a catalytic role (Asp206 and Glu230). This explains the inhibitory effect of calcium observed at higher concentrations. Neutral Aspergillus oryzae (TAKA) {alpha}-amylase was also refined in a new crystal at 2.1-{angstrom} resolution. The structure of this homologous (over 80%) enzyme and addition kinetic studies support all the structural conclusions regarding both calcium-binding sites.

Boel, E.; Jensen, V.J.; Petersen, S.B.; Thim, L. Woldike, H.F. (NOVO-Nordisk Industri AS, Bagsvaerd (Denmark)); Brady, L.; Brzozowski, AM.; Derewenda, Z.; Dodson, G.G.; Swift, H. (Univ. of York (England))

1990-07-03T23:59:59.000Z

469

Fibronectin type III domains engineered to bind CD40L: cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of two complexes  

Science Journals Connector (OSTI)

Tn3 proteins, a novel class of binding molecules based on a fibronectin type III domain, have been cloned, expressed, purified and crystallized in complex with their cognate target.

Oganesyan, V.

2013-08-21T23:59:59.000Z

470

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

471

Comparison Between the Many-Body Perturbative and Greens-Function Approaches for Calculating Electron Binding Energies and Affinities: Brueckner and Dyson Orbitals  

Science Journals Connector (OSTI)

The many-body perturbative and Greens-function approaches for evaluating electron binding energies and electron affinities are compared, and it is shown that they are equivalent and both virtually exact. The for...

Ingvar Lindgren

2004-01-01T23:59:59.000Z

472

Flexibility and binding affinity in proteinligand, proteinprotein and multi-component protein interactions: limitations of current computational approaches  

Science Journals Connector (OSTI)

...small ligands or protein-binding partners...conformational ensemble for docking will...intrinsically disordered proteins (IDPs), which...conformational ensembles in biomolecular...predictors of mostly disordered proteins. Biochemistry...

2012-01-01T23:59:59.000Z

473

Multiple Nucleic Acid Binding Sites and Intrinsic Disorder of Severe Acute Respiratory Syndrome Coronavirus Nucleocapsid Protein: Implications for Ribonucleocapsid Protein Packaging  

Science Journals Connector (OSTI)

...resonances in the disordered region of...the whole protein. The flexible...conformational ensemble and does...putative disordered regions of coronavirus N proteins are positively...binding with N protein self-association in the disordered regions...

Chung-Ke Chang; Yen-Lan Hsu; Yuan-Hsiang Chang; Fa-An Chao; Ming-Chya Wu; Yu-Shan Huang; Chin-Kun Hu; Tai-Huang Huang

2008-12-03T23:59:59.000Z

474

The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold  

Science Journals Connector (OSTI)

...figure S1). The ensemble of 18 monomer models...different sites of the two proteins (see electronic supplementary...binding to intrinsically disordered protein regions [24] such...the interactions of disordered proteins. J. Mol. Biol...

2014-01-01T23:59:59.000Z

475

Assembly of the Alu domain of the signal recognition particle (SRP): dimerization of the two protein components is required for efficient binding to SRP RNA.  

Science Journals Connector (OSTI)

...domain of the signal recognition particle (SRP): dimerization of the two protein components is required for efficient binding to SRP RNA. K Strub P Walter Department of Biochemistry...94143-0448. The signal recognition particle (SRP), a cytoplasmic ribonucleoprotein, plays...

K Strub; P Walter

1990-02-01T23:59:59.000Z

476

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

477

Structure-based characterization and antifreeze properties of a hyperactive ice-binding protein from the Antarctic bacterium Flavobacterium frigoris PS1  

Science Journals Connector (OSTI)

The high-resolution crystal structure of FfIBP was determined and the structure showed an intramolecular disulfide bond in the capping head loop region and a T-A/G-X-T/N ice-binding motif. The rigid capping head loop region and greater surface area of the ice-binding site are important for the antifreeze activity of FfIBP.

Do, H.

2014-03-19T23:59:59.000Z

478

Essential Residues in the C Terminus of the Bacteriophage T7 Gene 2.5 Single-stranded DNA-binding Protein*  

E-Print Network [OSTI]

/thioredoxin (T7 DNA pol/trx) complex (2). However, the host ssDNA-binding protein, E. coli SSB protein-binding core (OB-fold) (10). This OB-fold is essentially superimposable with the OB-fold found in the E. coli on structural homology and amino acid sequence conservation of amino acids known to contact ssDNA in the E. coli

Richardson, Charles C.

479

Probing the Topological Tolerance of Multimeric Protein Interactions: Evaluation of an Estrogen/Synthetic Ligand for FK506 Binding Protein Conjugate  

Science Journals Connector (OSTI)

They tethered Congo Red, which, in turn, binds rather poorly to ?-amyloid (i.e., IC50 = 2 ?M), to SLF (synthetic ligand for FK-506 binding proteins [FKBPs]). ... The effect was not seen in the absence of FKBP12, suggesting that the mechanism of inhibition was dependent on the steric hindrance of FKBP12 that followed from its recruitment by the SLF element in the Congo Red conjugate. ... Chart 1. Structures of SLF, Congo Red, and SLF-Congo Red Conjugate I ...

Terry W. Moore; Jillian R. Gunther; John A. Katzenellenbogen

2010-10-04T23:59:59.000Z

480

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

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 and Inactivation Mechanism of a Humanized Fatty Acid Amide Hydrolase by [alpha]-Ketoheterocycle Inhibitors Revealed from Cocrystal Structures  

SciTech Connect (OSTI)

The cocrystal X-ray structures of two isomeric {alpha}-ketooxazole inhibitors (1 (OL-135) and 2) bound to fatty acid amide hydrolase (FAAH), a key enzymatic regulator of endocannabinoid signaling, are disclosed. The active site catalytic Ser241 is covalently bound to the inhibitors electrophilic carbonyl groups, providing the first structures of FAAH bound to an inhibitor as a deprotonated hemiketal mimicking the enzymatic tetrahedral intermediate. The work also offers a detailed view of the oxyanion hole and an exceptional 'in-action' depiction of the unusual Ser-Ser-Lys catalytic triad. These structures capture the first picture of inhibitors that span the active site into the cytosolic port providing new insights that help to explain FAAH's interaction with substrate leaving groups and their role in modulating inhibitor potency and selectivity. The role for the activating central heterocycle is clearly defined and distinguished from that observed in prior applications with serine proteases, reconciling the large electronic effect of attached substituents found unique to this class of inhibitors with FAAH. Additional striking active site flexibility is seen upon binding of the inhibitors, providing insights into the existence of a now well-defined membrane access channel with the disappearance of a spatially independent portion of the acyl chain-binding pocket. Finally, comparison of the structures of OL-135 (1) and its isomer 2 indicates that they bind identically to FAAH, albeit with reversed orientations of the central activating heterocycle, revealing that the terminal 2-pyridyl substituent and the acyl chain phenyl group provide key anchoring interactions and confirming the distinguishing role of the activating oxazole.

Mileni, Mauro; Garfunkle, Joie; DeMartino, Jessica K.; Cravatt, Benjamin F.; Boger, Dale L.; Stevens, Raymond C.; (Scripps)

2010-08-17T23:59:59.000Z

482

Chapter Four - Carbohydrate-Binding Modules of Fungal Cellulases: Occurrence in Nature, Function, and Relevance in Industrial Biomass Conversion  

Science Journals Connector (OSTI)

Abstract In this review, the present knowledge on the occurrence of cellulases, with a special emphasis on the presence of carbohydrate-binding modules (CBMs) in various fungal strains, has been summarized. The importance of efficient fungal cellulases is growing due to their potential uses in biorefinery processes where lignocellulosic biomasses are converted to platform sugars and further to biofuels and chemicals. Most secreted cellulases studied in detail have a bimodular structure containing an active core domain attached to a CBM. \\{CBMs\\} are traditionally been considered as essential parts in cellulases, especially in cellobiohydrolases. However, presently available genome data indicate that many cellulases lack the binding domains in cellulose-degrading organisms. Recent data also demonstrate that \\{CBMs\\} are not necessary for the action of cellulases and they solely increase the concentration of enzymes on the substrate surfaces. On the other hand, in practical industrial processes where high substrate concentrations with low amounts of water are employed, the enzymes have been shown to act equally efficiently with and without CBM. Furthermore, available kinetic data show that enzymes without \\{CBMs\\} can desorb more readily from the often lignaceous substrates, that is, they are not stuck on the substrates and are thus available for new actions. In this review, the available data on the natural habitats of different wood-degrading organisms (with emphasis on the amount of water present during wood degradation) and occurrence of cellulose-binding domains in their genome have been assessed in order to identify evolutionary advantages for the development of CBM-less cellulases in nature.

Anik Vrnai; Miia R. Mkel; Demi T. Djajadi; Jenni Rahikainen; Annele Hatakka; Liisa Viikari

2014-01-01T23:59:59.000Z

483

High-energy nuclear quasielastic reactions: Decisive tests of nuclear-binding/pion models of the European Muon Collaboration effect  

Science Journals Connector (OSTI)

The light-cone nucleon momentum distributions obtained from nonrelativistic spectral functions or given by nuclear-binding/pion models are often used to analyze high-Q2 quasielastic and deep-inelastic (e,e) reactions. We demonstrate that in such models the presence of non-nucleonic components causes the scattering from forward and backward moving target protons to be significantly different. Other models do not have this property. The sensitivity of current (e,ep) and (p,pp) color transparency experiments is sufficient to observe these differences.

L. Frankfurt; G. A. Miller; M. Strikman

1992-01-06T23:59:59.000Z

484

High energy nuclear quasielastic reactions: Decisive tests of nuclear binding/pion models of the EMC effect  

SciTech Connect (OSTI)

The light-cone nucleon momentum distributions obtained from non- relativistic spectral functions or given by nuclear binding/pion models are often used to analyze high Q{sup 2} quasi-elastic and deep-inelastic (e,e{prime}) reactions. We demonstrate that in such models the presence of non-nucleonic components causes the scattering from forward and backward moving target protons to be significantly different. Other models do not have this property. The sensitivity of current (e,e{prime}p) and (p,pp) color transparency experiments is sufficient to observe these differences.

Frankfurt, L; Strikman, M [Washington Univ., Seattle, WA (United States). Inst. for Nuclear Theory AN SSSR, Leningrad (USSR). Inst. Yadernoj Fiziki; Miller, G A [Washington Univ., Seattle, WA (United States). Inst. for Nuclear Theory

1991-01-01T23:59:59.000Z

485

Binding of soluble immune complexes to adult Schistosoma mansoni: evidence for IgG-Fc and complement receptors  

E-Print Network [OSTI]

the complexes were incubated with parasites at 4 C and retention of bound complexes was dependent on the presence 0 of a metabolic inhib1tor, 2-deoxy-0-glucose in the incubat1on mixture. AgAb binding required the presence of an intact Fc on the Ig... fraction (top wel I ) and the intact IgG (lower well) of rabbit anti-BSA serum . . 17 Fi g. 3. Immunoelectrophorests of anti-mouse complement C3 (trough) versus normal mouse serum &top weil) and normal mouse serum-minus complement C3 &lower well...

Tarleton, Ricky Lee

2012-06-07T23:59:59.000Z

486

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

487

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

488

Caffeic acid phenethyl ester downregulates phospholipase D1 via direct binding and inhibition of NF?B transactivation  

SciTech Connect (OSTI)

Highlights: We found CAF, a natural product that suppresses expression and activity of PLD1. CAPE decreased PLD1 expression by inhibiting NF?B transactivation. CAPE rapidly inhibited PLD activity via its binding to a Cys837 of PLD1. PLD1 downregulation by CAPE inhibited invasion and proliferation of glioma cells. -- Abstract: Upregulation of phospholipase D (PLD) is functionally linked with oncogenic signals and tumorigenesis. Caffeic acid phenethyl ester (CAPE) is an active compound of propolis extract that exhibits anti-proliferative, anti-inflammatory, anti-oxidant, and antineoplastic properties. In this study, we demonstrated that CAPE suppressed the expression of PLD1 at the transcriptional level via inhibition of binding of NF?B to PLD1 promoter. Moreover, CAPE, but not its analogs, bound to a Cys837 residue of PLD1 and inhibited enzymatic activity of PLD. CAPE also decreased activation of matrix metalloproteinases-2 induced by phosphatidic acid, a product of PLD activity. Ultimately, CAPE-induced downregulation of PLD1 suppressed invasion and proliferation of glioma cells. Taken together, the results of this study indicate that CAPE might contribute to anti-neoplastic effect by targeting PLD1.

Park, Mi Hee; Kang, Dong Woo [Department of Molecular Biology, Pusan National University, Busan 609-735 (Korea, Republic of)] [Department of Molecular Biology, Pusan National University, Busan 609-735 (Korea, Republic of); Jung, Yunjin [College of Pharmacy, Pusan National University, Busan 609-735 (Korea, Republic of)] [College of Pharmacy, Pusan National University, Busan 609-735 (Korea, Republic of); Choi, Kang-Yell [Translational Research Center for Protein Function Control, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul (Korea, Republic of)] [Translational Research Center for Protein Function Control, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul (Korea, Republic of); Min, Do Sik, E-mail: minds@pusan.ac.kr [Department of Molecular Biology, Pusan National University, Busan 609-735 (Korea, Republic of)

2013-12-06T23:59:59.000Z

489

Quasi-Anharmonic Analysis Reveals Intermediate States In The Nuclear Co-Activator Receptor Binding Domain Ensemble  

SciTech Connect (OSTI)

The molten globule nuclear receptor co-activator binding domain (NCBD) of CREB binding protein (CBP) selectively recruits transcription co-activators (TCAs) during the formation of the transcription preinitiation complex. NCBD:TCA interactions have been implicated in several cancers, however, the mechanisms of NCBD:TCA recognition remain uncharacterized. NCBD:TCA intermolecular recognition has challenged traditional investigation as both NCBD and several of its corresponding TCAs are intrinsically disordered. Using 40 {micro}s of explicit solvent molecular dynamics simulations, we relate the conformational diversity of ligand-free NCBD to its bound configurations. We introduce two novel techniques to quantify the conformational heterogeneity of ligand-free NCBD, dihedral quasi-anharmonic analysis (dQAA) and hierarchical graph-based diffusive clustering. With this integrated approach we find that three of four ligand-bound states are natively accessible to the ligand-free NCBD simulations with root-mean squared deviation (RMSD) less than 2 {angstrom}. These conformations are accessible via diverse pathways while a rate-limiting barrier must be crossed in order to access the fourth bound state.

Agarwal, Pratul K [ORNL] [ORNL; Ramanathan, Arvind [ORNL] [ORNL

2012-01-01T23:59:59.000Z

490

Conformational changes in the bacterial SRP receptor FtsY upon binding of guanine nucleotides and SRP  

Science Journals Connector (OSTI)

In cotranslational preprotein targeting in Escherichia coli, the signal recognition particle (SRP) binds to the signal peptide emerging from the ribosome and, subsequently, interacts with the signal recognition particle receptor, FtsY, at the plasma membrane. Both FtsY and the protein moiety of the signal recognition particle, Ffh, are GTPases, and GTP is required for the formation of the SRP-FtsY complex. We have studied the binding of GTP/GDP to FtsY as well as the SRP-FtsY complex formation by monitoring the fluorescence of tryptophan 343 in the I box of mutant FtsY. Thermodynamic and kinetic parameters of the FtsY complexes with GDP, GTP, and signal recognition particle are reported. Upon SRP-FtsY complex formation in the presence of GTP, the fluorescence of tryptophan 343 increased by 50 % and was blue-shifted by 10 nm. We conclude that GTP-dependent SRP-FtsY complex formation leads to an extensive conformational change in the I box insertion in the effector region of FtsY.

Junutula R Jagath; Marina V Rodnina; Wolfgang Wintermeyer

2000-01-01T23:59:59.000Z

491

Regulation of steroid 5-{alpha} reductase type 2 (Srd5a2) by sterol regulatory element binding proteins and statin  

SciTech Connect (OSTI)

In this study, we show that sterol regulatory element binding proteins (SREBPs) regulate expression of Srd5a2, an enzyme that catalyzes the irreversible conversion of testosterone to dihydroxytestosterone in the male reproductive tract and is highly expressed in androgen-sensitive tissues such as the prostate and skin. We show that Srd5a2 is induced in livers and prostate from mice fed a chow diet supplemented with lovastatin plus ezitimibe (L/E), which increases the activity of nuclear SREBP-2. The three fold increase in Srd5a2 mRNA mediated by L/E treatment was accompanied by the induction of SREBP-2 binding to the Srd5a2 promoter detected by a ChIP-chip assay in liver. We identified a SREBP-2 responsive region within the first 300 upstream bases of the mouse Srd5a2 promoter by co-transfection assays which contain a site that bound SREBP-2 in vitro by an EMSA. Srd5a2 protein was also induced in cells over-expressing SREBP-2 in culture. The induction of Srd5a2 through SREBP-2 provides a mechanistic explanation for why even though statin therapy is effective in reducing cholesterol levels in treating hypercholesterolemia it does not compromise androgen production in clinical studies.

Seo, Young-Kyo [Department of Molecular Biology and Biochemistry, 3244 McGaugh Hall, University of California, UC Irvine, Irvine, CA 92697-3900 (United States)] [Department of Molecular Biology and Biochemistry, 3244 McGaugh Hall, University of California, UC Irvine, Irvine, CA 92697-3900 (United States); Zhu, Bing [Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0144 (United States)] [Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0144 (United States); Jeon, Tae-Il [Department of Molecular Biology and Biochemistry, 3244 McGaugh Hall, University of California, UC Irvine, Irvine, CA 92697-3900 (United States)] [Department of Molecular Biology and Biochemistry, 3244 McGaugh Hall, University of California, UC Irvine, Irvine, CA 92697-3900 (United States); Osborne, Timothy F., E-mail: tfosborn@uci.edu [Department of Molecular Biology and Biochemistry, 3244 McGaugh Hall, University of California, UC Irvine, Irvine, CA 92697-3900 (United States)

2009-11-01T23:59:59.000Z

492

Intracellular protein delivery activity of peptides derived from insulin-like growth factor binding proteins 3 and 5  

SciTech Connect (OSTI)

Insulin-like growth factor binding proteins (IGFBPs) have various IGF-independent cellular activities, including receptor-independent cellular uptake followed by transcriptional regulation, although mechanisms of cellular entry remain unclear. Herein, we focused on their receptor-independent cellular entry mechanism in terms of protein transduction domain (PTD) activity, which is an emerging technique useful for clinical applications. The peptides of 18 amino acid residues derived from IGFBP-3 and IGFBP-5, which involve heparin-binding regions, mediated cellular delivery of an exogenous protein into NIH3T3 and HeLa cells. Relative protein delivery activities of IGFBP-3/5-derived peptides were approximately 20-150% compared to that of the HIV-Tat peptide, a potent PTD. Heparin inhibited the uptake of the fusion proteins with IGFBP-3 and IGFBP-5, indicating that the delivery pathway is heparin-dependent endocytosis, similar to that of HIV-Tat. The delivery of GST fused to HIV-Tat was competed by either IGFBP-3 or IGFBP-5-derived synthetic peptides. Therefore, the entry pathways of the three PTDs are shared. Our data has shown a new approach for designing protein delivery systems using IGFBP-3/5 derived peptides based on the molecular mechanisms of IGF-independent activities of IGFBPs.

Goda, Natsuko [Division of Biophysics, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 (Japan); Division of Structural Biology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 650-0017 (Japan); Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Corporation (JST) (Japan); Tenno, Takeshi [Division of Structural Biology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 650-0017 (Japan); Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510 (Japan); Inomata, Kosuke; Shirakawa, Masahiro [Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Corporation (JST) (Japan); Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510 (Japan); Tanaka, Toshiki [Graduate School of Material Science, OMOHI-College, Nagoya Institute of Technology, Gokiso-cho, Nagoya 466-8555 (Japan); Hiroaki, Hidekazu [Division of Biophysics, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 (Japan); Division of Structural Biology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 650-0017 (Japan); Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Corporation (JST) (Japan)], E-mail: hiroakih@med.kobe-u.ac.jp

2008-08-01T23:59:59.000Z

493

The single-strand DNA binding activity of human PC4 preventsmutagenesis and killing by oxidative DNA damage  

SciTech Connect (OSTI)

Human positive cofactor 4 (PC4) is a transcriptional coactivator with a highly conserved single-strand DNA (ssDNA) binding domain of unknown function. We identified PC4 as a suppressor of the oxidative mutator phenotype of the Escherichia coli fpg mutY mutant and demonstrate that this suppression requires its ssDNA binding activity. Yeast mutants lacking their PC4 ortholog Sub1 are sensitive to hydrogen peroxide and exhibit spontaneous and peroxide induced hypermutability. PC4 expression suppresses the peroxide sensitivity of the yeast sub l{Delta} mutant, suggesting that the human protein has a similar function. A role for yeast and human proteins in DNA repair is suggested by the demonstration that Sub1 acts in a peroxide-resistance pathway involving Rad2 and by the physical interaction of PC4 with the human Rad2 homolog XPG. We show XPG recruits PC4 to a bubble-containing DNA substrate with resulting displacement of XPG and formation of a PC4-DNA complex. We discuss the possible requirement for PC4 in either global or transcription-coupled repair of oxidative DNA damage to mediate the release of XPG bound to its substrate.

Wang, Jen-Yeu; Sarker, Altaf Hossain; Cooper, Priscilla K.; Volkert, Michael R.

2004-02-01T23:59:59.000Z

494

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

495

Activation of Retinal Guanylyl Cyclase RetGC1 by GCAP1: Stoichiometry of Binding and Effect of New LCA-Related Mutations  

Science Journals Connector (OSTI)

Activation of Retinal Guanylyl Cyclase RetGC1 by GCAP1: Stoichiometry of Binding and Effect of New LCA-Related Mutations ... In a striking manner, the equimolar binding of RetGC1 with GCAP1 in transfected HEK293 cells typical for wild-type RetGC1 was eliminated by a substitution, D639Y, in the kinase homology domain of RetGC1 found in a patient with a severe form of retinal dystrophy, Leber congenital amaurosis (LCA). ... A similar effect was observed with another LCA-related mutation, R768W, in the same domain of RetGC1. ...

Igor V. Peshenko; Elena V. Olshevskaya; Suxia Yao; Hany H. Ezzeldin; Steven J. Pittler; Alexander M. Dizhoor

2010-01-05T23:59:59.000Z

496

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

497

Binding-induced Folding of Prokaryotic Ubiquitin-like Protein on the Mycobacterium Proteasomal ATPase Targets Substrates for Degradation  

SciTech Connect (OSTI)

Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an {alpha}-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.

T Wang; K Heran Darwin; H Li

2011-12-31T23:59:59.000Z

498

Binding-induced folding of prokaryotic ubiquitin-like protein on the mycobacterium proteasomal ATPase targets substrates for degradation  

SciTech Connect (OSTI)

Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an {alpha}-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.

Wang, T.; Li, H.; Darwin, K. H.

2010-11-01T23:59:59.000Z

499

Preliminary Crystallography Confirms that the Archaeal DNA-binding and Tryptophan-sensing Regulator TrpY is a Dimer  

SciTech Connect (OSTI)

TrpY regulates the transcription of the metabolically expensive tryptophan-biosynthetic operon in the thermophilic archaeon Methanothermobacter thermautotrophicus. TrpY was crystallized using the hanging-drop method with ammonium sulfate as the precipitant. The crystals belonged to the tetragonal space group P4{sub 3}2{sub 1}2 or P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 87, c = 147 {angstrom}, and diffracted to 2.9 {angstrom} resolution. The possible packing of molecules within the cell based on the values of the Matthews coefficient (V{sub M}) and analysis of the self-rotation function are consistent with the asymmetric unit being a dimer. Determining the structure of TrpY in detail will provide insight into the mechanisms of DNA binding, tryptophan sensing and transcription regulation at high temperature by this novel archaeal protein.

J Cafasso; B Manjasetty; E Karr; K Sandman; M Chance; J Reeve

2011-12-31T23:59:59.000Z

500

Initial Recognition of a Cellodextrin Chain in the Cellulose-Binding Tunnel May Affect Cellobiohydrolase Directional Specificity  

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

Initial Initial Recognition of a Cellodextrin Chain in the Cellulose-Binding Tunnel May Affect Cellobiohydrolase Directional Specificity Pavan K. GhattyVenkataKrishna, †‡ Emal M. Alekozai, §{ Gregg T. Beckham, k ** Roland Schulz, {‡‡ Michael F. Crowley, ‡†† * Edward C. Uberbacher, †‡ * and Xiaolin Cheng ‡{‡‡ * † Computational Biology and Bioinformatics Group and ‡ BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee; § Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg Germany; { UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee; k National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado; **Department of Chemical Engineering, Colorado School of Mines, Golden, Colorado; †† Biosciences Center, National