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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

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.

3

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.

4

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; Mondragón, Alfonso; (NWU)

2010-01-07T23:59:59.000Z

5

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.

6

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

7

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...

8

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

9

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.

10

Impact of the [delta]F508 Mutation in First Nucleotide-binding Domain of Human Cystic Fibrosis Transmembrane Conductance Regulator on Domain Folding and Structure  

SciTech Connect (OSTI)

Cystic fibrosis is caused by defects in the cystic fibrosis transmembrane conductance regulator (CFTR), commonly the deletion of residue Phe-508 (DeltaF508) in the first nucleotide-binding domain (NBD1), which results in a severe reduction in the population of functional channels at the epithelial cell surface. Previous studies employing incomplete NBD1 domains have attributed this to aberrant folding of DeltaF508 NBD1. We report structural and biophysical studies on complete human NBD1 domains, which fail to demonstrate significant changes of in vitro stability or folding kinetics in the presence or absence of the DeltaF508 mutation. Crystal structures show minimal changes in protein conformation but substantial changes in local surface topography at the site of the mutation, which is located in the region of NBD1 believed to interact with the first membrane spanning domain of CFTR. These results raise the possibility that the primary effect of DeltaF508 is a disruption of proper interdomain interactions at this site in CFTR rather than interference with the folding of NBD1. Interestingly, increases in the stability of NBD1 constructs are observed upon introduction of second-site mutations that suppress the trafficking defect caused by the DeltaF508 mutation, suggesting that these suppressors might function indirectly by improving the folding efficiency of NBD1 in the context of the full-length protein. The human NBD1 structures also solidify the understanding of CFTR regulation by showing that its two protein segments that can be phosphorylated both adopt multiple conformations that modulate access to the ATPase active site and functional interdomain interfaces.

Lewis, Hal A.; Zhao, Xun; Wang, Chi; Sauder, J. Michael; Rooney, Isabelle; Noland, Brian W.; Lorimer, Don; Kearins, Margaret C.; Conners, Kris; Condon, Brad; Maloney, Peter C.; Guggino, William B.; Hunt, John F.; Emtage, Spencer (SG); (Columbia); (JHU)

2010-07-19T23:59:59.000Z

11

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)–ribosome–nascent 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 Bär; Jörg-Oliver Thumfart; Hans-Georg Koch

2009-01-01T23:59:59.000Z

12

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

13

Solution Structure of an Arabidopsis WRKY DNA Binding Domain  

Science Journals Connector (OSTI)

...in the electrostatic energy gain for each domain...accurate comparison of free energies, including an evaluation...and the lowest total energies were selected as accepted...partially conducted using the resources in the Computer Center...responses to stress. Solar ultraviolet-B radiation...

Kazuhiko Yamasaki; Takanori Kigawa; Makoto Inoue; Masaru Tateno; Tomoko Yamasaki; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Yasuko Tomo; Nobuhiro Hayami; Takaho Terada; Mikako Shirouzu; Akiko Tanaka; Motoaki Seki; Kazuo Shinozaki; Shigeyuki Yokoyama

2005-02-10T23:59:59.000Z

14

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

15

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

16

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 233 nm...

Rui Yamaguchi; Tsutomu Arakawa; Hiroko Tokunaga; Matsujiro Ishibashi…

2012-03-01T23:59:59.000Z

17

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

18

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.

19

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

20

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

Note: This page contains sample records for the topic "bind deleted domain" 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

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.

22

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 75°C 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

23

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

Science Journals Connector (OSTI)

Precisely Defined Protein–Polymer 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.; Vögtle, F. Dendrimers and Dendrons:Concepts, Syntheses, Applications; Wiley-VCH: Weinheim, 2001. ...

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

2007-08-25T23:59:59.000Z

24

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.

25

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.

26

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

27

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

28

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

29

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

30

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

31

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

32

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

33

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

34

Construction of a Functional S-Layer Fusion Protein Comprising an Immunoglobulin G-Binding Domain for Development of Specific Adsorbents for Extracorporeal Blood Purification  

Science Journals Connector (OSTI)

...G-Binding Domain for Development of Specific Adsorbents for Extracorporeal Blood Purification...cellulose-based microbeads to generate specific adsorbents, which should find clinical application...advantage in comparison to commercial adsorbents can be seen in the fact that the ZZ-domains...

Christine Völlenkle; Stefan Weigert; Nicola Ilk; Eva Egelseer; Viktoria Weber; Fritz Loth; Dieter Falkenhagen; Uwe B. Sleytr; Margit Sára

2004-03-01T23:59:59.000Z

35

Integrative data analysis indicates an intrinsic disordered domain character of Argonaute-binding motifs  

Science Journals Connector (OSTI)

......in any of the known proteins. Based on structural...predictions of the GW182 protein family suggest that...motifs of eukaryotic proteins constitute a family of Intrinsically Disordered Domains (IDD) that exist as ensembles of rapidly interconverting......

Andrzej Zielezinski; Wojciech M. Karlowski

2014-11-01T23:59:59.000Z

36

A Generalized Deletion Machine  

E-Print Network [OSTI]

In this work we prescribe a more generalized quantum-deleting machine (input state dependent). The fidelity of deletion is dependent on some machine parameters such that on alteration of machine parameters we get back to standard deleting machines. We also carried out a various comparative study of various kinds of quantum deleting machines. We also plotted graphs, making a comparative study of fidelity of deletion of the deletion machines, obtained as particular cases on changing the machine parameters of our machine.

Indranil Chakrabarty; Satyabrata Adhikari

2005-11-22T23:59:59.000Z

37

Embargoed Deletion  

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

PNAS proof PNAS proof Embargoed Deletion of Cel48S Q:1 from Clostridium thermocellum ; 2 Daniel G. Olson a,b,c , Shital A. Tripathi a,c , Richard J. Giannone c,d , Jonathan Lo b,c , Nicky C. Caiazza a,c , David A. Hogsett a,c , Robert Hettich c,d , Adam M. Guss b,c , Genia Dubrovsky b,c , and Lee R. Lynd a,b,c,e,1 a Mascoma Corporation, NH 03766; b Thayer School of Engineering and e Department of Biological Sciences, Dartmouth College, NH 03755; and c BioEnergy Science Center, d Oak Ridge National Laboratory, TN 37830 Q:3 Edited* by Lonnie O'Neal Ingram, University of Florida, Gainesville, FL, and approved August 16, 2010 (received for review April 9, 2010) Clostridium thermocellum is a thermophilic anaerobic bacterium that rapidly solubilizes cellulose with the aid of a multienzyme cel- lulosome complex. Creation of knockout mutants for Cel48S (also known as CelS, S S , and S8), the most abundant cellulosome

38

Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2  

Science Journals Connector (OSTI)

The high-resolution crystal structures of the human tankyrase 2 poly(ADP-ribose) polymerase (PARP) domain in complex with 16 various PARP inhibitors are reported, including the compounds BSI-201, AZD-2281 and ABT-888, which are currently in Phase 2 or 3 clinical trials.

Qiu, W.

2014-09-27T23:59:59.000Z

39

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

40

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

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
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41

Identification of High Affinity Polo-like Kinase 1 (Plk1) Polo-box Domain Binding Peptides Using Oxime-Based Diversification  

E-Print Network [OSTI]

In an effort to develop improved binding antagonists of the polo-like kinase 1 (Plk1) polo-box domain (PBD), we optimized interactions of the known high affinity 5-mer peptide PLHSpT using oxime-based post solid-phase ...

Liu, Fa

42

Crystal structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains  

SciTech Connect (OSTI)

The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged helix (WH) DNA-binding domains and diverse C-terminal, regulatory domains, which provide a basis for the classification of the constituent families. The largest of these families, FadR, contains nearly 3000 proteins with all a-helical regulatory domains classified into two related Pfam families: FadR{_}C and FCD. Only two crystal structures of the FadR family members, i.e. the E. coli FadR protein and the LldR from C. glutamicum, have been described to date in literature. Here we describe the crystal structure of TM0439, a GntR regulator with an FCD domain, found in the Thermotoga maritima genome. The FCD domain is similar to that of the LldR regulator, and contains a buried metal binding site. Using atomic absorption spectroscopy and Trp fluorescence, we show that the recombinant protein contains bound Ni{sup 2+} ions, but it is able to bind Zn{sup 2+} with K{sub D} < 70 nM . We conclude that Zn{sup 2+} is the likely physiological metal, where it may perform either or both structural and regulatory roles. Finally, we compare the TM0439 structure to two other FadR family structures recently deposited by Structural Genomics consortia. The results call for a revision in the classification of the FadR family of transcription factors.

Zheng, Meiying; Cooper, David; Grossoehmerb, Nickolas; Yu, Minmin; Hung, Li-Wei; Cieslik, Murcin; Derewendaro, Urszula; Lesley, Scott; Wilson, Ian; Giedrocb, David; Derewenda, Zygmunt

2009-06-06T23:59:59.000Z

43

Redox-sensitive structural change in the A-domain of HMGB1 and its implication for the binding to cisplatin modified DNA  

SciTech Connect (OSTI)

Highlights: •The structure of the oxidized A-domain of human HMGB1 was solved. •Phe38 ring was flipped in the oxidized structure from that in the reduced form. •The flipped ring disables the intercalation into the cisplatinated lesions. •The functionally relevant redox-dependent structural change was described. -- Abstract: HMGB1 (high-mobility group B1) is a ubiquitously expressed bifunctional protein that acts as a nuclear protein in cells and also as an inflammatory mediator in the extracellular space. HMGB1 changes its functions according to the redox states in both intra- and extra-cellular environments. Two cysteines, Cys23 and Cys45, in the A-domain of HMGB1 form a disulfide bond under oxidative conditions. The A-domain with the disulfide bond shows reduced affinity to cisplatin modified DNA. We have solved the oxidized A-domain structure by NMR. In the structure, Phe38 has a flipped ring orientation from that found in the reduced form; the phenyl ring in the reduced form intercalates into the platinated lesion in DNA. The phenyl ring orientation in the oxidized form is stabilized through intramolecular hydrophobic contacts. The reorientation of the Phe38 ring by the disulfide bond in the A-domain may explain the reduced HMGB1 binding affinity towards cisplatinated DNA.

Wang, Jing [Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526 (Japan)] [Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526 (Japan); Tochio, Naoya [Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526 (Japan)] [Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526 (Japan); Takeuchi, Aya [Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526 (Japan)] [Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526 (Japan); Uewaki, Jun-ichi [Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526 (Japan) [Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526 (Japan); Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526 (Japan); Kobayashi, Naohiro [Protein Research Institute, Osaka University, 3-2 Yamadaoka, Suita 565-0871 (Japan)] [Protein Research Institute, Osaka University, 3-2 Yamadaoka, Suita 565-0871 (Japan); Tate, Shin-ichi, E-mail: tate@hiroshima-u.ac.jp [Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526 (Japan) [Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526 (Japan); Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526 (Japan)

2013-11-29T23:59:59.000Z

44

Improving the fidelity of deletion  

Science Journals Connector (OSTI)

In this work we study the quantum deletion machine with two transformers, and show that the deletion machine with a single transformer performs better than the deletion machine with more than two transformers. We also observe that the fidelity of deletion depends on the blank state used in the deleter, and so for different blank states the fidelity is different. Further, we study the Pati-Braunsein deleter with transformer.

Satyabrata Adhikari and B. S. Choudhury

2006-05-24T23:59:59.000Z

45

The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors  

SciTech Connect (OSTI)

Signaling through the programmed death 1 (PD-1) inhibitory receptor upon binding its ligand, PD-L1, suppresses immune responses against autoantigens and tumors and plays an important role in the maintenance of peripheral immune tolerance. Release from PD-1 inhibitory signaling revives 'exhausted' virus-specific T cells in chronic viral infections. Here we present the crystal structure of murine PD-1 in complex with human PD-L1. PD-1 and PD-L1 interact through the conserved front and side of their Ig variable (IgV) domains, as do the IgV domains of antibodies and T cell receptors. This places the loops at the ends of the IgV domains on the same side of the PD-1/PD-L1 complex, forming a surface that is similar to the antigen-binding surface of antibodies and T cell receptors. Mapping conserved residues allowed the identification of residues that are important in forming the PD-1/PD-L1 interface. Based on the structure, we show that some reported loss-of-binding mutations involve the PD-1/PD-L1 interaction but that others compromise protein folding. The PD-1/PD-L1 interaction described here may be blocked by antibodies or by designed small-molecule drugs to lower inhibitory signaling that results in a stronger immune response. The immune receptor-like loops offer a new surface for further study and potentially the design of molecules that would affect PD-1/PD-L1 complex formation and thereby modulate the immune response.

Lin, David Yin-wei; Tanaka, Yoshimasa; Iwasaki, Masashi; Gittis, Apostolos G.; Su, Hua-Poo; Mikami, Bunzo; Okazaki, Taku; Honjo, Tasuku; Minato, Nagahiro; Garboczi, David N. (NIH); (Kyoto)

2008-07-29T23:59:59.000Z

46

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

47

Crystal Structure of the Receptor Binding Domain of the botulinum C-D Mosiac Neurotoxin Reveals Potential Roles of Lysines 1118 and 1136 in Membrane Interactions  

SciTech Connect (OSTI)

The botulinum neurotoxins (BoNTs) produced by different strains of the bacterium Clostridium botulinum are responsible for the disease botulism and include a group of immunologically distinct serotypes (A, B, E, and F) that are considered to be the most lethal natural proteins known for humans. Two BoNT serotypes, C and D, while rarely associated with human infection, are responsible for deadly botulism outbreaks afflicting animals. Also associated with animal infections is the BoNT C-D mosaic protein (BoNT/CD), a BoNT subtype that is essentially a hybrid of the BoNT/C ({approx}two-third) and BoNT/D ({approx}one-third) serotypes. While the amino acid sequence of the heavy chain receptor binding (HCR) domain of BoNT/CD (BoNT/CD-HCR) is very similar to the corresponding amino acid sequence of BoNT/D, BoNT/CD-HCR binds synaptosome membranes better than BoNT/D-HCR. To obtain structural insights for the different membrane binding properties, the crystal structure of BoNT/CD-HCR (S867-E1280) was determined at 1.56 {angstrom} resolution and compared to previously reported structures for BoNT/D-HCR. Overall, the BoNT/CD-HCR structure is similar to the two sub-domain organization observed for other BoNT HCRs: an N-terminal jellyroll barrel motif and a C-terminal {beta}-trefoil fold. Comparison of the structure of BoNT/CD-HCR with BoNT/D-HCR indicates that K1118 has a similar structural role as the equivalent residue, E1114, in BoNT/D-HCR, while K1136 has a structurally different role than the equivalent residue, G1132, in BoNT/D-HCR. Lysine-1118 forms a salt bridge with E1247 and may enhance membrane interactions by stabilizing the putative membrane binding loop (K1240-N1248). Lysine-1136 is observed on the surface of the protein. A sulfate ion bound to K1136 may mimic a natural interaction with the negatively changed phospholipid membrane surface. Liposome-binding experiments demonstrate that BoNT/CD-HCR binds phosphatidylethanolamine liposomes more tightly than BoNT/D-HCR.

Y Zhang; G Buchko; L Qin; H Robinson; S Varnum

2011-12-31T23:59:59.000Z

48

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

49

Hierarchy of Simulation Models in Predicting Structure and Energetics of the Src SH2 Domain Binding to Tyrosyl Phosphopeptides  

Science Journals Connector (OSTI)

Gennady M. Verkhivker ,* Djamal Bouzida , Daniel K. Gehlhaar , Paul A. Rejto , Lana Schaffer , Sandra Arthurs , Anthony B. Colson , Stephan T. Freer , Veda Larson , Brock A. Luty , Tami Marrone , and Peter W. Rose ... (33)?Shakespeare, W. C.; Bohacek, R. S.; Azimioara, M. D.; Macek, K. J.; Luke, G. P.; Dalgarno, D. C.; Hatada, M. H.; Lu, X.; Violette, S. M.; Bartlett, C.; Sawyer, T. K. Structure-based Design of Novel Bicyclic Nonpeptide Inhibitors for the Src SH2 Domain. ...

Gennady M. Verkhivker; Djamal Bouzida; Daniel K. Gehlhaar; Paul A. Rejto; Lana Schaffer; Sandra Arthurs; Anthony B. Colson; Stephan T. Freer; Veda Larson; Brock A. Luty; Tami Marrone; Peter W. Rose

2001-11-09T23:59:59.000Z

50

The Escherichia coli RhaS Transcriptional Activator: Transcriptional Activation by the DNA-Binding Domain, The Interdomain Effector Response, and Negative Autoregulation  

E-Print Network [OSTI]

) in 100 µL of RNAP storage buffer (50 mM Tris-HCl, pH 8.0; 50% glycerol; 0.1 mM NaEDTA; 0.1 mM DTT; 50 mM NaCl) and incubating at 25°C for 10 minutes, then storing at –20°C. To prepare the transcription reaction, His6-RhaS-CTD and/or CRP was incubated... using a Cyclone Storage Phosphor System (PerkinElmer). The results shown are representative of three similar experiments. 16 RESULTS In vitro DNA binding by His6-RhaS-CTD and His6-RhaR-CTD. Specific residues in the C-terminal domains of Rha...

Skredenske, Jeffrey M.

2012-05-31T23:59:59.000Z

51

Activated RhoA Binds to the Pleckstrin Homology (PH) Domain of PDZ-RhoGEF, a Potential Site for Autoregulation  

SciTech Connect (OSTI)

Guanine nucleotide exchange factors (GEFs) catalyze exchange of GDP for GTP by stabilizing the nucleotide-free state of the small GTPases through their Dbl homology/pleckstrin homology (DH {center_dot} PH) domains. Unconventionally, PDZ-RhoGEF (PRG), a member of the RGS-RhoGEFs, binds tightly to both nucleotide-free and activated RhoA (RhoA {center_dot} GTP). We have characterized the interaction between PRG and activated RhoA and determined the structure of the PRG-DH {center_dot} PH-RhoA {center_dot} GTP{gamma}S (guanosine 5{prime}-O-[{gamma}-thio]triphosphate) complex. The interface bears striking similarity to a GTPase-effector interface and involves the switch regions in RhoA and a hydrophobic patch in PRG-PH that is conserved among all Lbc RhoGEFs. The two surfaces that bind activated and nucleotide-free RhoA on PRG-DH {center_dot} PH do not overlap, and a ternary complex of PRG-DH {center_dot} PH bound to both forms of RhoA can be isolated by size-exclusion chromatography. This novel interaction between activated RhoA and PH could play a key role in regulation of RhoGEF activity in vivo.

Chen, Zhe; Medina, Frank; Liu, Mu-ya; Thomas, Celestine; Sprang, Stephen R.; Sternweis, Paul C. (UTSMC); (Montana)

2010-07-19T23:59:59.000Z

52

Identification of new functions for BRCT domains  

E-Print Network [OSTI]

Our lab identified the tandem BRCT domains of PTIP function as a DNA damage responsive phospho binding domain that recognizes proteins phosphorylated by ATM and ATR after DNA damage. The PTIP tandem BRCT domains are ...

Mohammad, Duaa H

2008-01-01T23:59:59.000Z

53

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

54

Help:Deleting pages | Open Energy Information  

Open Energy Info (EERE)

pages pages Jump to: navigation, search See Category:Proposed deletion for the listing of all articles currently proposed for deletion. Proposed deletion is the way to suggest that an article is a candidate for uncontroversial deletion. If nobody objects, the article is deleted after seven days. An article may not be proposed for deletion ("PRODed") if it has been PRODed before. Proposed deletion is only applicable to mainspace articles, lists, and disambiguation pages; it cannot be used with redirects, userspace pages, templates, categories, or pages in any other namespace. There are three steps to the PROD process An article or disambiguation page is nominated when an editor carefully reviews the article and inserts the {{subst:proposed deletion}} tag by placing {{subst:proposed deletion}} on the page. This lists the

55

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

56

Novel Activity of RGS14 on Go? and Gi? Nucleotide Binding and Hydrolysis Distinct from Its RGS Domain and GDI Activity  

Science Journals Connector (OSTI)

The bifunctional protein RGS14 is both a GTPase activating protein (GAP) for Gi? and Go? and a guanine nucleotide dissociation inhibitor (GDI) for Gi?. This GDI activity is isolated to a region of the protein distinct from the RGS domain that contains an ...

John R. Hepler; Wendy Cladman; Suneela Ramineni; Susanne Hollinger; Peter Chidiac

2005-03-18T23:59:59.000Z

57

Cloning and characterization of an alternatively spliced gene in proximal Xq28 deleted in two patients with intersexual genitalia and myotubular myopathy  

SciTech Connect (OSTI)

We have identified a novel human gene that is entirely deleted in two boys with abnormal genital development and myotubular myopathy (MTM1). The gene, F18, is located in proximal Xq28, approximately 80 kb centromeric to the recently isolated MTM1 gene. Northern analysis of mRNA showed a ubiquitous pattern and suggested high levels of expression in skeletal muscle, brain, and heart. A transcript of 4.6 kb was detected in a range of tissues, and additional alternate forms of 3.8 and 2.6 kb were present in placenta and pancreas, respectively. The gene extends over 100 kb and is composed of at least seven exons, of which two are non-coding. Sequence analysis of a 4.6-kb cDNA contig revealed two overlapping open reading frames (ORFs) that encode putative proteins of 701 and 424 amino acids, respectively. Two alternative spliced transcripts affecting the large open reading frame were identified that, together with the Northern blot results, suggest that distinct proteins are derived from the gene. No significant homology to other known proteins was detected, but segments of the first ORF encode polyglutamine tracts and proline-rich domains, which are frequently observed in DNA-binding proteins. The F18 gene is a strong candidate for being implicated in the intersexual genitalia present in the two MTM1-deleted patients. The gene also serves as a candidate for other disorders that map to proximal Xq28. 15 refs., 3 figs., 1 tab.

Laporte, J.; Hu, Ling-Jia; Kretz, C. [Institut de Genetique et de Biologie Moleculaire et Cellulaire, Strasbourg (France)] [and others] [Institut de Genetique et de Biologie Moleculaire et Cellulaire, Strasbourg (France); and others

1997-05-01T23:59:59.000Z

58

Help:Sysop deleting and undeleting | Open Energy Information  

Open Energy Info (EERE)

Sysop deleting and undeleting Sysop deleting and undeleting Jump to: navigation, search Deleting a page is a straightforward operation for anyone with sysop permissions. Users without such permissions can still remove text from wiki pages, or propose/request that a page should be deleted. See Help:Deleting a page. Contents 1 Before deleting 2 Use the 'delete' tab 3 Undeleting 4 Configuring deletion reasons Before deleting Sysops should also be aware of the general advice given on Help:Deleting a page (In particular, note that there are many situations where a deleting is too drastic. Often a redirect is more appropriate for example) Before deleting you could perform various checks: Use the "What links here" tool. This gives an indication as to how important a page is, and what subjects it relates to. Perhaps the page is

59

PartialDeletion for web.cdr  

Office of Legacy Management (LM)

States Department of Energy Grand Junction Office F A C T S H E E T Partial Deletion of Monticello Mill Tailings Site From the National Priorities List July 2003 The U.S....

60

Probabilistic cloning and deleting of quantum states Yuan Feng, Shengyu Zhang, and Mingsheng Ying*  

E-Print Network [OSTI]

, deleting unknown quantum states was also found to be impossible, where ``deleting'' means ``uncopy- ing

Zhang, Shengyu

Note: This page contains sample records for the topic "bind deleted domain" 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

Method for introducing unidirectional nested deletions  

DOE Patents [OSTI]

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment in the context of a cloning vector which contains an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment. Also disclosed is a method for producing single-stranded DNA probes utilizing the same cloning vector. An optimal vector, PZIP is described. Methods for introducing unidirectional deletions into a terminal location of a cloned DNA sequence which is inserted into the vector of the present invention are also disclosed. These methods are useful for introducing deletions into either or both ends of a cloned DNA insert, for high throughput sequencing of any DNA of interest.

Dunn, John J. (Bellport, NY); Quesada, Mark A. (Horseheads, NY); Randesi, Matthew (New York, NY)

2001-01-01T23:59:59.000Z

62

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 Å resolution reveal multiple overlapping nucleotide binding modes.

Ramirez, U.D.

2008-09-19T23:59:59.000Z

63

Binding of the Inhibitor Protein IF1 to Bovine F1-ATPase  

Science Journals Connector (OSTI)

In the structure of bovine F1-ATPase inhibited with residues 1–60 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

64

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

65

Binding sites of the 9- and 14-kilodalton heterodimeric protein subunit of the signal recognition particle (SRP) are contained exclusively in the Alu domain of SRP RNA and contain a sequence motif that is conserved in evolution.  

Science Journals Connector (OSTI)

...subunit of the signal recognition particle (SRP) are contained exclusively in the Alu domain of SRP RNA and contain a sequence motif that is conserved...The mammalian signal recognition particle (SRP) is a small cytoplasmic ribonucleoprotein required...

K Strub; J Moss; P Walter

1991-08-01T23:59:59.000Z

66

Method for introducing unidirectional nested deletions  

DOE Patents [OSTI]

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

Dunn, John J. (Bellport, NY); Quesada, Mark A. (Middle Island, NY); Randesi, Matthew (Upton, NY)

1999-07-27T23:59:59.000Z

67

Method for introducing unidirectional nested deletions  

DOE Patents [OSTI]

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector. The cloning vector has an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe. 1 fig.

Dunn, J.J.; Quesada, M.A.; Randesi, M.

1999-07-27T23:59:59.000Z

68

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.

69

The effect on chromosome stability of deleting replication origins.  

Science Journals Connector (OSTI)

...is the result of breakage of bubble-containing replication intermediates...deletion. The transition from bubble arc to Y arc characteristic...external origin and therefore BUBBLE D that deleting ARS309 removes...ARS elements to chromosome stability. It is part of the 200-kb...

A Dershowitz; C S Newlon

1993-01-01T23:59:59.000Z

70

Phase behavior and the partitioning of caveolin-1 scaffolding domain peptides in model lipid bilayers  

E-Print Network [OSTI]

The membrane binding and model lipid raft interaction of synthetic peptides derived from the caveolin scaffolding domain (CSD) of the protein caveolin-1 have been investigated. CSD peptides bind preferentially to ...

Rädler, Joachim

71

Flag rates for deletion? | OpenEI Community  

Open Energy Info (EERE)

Flag rates for deletion? Flag rates for deletion? Home > Groups > Utility Rate I found some "rates" that don't belong; they are one-time connection fees instead of rates (e.g. with a $2,500 connection fee as a "fixed monthly charge"). Is there some way to flag rates for suggested deletion? Submitted by Ewilson on 22 June, 2012 - 11:27 1 answer Points: 1 Hi Ewilson, Thank you for pointing this out! We are currently working on a way for users to propose deletion: http://en.openei.org/wiki/Help:Deleting_pages. Let me know if you have any questions! Wzeng on 12 July, 2012 - 08:19 Groups Menu You must login in order to post into this group. Recent content There is currently no way to s... ranking of utilities by demand charge? FYI, OpenEI now accommodates t... Very useful information. Thank...

72

Help:Deleting a page | Open Energy Information  

Open Energy Info (EERE)

page page Jump to: navigation, search Contents 1 When not to delete a page 1.1 Proposing changes 1.2 Unlinking a page 2 Deletion itself 3 See also When not to delete a page Typically you would delete a page if the contents are entirely inappropriate and do not match the purposes of the Wiki. In other situations, you would take a less extreme course of action, for example: The page should have a different title -- See Help:Moving a page The contents should have been placed on a different page -- Add the contents to the other page, and then supply a redirect. See Help:Redirects The contents are already on a different page -- Delete the duplicate content and leave a redirect. That way, the page title, which made sense to somebody, will helpfully redirect to the information. See Help:Redirects

73

Eminent Domain Law (Iowa)  

Broader source: Energy.gov [DOE]

These regulations confer the power of eminent domain and describe procedures for exercising eminent domain in Iowa.

74

DMBC: Domain Names & Web Hosting Domain Names  

E-Print Network [OSTI]

DMBC: Domain Names & Web Hosting Domain Names Top Level Domains · .com · .net · .org · .edu · .gov.9% of the web-viewing audience is used to typing in. Chances are, a visitor will type in ".com" even if you tell and simple · Try to avoid dashes or underscores in the domain name unless there is no other option Web

Stowell, Michael

75

Planar F-Deletion: Approximation and Optimal FPT Algorithms  

E-Print Network [OSTI]

Let F be a finite set of graphs. In the F-Deletion problem, we are given an n-vertex, m-edge graph G and an integer k as input, and asked whether at most k vertices can be deleted from G such that the resulting graph does not contain a graph from F as a minor. F-Deletion is a generic problem and by selecting different sets of forbidden minors F, one can obtain various fundamental problems such as Vertex Cover, Feedback Vertex Set or Treewidth t-Deletion. In this paper we obtain a number of generic algorithmic results about Planar F-Deletion, when F contains at least one planar graph. The highlights of our work are - A randomized O(nm) time constant factor approximation algorithm for the optimization version of Planar F-Deletion. - A randomized O(2^{O(k)} n) time parameterized algorithm for Planar F-Deletion when F is connected. Here a family F is called connected if every graph in F is connected. The algorithm can be made deterministic at the cost of making the polynomial factor in the running time n\\log^2 n ...

Fomin, Fedor; Misra, Neeldhara; Saurabh, Saket

2012-01-01T23:59:59.000Z

76

Formalizing Synthetic Domain Theory  

Science Journals Connector (OSTI)

Synthetic Domain Theory (SDT) is a constructive variant of Domain Theory where all functions are continuous following Dana Scott‘s idea of “domains as sets”. Recently there have been suggested more abstract axiomatizations encompassing ... Keywords: LCF, domain theory, formal verification, programming logics, synthetic domain theory, type theory

Bernhard Reus

1999-11-01T23:59:59.000Z

77

Multi-Domain Modeling  

Science Journals Connector (OSTI)

This chapter presents several multi-domain system models. Multi-domain models are characterized by the fact that they have components belonging to different engineering domains. In this chapter, we will see mo...

Michael Tiller Ph.D.

2001-01-01T23:59:59.000Z

78

Complex Domain Chemical Process Simulation in Theory and in Practice  

Science Journals Connector (OSTI)

Complex Domain Chemical Process Simulation in Theory and in Practice† ... However, care must be exercised in developing algorithms where signs of variables or other quantities are used to make decisions (e.g., in exchanging basic and nonbasic variables in simplex tableaus, adding and deleting inequalities in active set strategies, etc.). ... However, I cannot decide if I am enthusiastic about the usefulness of such an approach for optimization or not. ...

Angelo Lucia

2000-05-02T23:59:59.000Z

79

Targeted Genomic Deletion of the Lens-Specific Intermediate Filament Protein CP49  

E-Print Network [OSTI]

Targeted Genomic Deletion of the Lens-Specific Intermediate Filament Protein CP49 Azita Alizadeh,1, by blocking expression of the fiber cell­specific beaded filament protein CP49. METHODS. The first exon of the mouse CP49 gene was deleted by using targeted genomic deletion techniques. Gene deletion was assessed

Clark, John

80

PABPN1 polyalanine tract deletion and long expansions modify its aggregation pattern and expression  

Science Journals Connector (OSTI)

Expansions of a (GCN)10/polyalanine tract in the Poly(A) Binding Protein Nuclear 1 (PABPN1) cause autosomal dominant oculopharyngeal muscular dystrophy (OPMD). In OPMD muscles, as in models, PABPN1 accumulates in intranuclear inclusions (INIs) whereas in other diseases caused by similar polyalanine expansions, the mutated proteins have been shown to abnormally accumulate in the cytoplasm. This study presents the impact on the subcellular localization of PABPN1 produced by large expansions or deletion of its polyalanine tract. Large tracts of more than 24 alanines result in the nuclear accumulation of PABPN1 in SFRS2-positive functional speckles and a significant decline in cell survival. These large expansions do not cause \\{INIs\\} formation nor do they lead to cytoplasmic accumulation. Deletion of the polyalanine tract induces the formation of aggregates that are located on either side and cross the nuclear membrane, highlighting the possible role of the N-terminal polyalanine tract in PABPN1 nucleo-cytoplasmic transport. We also show that even though five other proteins with polyalanine tracts tend to aggregate when over-expressed they do not co-aggregate with PABPN1 INIs. This study presents the first experimental evidence that there may be a relative loss of function in OPMD by decreasing the availability of PABPN1 through an INI-independent mechanism.

Arnaud F. Klein; Mitsuru Ebihara; Christine Alexander; Marie-Josée Dicaire; A. Marie-Josée Sasseville; Yves Langelier; Guy A. Rouleau; Bernard Brais

2008-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" 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 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

82

Detection of frame deletion for digital video forensics  

Science Journals Connector (OSTI)

The abundance of digital video forms a potential piece of evidence in courtrooms. Augmenting subjective assessment of digital video evidence by an automated objective assessment helps increase the accuracy of deciding whether or not to admit the digital ... Keywords: Digital forensics, Frame deletion, Video compression

Tamer Shanableh

2013-12-01T23:59:59.000Z

83

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

84

Quantum Fusion of Domain Walls with Fluxes  

E-Print Network [OSTI]

We study how fluxes on the domain wall world volume modify quantum fusion of two distant parallel domain walls into a composite wall. The elementary wall fluxes can be separated into parallel and antiparallel components. The parallel component affects neither the binding energy nor the process of quantum merger. The antiparallel fluxes, instead, increase the binding energy and, against naive expectations, suppress quantum fusion. In the small flux limit we explicitly find the bounce solution and the fusion rate as a function of the flux. We argue that at large (antiparallel) fluxes there exists a critical value of the flux (versus the difference in the wall tensions), which switches off quantum fusion altogether. This phenomenon of flux-related wall stabilization is rather peculiar: it is unrelated to any conserved quantity. Our consideration of the flux-related all stabilization is based on substantiated arguments that fall short of complete proof.

S. Bolognesi; M. Shifman; M. B. Voloshin

2009-07-20T23:59:59.000Z

85

Structure of the Response Regulator PhoP from Mycobacterium tuberculosis Reveals a Dimer Through the Receiver Domain  

SciTech Connect (OSTI)

The PhoP protein from Mycobacterium tuberculosis is a response regulator of the OmpR/PhoB subfamily, whose structure consists of an N-terminal receiver domain and a C-terminal DNA-binding domain. How the DNA-binding activities are regulated by phosphorylation of the receiver domain remains unclear due to a lack of structural information on the full-length proteins. Here we report the crystal structure of the full-length PhoP of M. tuberculosis. Unlike other known structures of full-length proteins of the same subfamily, PhoP forms a dimer through its receiver domain with the dimer interface involving {alpha}4-{beta}5-{alpha}5, a common interface for activated receiver domain dimers. However, the switch residues, Thr99 and Tyr118, are in a conformation resembling those of nonactivated receiver domains. The Tyr118 side chain is involved in the dimer interface interactions. The receiver domain is tethered to the DNA-binding domain through a flexible linker and does not impose structural constraints on the DNA-binding domain. This structure suggests that phosphorylation likely facilitates/stabilizes receiver domain dimerization, bringing the DNA-binding domains to close proximity, thereby increasing their binding affinity for direct repeat DNA sequences.

S Menon; S Wang

2011-12-31T23:59:59.000Z

86

Sixth CREST Conference: 'Ctrl, Alt, Delete: Re-booting the State via  

E-Print Network [OSTI]

Sixth CREST Conference: 'Ctrl, Alt, Delete: Re-booting the State via E-Government in Europe, Delete: Re-booting the State via E-Government in Europe' Convenors: Dr Liki Koutrakou, UEA and Dr Paul

Feigon, Brooke

87

Starch-Binding Domain Affects Catalysis in Two Lactobacillus ?-Amylases  

Science Journals Connector (OSTI)

...Starch. Amylase activity...starch, amylose, amylopectin, or corn...starch. Amylase activity...starch, amylose, amylopectin, or raw...B) a-amylases as measured...and 63C. , amylose; , soluble...starch; , amylopectin; , corn...

R. Rodríguez-Sanoja; B. Ruiz; J. P. Guyot; S. Sanchez

2005-01-01T23:59:59.000Z

88

Structure of the p53 Transactivation Domain in Complex with the Nuclear Receptor Coactivator Binding Domain of CREB Binding Protein  

Science Journals Connector (OSTI)

The initial set of 100 structures generated in CYANA version 2.1 with the redundant dihedral angle constraints (REDAC) (56) was further refined by molecular dynamics calculations with AMBER9 under in vacuo conditions with 20% reduced charges (57). ... Biol., 186, 611) is described, which makes use of redundant dihedral angle constraints (REDAC) derived from preliminary calculations of the complete structure. ... The REDAC approach reduces the computation time for obtaining a group of acceptable conformers with the program DIANA 5-100-fold, depending on the complexity of the protein structure, and retains good sampling of conformation space. ...

Chul Won Lee; Maria A. Martinez-Yamout; H. Jane Dyson; Peter E. Wright

2010-10-20T23:59:59.000Z

89

Domain formation on oxidized graphene  

Science Journals Connector (OSTI)

Using first-principles calculations within density functional theory, we demonstrate that the adsorption of a single oxygen atom results in significant electron transfer from graphene to oxygen. This strongly disturbs the charge landscape of the C-C bonds at the proximity. Additional oxygen atoms adsorbing to graphene prefer always the C-C bonds having the highest charge density and, consequently, they have the tendency to form domain structure. While oxygen adsorption to one side of graphene ends with significant buckling, the adsorption to both sides with similar domain pattern is favored. The binding energy displays an oscillatory variation and the band gap widens with increasing oxygen coverage. While a single oxygen atom migrates over the C-C bonds on the graphene surface, a repulsive interaction prevents two oxygen adatoms from forming an oxygen molecule. Our first-principles study together with finite-temperature ab initio molecular dynamics calculations conclude that oxygen adatoms on graphene can not desorb easily without the influence of external agents.

M. Topsakal and S. Ciraci

2012-11-01T23:59:59.000Z

90

Eminent Domain Rights (Florida)  

Broader source: Energy.gov [DOE]

Developers of certain facilities, including dams to be used for hydropower, natural gas companies, wastewater systems, and coal pipelines, may be eligible to exercise eminent domain powers in...

91

Structure and function of the deleted in azoospermia gene  

E-Print Network [OSTI]

and DAZL RRMs fit both of these criteria. At least for the U1 spliceosomal protein, the RRM domain folds into an alternating series of alpha helices and beta sheets with the RNP domains next to each other on opposite beta sheets in an antiparallel... and DAZL RRMs fit both of these criteria. At least for the U1 spliceosomal protein, the RRM domain folds into an alternating series of alpha helices and beta sheets with the RNP domains next to each other on opposite beta sheets in an antiparallel...

Sprague, David Chase Cameron

2009-05-15T23:59:59.000Z

92

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

93

The Second Ca2+-Binding Domain of NCX1 Binds Mg2+ with High Affinity  

Science Journals Connector (OSTI)

(26) The cross-peaks of several other residues, for example, Ile518 and Gly548, are clearly present at 10 mM Mg2+ and are approximately midway between the apo and Ca2+-bound forms (cf. Figure 5C,D). ... Malmendal, A., Linse, S., Evenäs, J., Forsén, S., and Drakenberg, T. ( 1999) Battle for the EF-hands: Magnesium-calcium interference in calmodulin Biochemistry 38, 11844– 11850 ...

Vincent Breukels; Albert Konijnenberg; Sanne M. Nabuurs; Wouter G. Touw; Geerten W. Vuister

2011-09-19T23:59:59.000Z

94

The effect of two deletion schemes upon the comprehension and reading rate of five levels of telegraphic prose  

E-Print Network [OSTI]

between the two deletion schemes that would involve a relative increase in comprehension, reading rate, and efficiency for the subject generated scheme with 1ncreasing percentages of deletion. (5) The index of agreement among subjects on the rank... Reduced Version of the Passage Based on 50% Deletion (S5) Randomly Reduced Version of the Passage Based on IOX Deletion (Rl) Randomly Reduced Version of the Passage Based on 20% Deletion (R2) Randomly Reduced Version of the Passage Based on 30K...

Pantalion, Charles Adrian

1972-01-01T23:59:59.000Z

95

UNCORRECTED Three-dimensional structure topology of the calreticulin P-domain based  

E-Print Network [OSTI]

a single hairpin fold formed by the entire polypeptide chain. The loop at the bottom of the hairpin as a quality control system to ensure their structural integrity [1,2]. The calcium-binding molecular chaperone of the major calcium- binding proteins of the ER. Much interest has been focused on the proline-rich domain (P

Riek, Roland

96

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

97

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.

98

Domain boundary prediction based on profile domain linker propensity index  

Science Journals Connector (OSTI)

Successful prediction of protein domain boundaries provides valuable information not only for the computational structure prediction of multi-domain proteins but also for the experimental structure determination. In this work, a novel index at the profile ... Keywords: Domain, Domain linker, Profile

Qiwen Dong; Xiaolong Wang; Lei Lin; Zhiming Xu

2006-04-01T23:59:59.000Z

99

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

100

Domain analysis for estrogen receptor/Sp1-mediated transactivation and detection of estrogen receptor/Sp1 protein interactions in living cells  

E-Print Network [OSTI]

-induced activation of hER?/Sp1 was lost using hER? mutants deleted in zinc finger 1 (amino acids (aa) 185-205), zinc finger 2 (aa 218-245), and the hinge/helix 1 (aa 265-330) domains. In contrast with antiestrogens, E2-dependent activation of hER?/Sp1 required the C...

Kim, KyoungHyun

2005-11-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" 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

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

102

Comparative Characterization of a Wild Type and Transmembrane Domain-Deleted Fatty Acid Amide Hydrolase:? Identification of the Transmembrane Domain as a Site for Oligomerization  

Science Journals Connector (OSTI)

Matthew P. Patricelli ,‡ Hilal A. Lashuel ,§ Dan K. Giang ,‡ Jeffery W. Kelly ,§ and Benjamin F. Cravatt *‡ ... Giang, Dan K.; Cravatt, Benjamin F. ...

Matthew P. Patricelli; Hilal A. Lashuel; Dan K. Giang; Jeffery W. Kelly; Benjamin F. Cravatt

1998-10-08T23:59:59.000Z

103

Data Domain to Model Domain Conversion Package | Argonne National  

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

Data Domain to Model Domain Conversion Package Data Domain to Model Domain Conversion Package Data Domain to Model Domain Conversion Package The Data Domain to Model Domain Conversion Package project will develop methods and implement a novel approach for generating data ensembles by using the latest available statistical modeling tools and knowledge of relevant physical and chemical process to develop climatologically aware methods for processing ACRF and other spatially sparse data sets. Data collected at the Atmospheric Radiation Measurement Program Climate Research Facility (ACRF) sites are employed mainly in column radiation models, to validate the models and develop new parameterizations. Currently, no single methodology can be used with data collected at the spatial scale of the ACRF sites or from specific AmeriFlux locations, to

104

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

105

Identification of interstitial deletions in human neoplasia by FISH-technique  

SciTech Connect (OSTI)

Undoubtedly, the discovery of the minute chromosome in chronic myelogenous leukemia (CML), termed the Philadelphia chromosome, has revolutionized cancer cytogenetics. Rowely`s seminal findings of a balanced translocation between chromosomes 9 and 22 opened new avenues where a simple deletion was clearly refuted. Even today, thousands of cases are being identified as simple terminal deletions by routine banding techniques in various human neoplasias. If these deletions are terminal, then how is the instability of the chromosome retained? Apparently, the precise characterization of telomeric ends has gone undetected in the past by conventional methods. It is evident that telomeres of chromosomes consist of short tandemly repeated DNA sequences (TTAGGG){sub n} which are conserved on both ends. The recent availability of chromosome-specific telomeric probes has become a cytogenetic icon for many perplexing questions. For example, we were referred a patient with acute myelogenous leukemia evolving from agnogenic myloid metaplasia. Routine cytogenetic techniques revealed a terminal deletion of one of the chromosomes 7 [del(7)(q21)]. When we hybridized the metaphases with chromosome 7q-specific telomeric probe [Oncor, Gaithersburg, MD], signal was detected at the distal q arms of the deleted chromosomes, apparently suggesting an interstial deletion. The cytogenetic diagnosis was changed to 46,SY,del(7)(q21.lq36.2). All deletions must be identified by FISH.

Gogineni, S.K.; Sanchez, M.A.; Elizalde, S.A. [Long Island College Hospital, Brooklyn, NY (United States)]|[New York Methodist Hospital, Brooklyn, NY (United States)] [and others

1994-09-01T23:59:59.000Z

106

Why did someone delete the Utility Rate Database Page? | OpenEI...  

Open Energy Info (EERE)

Why did someone delete the Utility Rate Database Page? Home > Groups > Utility Rate Can someone fix this? I can't access the Utility Rate Database Page It looks like someone...

107

Cold Urticaria, Immunodeficiency, and Autoimmunity Related to PLCG2 Deletions  

Science Journals Connector (OSTI)

...Supplementary Appendix) and generalized exposure to cold air, findings that are consistent with their reports that symptoms were often elicited by cold wind rather than contact with cold objects. Of the 27 subjects who were tested, 26 had immunologic abnormalities in addition to cold urticaria (Table S1... Analyses of families affected by cold urticaria, immunodeficiency, and autoimmunity implicate mutations that activate phospholipase C?2 (PLC?2), an enzyme pivotal to the translation of binding events at the cell surface to the intracellular milieu, as a cause of the disease.

Ombrello M.J.; Remmers E.F.; Sun G.

2012-01-26T23:59:59.000Z

108

Pinkbar is an epithelial-specific BAR domain protein that generates planar membrane structures  

SciTech Connect (OSTI)

Bin/amphipysin/Rvs (BAR)-domain proteins sculpt cellular membranes and have key roles in processes such as endocytosis, cell motility and morphogenesis. BAR domains are divided into three subfamilies: BAR- and F-BAR-domain proteins generate positive membrane curvature and stabilize cellular invaginations, whereas I-BAR-domain proteins induce negative curvature and stabilize protrusions. We show that a previously uncharacterized member of the I-BAR subfamily, Pinkbar, is specifically expressed in intestinal epithelial cells, where it localizes to Rab13-positive vesicles and to the plasma membrane at intercellular junctions. Notably, the BAR domain of Pinkbar does not induce membrane tubulation but promotes the formation of planar membrane sheets. Structural and mutagenesis analyses reveal that the BAR domain of Pinkbar has a relatively flat lipid-binding interface and that it assembles into sheet-like oligomers in crystals and in solution, which may explain its unique membrane-deforming activity.

Pykäläinen, Anette; Boczkowska, Malgorzata; Zhao, Hongxia; Saarikangas, Juha; Rebowski, Grzegorz; Jansen, Maurice; Hakanen, Janne; Koskela, Essi V.; Peränen, Johan; Vihinen, Helena; Jokitalo, Eija; Salminen, Marjo; Ikonen, Elina; Dominguez, Roberto; Lappalainen, Pekka (Helsinki); (Penn)

2013-05-29T23:59:59.000Z

109

Chemistry & Biology 13, 139147, February 2006 2006 Elsevier Ltd All rights reserved DOI 10.1016/j.chembiol.2005.10.015 Directed Evolution of ATP Binding Proteins  

E-Print Network [OSTI]

.chembiol.2005.10.015 Directed Evolution of ATP Binding Proteins from a Zinc Finger Domain by Using mRNA Display recognize adenosine triphosphate (ATP), dem- onstrating a significant alteration of the function of this protein domain from DNA binding to ATP recogni- tion. Many novel independent sequences were recov- ered

Heller, Eric

110

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

111

Calcium-dependent Membrane Penetration Is a Hallmark of the C2 Domain of Cytosolic Phospholipase A2 Whereas the C2A Domain  

E-Print Network [OSTI]

-stranded anti-parallel -sandwich. The most notable structural differ- ences occur in three loops at the calciumCalcium-dependent Membrane Penetration Is a Hallmark of the C2 Domain of Cytosolic Phospholipase A2 of their structures and calcium binding. Here we demonstrate that the protein-lipid interaction is dramatically

Williams, Roger L.

112

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, Niccolò; 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

113

Domain walls in SU(5)  

Science Journals Connector (OSTI)

We consider the grand unified SU(5) model with a small or vanishing cubic term in the adjoint scalar field in the potential. This gives the model an approximate or exact Z2 symmetry whose breaking leads to domain walls. The simplest domain wall has the structure of a kink across which the Higgs field changes sign (??-?) and inside which the full SU(5) is restored. The kink is shown to be perturbatively unstable for all parameters. We then construct a domain wall solution that is lighter than the kink and show it to be perturbatively stable for a range of parameters. The symmetry in the core of this domain wall is smaller than that outside. The interactions of the domain wall with magnetic monopoles are discussed and it is shown that magnetic monopoles with certain internal space orientations relative to the wall pass through the domain wall. Magnetic monopoles in other relative internal space orientations are likely to be swept away on collision with the domain walls, suggesting a scenario where the domain walls might act like optical polarization filters, allowing certain monopole “polarizations” to pass through but not others. As SU(5) domain walls will also be formed at small values of the cubic coupling, this leads to a very complicated picture of the evolution of defects after the grand unified phase transition.

Levon Pogosian and Tanmay Vachaspati

2000-11-21T23:59:59.000Z

114

Domain Walls in Gapped Graphene  

Science Journals Connector (OSTI)

The electronic properties of a particular class of domain walls in gapped graphene are investigated. We show that they can support midgap states which are localized in the vicinity of the domain wall and propagate along its length. With a finite density of domain walls, these states can alter the electronic properties of gapped graphene significantly. If the midgap band is partially filled, the domain wall can behave like a one-dimensional metal embedded in a semiconductor and could potentially be used as a single-channel quantum wire.

G. W. Semenoff; V. Semenoff; Fei Zhou

2008-08-21T23:59:59.000Z

115

Domain lines as fractional strings  

Science Journals Connector (OSTI)

We consider N=2 supersymmetric quantum electrodynamics with two flavors, the Fayet-Iliopoulos parameter, and a mass term ? which breaks the extended supersymmetry down to N=1. The bulk theory has two vacua; at ?=0 the Bogomol’nyi-Prasad-Sommerfield (BPS) monopoles-saturated domain wall interpolating between them has a moduli space parameterized by a U(1) phase ? which can be promoted to a scalar field in the effective low-energy theory on the wall world-volume. At small nonvanishing ? this field gets a sine-Gordon potential. As a result, only two discrete degenerate BPS domain walls survive. We find an explicit solitonic solution for domain lines—stringlike objects living on the surface of the domain wall which separate wall I from wall II. The domain line is seen as a BPS kink in the world-volume effective theory. We expect that the wall with the domain line on it saturates both the {1,0} and the {12,12} central charges of the bulk theory. The domain line carries a magnetic flux which is exactly 12 of the flux carried by the flux tube living in the bulk on each side of the wall. Thus, the domain lines on the wall confine charges living on the wall, resembling Polyakov’s three-dimensional confinement.

R. Auzzi; M. Shifman; A. Yung

2006-08-11T23:59:59.000Z

116

Domain Lines as Fractional Strings  

E-Print Network [OSTI]

We consider N=2 supersymmetric quantum electrodynamics (SQED) with 2 flavors, the Fayet--Iliopoulos parameter, and a mass term $\\beta$ which breaks the extended supersymmetry down to N=1. The bulk theory has two vacua; at $\\beta=0$ the BPS-saturated domain wall interpolating between them has a moduli space parameterized by a U(1) phase $\\sigma$ which can be promoted to a scalar field in the effective low-energy theory on the wall world-volume. At small nonvanishing $\\beta$ this field gets a sine-Gordon potential. As a result, only two discrete degenerate BPS domain walls survive. We find an explicit solitonic solution for domain lines -- string-like objects living on the surface of the domain wall which separate wall I from wall II. The domain line is seen as a BPS kink in the world-volume effective theory. We expect that the wall with the domain line on it saturates both the $\\{1,0\\}$ and the $\\{{1/2},{1/2}\\}$b central charges of the bulk theory. The domain line carries the magnetic flux which is exactly 1/2 of the flux carried by the flux tube living in the bulk on each side of the wall. Thus, the domain lines on the wall confine charges living on the wall, resembling Polyakov's three-dimensional confinement.

R. Auzzi; M. Shifman; A. Yung

2006-06-07T23:59:59.000Z

117

Brief Report: Spermatogenesis in a Man with Complete Deletion of USP9Y  

Science Journals Connector (OSTI)

...guidelines. In order to define the extent of deletion, we used several sequence-tagged sites (sY82, sY88, sY83, G64723, AZFa-prox2, G66179, G66183, SHGC-3904, G65852, G49201, G65840, G66201, G49206, G66189, sY87, GY6, and G38346) and gene-specific primers to localize the breakpoints to an interval spanning... The azoospermia factor region A (AZFA) on chromosome Y contains two genes, one of which is USP9Y. Deletions in this region have been associated with male infertility. However, a man and his father and brother, all of whom carry a deletion that encompasses USP9Y, are normospermic, providing definitive evidence that USP9Y is not required for spermatogenesis.

Luddi A.; Margollicci M.; Gambera L.

2009-02-26T23:59:59.000Z

118

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

119

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

120

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

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121

Protein domain organisation: adding order  

E-Print Network [OSTI]

4 81811 membrane_organization_and_biogenesis 4 81811 vesicle-mediated_transport 4 81811 intracellular_protein_transport 4 54117 immune_response 3 54117 negative_regulation_of_cell_proliferation 3 54117 signal_transducer_activity 3 50715 ligase... -type_endopeptidase_activity 4 69055 binding 3 52788 identical_protein_binding 4 54585 nucleoside-triphosphatase_activity 3 54585 ATPase_activity 3 54585 protein_transport 3 54585 caspase_activation 3 54585 unfolded_protein_response 3 54585 magnesium_ion_binding 3 54585 protein...

Kummerfeld, Sarah K; Teichmann, Sarah A

2009-01-29T23:59:59.000Z

122

Domain assignments for FSSP representative set using DomainParser  

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

Domain assignments for the FSSP representative set Domain assignments for the FSSP representative set The following are the domain assignments for the FSSP representative set (released on January 31, 2000, 1987 chains in total) using DomainParser. Each line shows a PDB entry (with a chain identifier if any), total number of residues, number of domains, and domain assignments. The result is obtained fully automatically without manual editing. 12asa 327 2 (33-86; 271-288) (4-32; 87-270; 289-330) 153l 185 1 16pk 415 2 (5-205; 409-419) (206-408) 16vpa 311 2 (47-130; 164-233; 324-349) (131-163; 234-323; 395-402) 1914 171 1 19hca 292 2 (45-107) (1-44; 108-292) 1a02f 53 1 1a02j 52 1 1a02n 280 2 (399-569) (570-678) 1a04a 205 2 (5-126) (127-216) 1a0aa 63 1 1a0ca 437 1 1a0fa 201 2 (1-81) (82-201) 1a0ha 159 1 1a0i 332 2 (2-239) (240-349)

123

Fusion protein based on Grb2-SH2 domain for cancer therapy  

SciTech Connect (OSTI)

Research highlights: {yields} Grb2 mediates EGFR signaling through binding to phosphorylate EGFR with SH2 domain. {yields} We generated fusion proteins containing 1 or 2 SH2 domains of Grb2 added with TAT. {yields} The one with 2 SH2 domains (TSSF) interfered ERK phosphorylation. {yields} TSSF significantly delayed the growth of EGFR overexpressing tumor in a mouse model. -- Abstract: Epidermal growth factor receptor (EGFR) is one of the very attractive targets for cancer therapy. In this study, we generated fusion proteins containing one or two Src-homology 2 (SH2) domains of growth factor receptor bound protein 2 (Grb2), which bind to phosphorylated EGFR, added with HIV-1 transactivating transcription for cell membrane penetration (termed TSF and TSSF, respectively). We examined if they can interfere Grb2-mediated signaling pathway and suppress tumor growth as expected from the lack of SH3 domain, which is necessary to intermediate EGFR-Grb2 cell signaling, in the fusion proteins. The transduction efficiency of TSSF was similar to that of TSF, but the binding activity of TSSF to EGFR was higher than that of TSF. Treatment of EGFR-overexpressing cells showed that TSSF decreased p42-ERK phosphorylation, while TSF did not. Both the proteins delayed cell growth but did not induce cell death in culture. TSSF also significantly suppressed tumor growth in vivo under consecutive administration. In conclusion, TSSF showed an ability to inhibit EGFR-Grb2 signaling and could have a potential to treat EGFR-activated cancer.

Saito, Yuriko [Molecular Imaging Center, National Institute of Radiological Sciences (Japan) [Molecular Imaging Center, National Institute of Radiological Sciences (Japan); Graduate School of Pharmaceutical Sciences, Chiba University (Japan); Furukawa, Takako, E-mail: tfuru@nirs.go.jp [Molecular Imaging Center, National Institute of Radiological Sciences (Japan) [Molecular Imaging Center, National Institute of Radiological Sciences (Japan); Biomedical Imaging Research Center, University of Fukui (Japan); Arano, Yasushi [Graduate School of Pharmaceutical Sciences, Chiba University (Japan)] [Graduate School of Pharmaceutical Sciences, Chiba University (Japan); Fujibayashi, Yasuhisa [Molecular Imaging Center, National Institute of Radiological Sciences (Japan) [Molecular Imaging Center, National Institute of Radiological Sciences (Japan); Biomedical Imaging Research Center, University of Fukui (Japan); Saga, Tsuneo [Molecular Imaging Center, National Institute of Radiological Sciences (Japan)] [Molecular Imaging Center, National Institute of Radiological Sciences (Japan)

2010-08-20T23:59:59.000Z

124

The C-Terminal RpoN Domain of sigma54 Forms an unpredictedHelix-Turn-Helix Motif Similar to domains of sigma70  

SciTech Connect (OSTI)

The ''{delta}'' subunit of prokaryotic RNA-polymerase allows gene-specific transcription initiation. Two {sigma} families have been identified, {sigma}{sup 70} and {sigma}{sup 54}, which use distinct mechanisms to initiate transcription and share no detectable sequence homology. Although the {sigma}{sup 70}-type factors have been well characterized structurally by x-ray crystallography, no high-resolution structural information is available for the {sigma}{sup 54}-type factors. Here we present the NMR derived structure of the C-terminal domain of {sigma}{sup 54} from Aquifex aeolicus. This domain (Thr323 to Gly389), which contains the highly conserved RpoN box sequence, consists of a poorly structured N-terminal tail followed by a three-helix bundle, which is surprisingly similar to domains of the {sigma}{sup 70}-type proteins. Residues of the RpoN box, which have previously been shown to be critical for DNA binding, form the second helix of an unpredicted helix-turn-helix motif. This structure's homology with other DNA binding proteins, combined with previous biochemical data, suggest how the C-terminal domain of {sigma}{sup 54} binds to DNA.

Doucleff, Michaeleen; Malak, Lawrence T.; Pelton, Jeffrey G.; Wemmer, David E.

2005-11-01T23:59:59.000Z

125

Collaborative Networks for Biodiversity Domain Organizations  

E-Print Network [OSTI]

, conservation groups, etc., referred to in this paper as BOs (Biodiversity-domain OrganizationsCollaborative Networks for Biodiversity Domain Organizations Ekaterina Ermilova, Hamideh, operating in the domains of biology, ecology, and biodiversity, strongly need to cooperate

Boyer, Edmond

126

Electron Microscope Studies of Heteroduplex DNA from a Deletion Mutant of Bacteriophage ?X-174  

Science Journals Connector (OSTI)

...Accordingly, in Fig. 3 we depict the hetero- duplexes as having a nick in'the deleted strand.) Structure B can only occur for a...migration. Several points, however, are sufficiently clear to merit discussion. Since branch migration processes involve successive...

Jung-Suh Kim; Phillip A. Sharp; Norman Davidson

1972-01-01T23:59:59.000Z

127

Proposed FMP amendment language for GOA Amendment 72 Deletions are removed; additions are in bold.  

E-Print Network [OSTI]

Proposed FMP amendment language for GOA Amendment 72 Deletions are removed; additions are in bold. p. ES-4, Table ES-2: remove entire row tittles Bycatch Reduction Programs: Bycatch Reduction. The Council may recommend that NMFS initiate rulemaking to add or remove a fishery from shallow-water flatfish

128

Early Deletion of Fillers In Processing Conversational Speech Matthew Lease and Mark Johnson  

E-Print Network [OSTI]

Early Deletion of Fillers In Processing Conversational Speech Matthew Lease and Mark Johnson Brown to parsing has been shown to improve its accuracy (Charniak and Johnson, 2001). We ex- plore whether- pairs or evaluating our ability to do so (Charniak and Johnson, 2001). Moreover, this work showed

Lease, Matthew

129

The Frequency of DYT1 (GAG Deletion) Mutation in Primary Dystonia Patients from Iran  

E-Print Network [OSTI]

The Frequency of DYT1 (GAG Deletion) Mutation in Primary Dystonia Patients from Iran Mohammad Hamid. Molecular Medicine Division, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran 2. Medical Genetics Department, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran 3

Boyer, Edmond

130

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

131

Split Vertex Deletion meets Vertex Cover: New fixed-parameter and exact exponential-time algorithms  

Science Journals Connector (OSTI)

In the Split Vertex Deletion problem, given a graph G and an integer k, we ask whether one can delete k vertices from the graph G to obtain a split graph (i.e., a graph, whose vertex set can be partitioned into two sets: one inducing a clique and the second one inducing an independent set). In this paper we study exact (exponential-time) and fixed-parameter algorithms for Split Vertex Deletion.• We show that, up to a factor quasipolynomial in k and polynomial in n, the Split Vertex Deletion problem can be solved in the same time as the well-studied Vertex Cover problem. By plugging in the currently best fixed-parameter algorithm for Vertex Cover due to Chen et al. [Theor. Comput. Sci. 411 (40–42) (2010) 3736–3756], we obtain an algorithm that solves Split Vertex Deletion in time O ( 1.2738 k k O ( log k ) + n 3 ) . • We show that all maximal induced split subgraphs of a given n-vertex graph can be listed in O ( 3 n / 3 n O ( log n ) ) time. To achieve our goals, we prove the following structural result that may be of independent interest: for any graph G we may compute a family P of size n O ( log n ) containing partitions of V ( G ) into two parts, such that for any two disjoint sets X C , X I ? V ( G ) where G [ X C ] is a clique and G [ X I ] is an independent set, there is a partition in P which contains all vertices of X C on one side and all vertices of X I on the other. Moreover, the family P can be enumerated in O ( n O ( log n ) ) time.

Marek Cygan; Marcin Pilipczuk

2013-01-01T23:59:59.000Z

132

Selective Binding by the RNA Binding Domain of PKR Revealed by Affinity Richard J. Spanggord and Peter A. Beal*  

E-Print Network [OSTI]

. Spanggord and Peter A. Beal* Department of Chemistry, UniVersity of Utah, Salt Lake City, Utah 84112 Recei

Beal, Peter A.

133

Domain walls riding the wave.  

SciTech Connect (OSTI)

Recent years have witnessed a rapid proliferation of electronic gadgets around the world. These devices are used for both communication and entertainment, and it is a fact that they account for a growing portion of household energy consumption and overall world consumption of electricity. Increasing the energy efficiency of these devices could have a far greater and immediate impact than a gradual switch to renewable energy sources. The advances in the area of spintronics are therefore very important, as gadgets are mostly comprised of memory and logic elements. Recent developments in controlled manipulation of magnetic domains in ferromagnet nanostructures have opened opportunities for novel device architectures. This new class of memories and logic gates could soon power millions of consumer electronic devices. The attractiveness of using domain-wall motion in electronics is due to its inherent reliability (no mechanical moving parts), scalability (3D scalable architectures such as in racetrack memory), and nonvolatility (retains information in the absence of power). The remaining obstacles in widespread use of 'racetrack-type' elements are the speed and the energy dissipation during the manipulation of domain walls. In their recent contribution to Physical Review Letters, Oleg Tretiakov, Yang Liu, and Artem Abanov from Texas A&M University in College Station, provide a theoretical description of domain-wall motion in nanoscale ferromagnets due to the spin-polarized currents. They find exact conditions for time-dependent resonant domain-wall movement, which could speed up the motion of domain walls while minimizing Ohmic losses. Movement of domain walls in ferromagnetic nanowires can be achieved by application of external magnetic fields or by passing a spin-polarized current through the nanowire itself. On the other hand, the readout of the domain state is done by measuring the resistance of the wire. Therefore, passing current through the ferromagnetic wire is the preferred method, as it combines manipulation and readout of the domain-wall state. The electrons that take part in the process of readout and manipulation of the domain-wall structure in the nanowire do so through the so-called spin transfer torque: When spin-polarized electrons in the ferromagnet nanowire pass through the domain wall they experience a nonuniform magnetization, and they try to align their spins with the local magnetic moments. The force that the electrons experience has a reaction force counterpart that 'pushes' the local magnetic moments, resulting in movement of the domain wall in the direction of the electron flow through the spin-transfer torque. The forces between the electrons and the local magnetic moments in the ferromagnet also create additional electrical resistance for the electrons passing through the domain wall. By measuring resistance across a segment of the nanowire, one determines if a domain wall is present; i.e., one can read the stored information. The interaction of the spin-polarized electrons with the domain wall in the ferromagnetic nanowire is not very efficient. Even for materials achieving high polarization of the free electrons, it is very difficult to move the magnetic domain wall. Several factors contribute to this problem, with imperfections of the ferromagnetic nanowire that cause domain-wall pinning being the dominant one. Permalloy nanowires, one of the best candidates for domain-wall-based memory and logic devices, require current densities of the order of 10{sup 8} A/cm{sup 2} in order to move a domain wall from a pinning well. Considering that this current has to pass through a relatively long wire, it is not very difficult to imagine that most of the energy will go to Joule heating. The efficiency of the process - the ratio of the energy converted to domain-wall motion to the total energy consumed - is comparable to that of an incandescent light bulb converting electricity to light. A step towards more efficient domain-wall-based memory devices is the advance of using alternating currents or curren

Karapetrov, G.; Novosad, V.; Materials Science Division

2010-11-01T23:59:59.000Z

134

Domain Walls, Triples and Acceleration  

E-Print Network [OSTI]

We present a construction of domain walls in string theory. The domain walls can bridge both Minkowski and AdS string vacua. A key ingredient in the construction are novel classical Yang-Mills configurations, including instantons, which interpolate between toroidal Yang-Mills vacua. Our construction provides a concrete framework for the study of inflating metrics in string theory. In some cases, the accelerating space-time comes with a holographic description. The general form of the holographic dual is a field theory with parameters that vary over space-time.

Travis Maxfield; Savdeep Sethi

2014-04-09T23:59:59.000Z

135

Non-algebraic quadrature domains  

E-Print Network [OSTI]

May 28, 2012 ... “Quadrature domain in the classical sense” is used to specify the restricted case we ...... monotonically” on ?. 4. The procedure used in the proof of Theorem 3.1 can also be used to ... Royal Inst. of Technology, Stockholm.

2012-05-28T23:59:59.000Z

136

Making recommendations from multiple domains  

Science Journals Connector (OSTI)

Given the vast amount of information on the World Wide Web, recommender systems are increasingly being used to help filter irrelevant data and suggest information that would interest users. Traditional systems make recommendations based on a single domain ... Keywords: collaborative filtering, personalization, recommendation, social trust

Wei Chen; Wynne Hsu; Mong Li Lee

2013-08-01T23:59:59.000Z

137

Structure of the Chloroplast Signal Recognition Particle (SRP) Receptor: Domain Arrangement Modulates SRP–Receptor Interaction  

Science Journals Connector (OSTI)

The signal recognition particle (SRP) pathway mediates co-translational targeting of nascent proteins to membranes. Chloroplast SRP is unique in that it does not contain the otherwise universally conserved SRP RNA, which accelerates the association between the SRP guanosine-5?-triphosphate (GTP) binding protein and its receptor FtsY in classical SRP pathways. Recently, we showed that the SRP and SRP receptor (SR) \\{GTPases\\} from chloroplast (cpSRP54 and cpFtsY, respectively) can interact with one another 400-fold more efficiently than their bacterial homologues, thus providing an explanation as to why this novel chloroplast SRP pathway bypasses the requirement for the SRP RNA. Here we report the crystal structure of cpFtsY from Arabidopsis thaliana at 2.0 Å resolution. In this chloroplast SR, the N-terminal “N” domain is more tightly packed, and a more extensive interaction surface is formed between the \\{GTPase\\} “G” domain and the N domain than was previously observed in many of its bacterial homologues. As a result, the overall conformation of apo-cpFtsY is closer to that found in the bacterial SRP•FtsY complex than in free bacterial FtsY, especially with regard to the relative orientation of the N and G domains. In contrast, active-site residues in the G domain are mispositioned, explaining the low basal GTP binding and hydrolysis activity of free cpFtsY. This structure emphasizes proper N–G domain arrangement as a key factor in modulating the efficiency of SRP–receptor interaction and helps account, in part, for the faster kinetics at which the chloroplast SR interacts with its binding partner in the absence of an SRP RNA.

Sowmya Chandrasekar; Justin Chartron; Peera Jaru-Ampornpan; Shu-ou Shan

2008-01-01T23:59:59.000Z

138

Structural Basis for Ubiquitin Recognition by the Otu1 Ovarian Tumor Domain Protein  

SciTech Connect (OSTI)

Ubiquitination of proteins modifies protein function by either altering their activities, promoting their degradation, or altering their subcellular localization. Deubiquitinating enzymes are proteases that reverse this ubiquitination. Previous studies demonstrate that proteins that contain an ovarian tumor (OTU) domain possess deubiquitinating activity. This domain of {approx}130 amino acids is weakly similar to the papain family of proteases and is highly conserved from yeast to mammals. Here we report structural and functional studies on the OTU domain-containing protein from yeast, Otu1. We show that Otu1 binds polyubiquitin chain analogs more tightly than monoubiquitin and preferentially hydrolyzes longer polyubiquitin chains with Lys{sup 48} linkages, having little or no activity on Lys{sup 63}- and Lys{sup 29}-linked chains. We also show that Otu1 interacts with Cdc48, a regulator of the ER-associated degradation pathway. We also report the x-ray crystal structure of the OTU domain of Otu1 covalently complexed with ubiquitin and carry out structure-guided mutagenesis revealing a novel mode of ubiquitin recognition and a variation on the papain protease catalytic site configuration that appears to be conserved within the OTU family of ubiquitin hydrolases. Together, these studies provide new insights into ubiquitin binding and hydrolysis by yeast Otu1 and other OTU domain-containing proteins.

T Messick; N Russel; A Iwata; K Sarachan; R Shiekhattar; I Shanks; F Reyes-Turcu; K Wilkinson; R Marmorstein

2011-12-31T23:59:59.000Z

139

Effect of GPD1 and GPD2 Deletion on the Production of Glycerol and Ethanol in the Yeast Saccharomyces cerevisiae  

Science Journals Connector (OSTI)

Glycerol is the main by-product in ethanol production during the very high gravity (VHG...Saccharomyces cerevisiae. This study investigates the effect of GPD1 or GPD...2 (encoding 3-phosphate dehydrogenase) delet...

Jingjing Yu; Jian Dong; Cuiying Zhang…

2014-01-01T23:59:59.000Z

140

The Fas-FADD Death Domain Complex Structure Unravels Signalling by Receptor Clustering  

SciTech Connect (OSTI)

The death inducing signalling complex (DISC) formed by Fas receptor, FADD (Fas-associated death domain protein) and caspase 8 is a pivotal trigger of apoptosis1, 2, 3. The Fas-FADD DISC represents a receptor platform, which once assembled initiates the induction of programmed cell death. A highly oligomeric network of homotypic protein interactions comprised of the death domains of Fas and FADD is at the centre of DISC formation4, 5. Thus, characterizing the mechanistic basis for the Fas-FADD interaction is crucial for understanding DISC signalling but has remained unclear largely because of a lack of structural data. We have successfully formed and isolated the human Fas-FADD death domain complex and report the 2.7 A crystal structure. The complex shows a tetrameric arrangement of four FADD death domains bound to four Fas death domains. We show that an opening of the Fas death domain exposes the FADD binding site and simultaneously generates a Fas-Fas bridge. The result is a regulatory Fas-FADD complex bridge governed by weak protein-protein interactions revealing a model where the complex itself functions as a mechanistic switch. This switch prevents accidental DISC assembly, yet allows for highly processive DISC formation and clustering upon a sufficient stimulus. In addition to depicting a previously unknown mode of death domain interactions, these results further uncover a mechanism for receptor signalling solely by oligomerization and clustering events.

Scott, F.; Stec, B; Pop, C; Dobaczewska, M; Lee, J; Monosov, E; Robinson, H; Salvesen, G; Schwarzenbacher, R; Riedl, S

2009-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" 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

Determination of the Sequence Specificity of XIAP BIR Domains by Screening a Combinatorial Peptide Library  

Science Journals Connector (OSTI)

Database searches with the BIR2- and BIR3-binding consensus sequences revealed a large number of potential target proteins. ... Since BIR domains appear to recognize only the N-terminal few residues of a protein, in principle, one should be able to identify their partner proteins by determining their sequence specificities and then using the resulting binding motifs to search the protein and/or genomic databases. ... To facilitate unambiguous sequence determination by mass spectrometry, 5% Ac-Gly was added to the coupling reactions of Leu and Lys, whereas 5% Ac-Ala was added to the coupling reactions of Nle (18, 23). ...

Michael C. Sweeney; Xianxi Wang; Junguk Park; Yusen Liu; Dehua Pei

2006-11-09T23:59:59.000Z

142

Allostery Is an Intrinsic Property of the Protease Domain of DegS Implications for Enzyme Function and Evolution  

SciTech Connect (OSTI)

DegS is a periplasmic Escherichia coli protease, which functions as a trimer to catalyze the initial rate-limiting step in a proteolytic cascade that ultimately activates transcription of stress response genes in the cytoplasm. Each DegS subunit consists of a protease domain and a PDZ domain. During protein folding stress, DegS is allosterically activated by peptides exposed in misfolded outer membrane porins, which bind to the PDZ domain and stabilize the active protease. It is not known whether allostery is conferred by the PDZ domains or is an intrinsic feature of the trimeric protease domain. Here, we demonstrate that free DegS{sup {Delta}PDZ} equilibrates between active and inactive trimers with the latter species predominating. Substrate binding stabilizes active DegS{sup {Delta}PDZ} in a positively cooperative fashion. Mutations can also stabilize active DegS{sup {Delta}PDZ} and produce an enzyme that displays hyperbolic kinetics and degrades substrate with a maximal velocity within error of that for fully activated, intact DegS. Crystal structures of multiple DegS{sup {Delta}PDZ} variants, in functional and non-functional conformations, support a two-state model in which allosteric switching is mediated by changes in specific elements of tertiary structure in the context of an invariant trimeric base. Overall, our results indicate that protein substrates must bind sufficiently tightly and specifically to the functional conformation of DegS{sup {Delta}PDZ} to assist their own degradation. Thus, substrate binding alone may have regulated the activities of ancestral DegS trimers with subsequent fusion of the protease domain to a PDZ domain, resulting in ligand-mediated regulation.

Sohn, Jungsan; Grant, Robert A.; Sauer, Robert T. (MIT)

2010-12-02T23:59:59.000Z

143

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

144

Determining the DUF55-domain structure of human thymocyte nuclear protein 1 from crystals partially twinned by tetartohedry  

SciTech Connect (OSTI)

Human thymocyte nuclear protein 1 (hTHYN1) contains a unique DUF55 domain of 167 residues (55-221), but its cellular function is unclear. Crystals of DUF55 belong to the trigonal space group P3{sub 1}, but twinning causes the data to approach an apparent 622 symmetry. Two datasets to 2.3 {angstrom} resolution were collected. Statistical analysis confirmed that both datasets were partially twinned by tetartohedry. Tetartohedral twin fractions were estimated. After the structure was determined, only one twofold axis of rotational pseudosymmetry was found in the crystal structure. Using the DALI program, a YTH domain, which is a potential RNA binding domain from human YTH domain-containing protein 2, was identified to have the most similar three-dimensional fold to DUF55. It is implied that DUF55 might be a potential RNA-related domain.

Yu, Feng; Song, Aixin; Xu, Chunyan; Sun, Lihua; Li, Jian; Tang, Lin; Yu, Minmin; Yeates, Todd O.; Hu, Hongyu; He, Jianhua

2009-06-06T23:59:59.000Z

145

How to Run DomainParser  

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

Run DomainParser Run DomainParser The structure for partition needs to be prepared in the PDB format. In most cases, running DomainParser using defaults should give satisfactory partitions. However, several options offered in DomainParser can provide a partition that a user desires or correct some overcut/undercut partitions. Here, we use a PDB file 1atna.pdb as an example to show how to use the DomainParser program. Run DomainParser using defaults: domainparser 1atna.pdb The output shows the partition for each domain in terms of ranges of residue numbers: 4 domains have been found for 1atna: Domain 1 : 34-96. Domain 2 : 181-272. Domain 3 : 148-180; 273-336. Domain 4 : 0-33; 97-147; 337-372. The program also generates a new file 1atna_dom.pdb, with the "temperature factor" column (column 61-66 of an "ATOM" entry) showing domain numbers. A

146

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

147

Dynamics of Domain Wall Networks  

E-Print Network [OSTI]

Networks or webs of domain walls are admitted in Abelian or non-Abelian gauge theory coupled to fundamental Higgs fields with complex masses. We examine the dynamics of the domain wall loops by using the moduli approximation and find a phase rotation induces a repulsive force which can be understood as a Noether charge of Q-solitons. Non-Abelian gauge theory allows different types of loops which can be deformed to each other by changing a modulus. This admits the moduli geometry like a sandglass made by gluing the tips of the two cigar-(cone-)like metrics of a single triangle loop. We conclude that the sizes of all loops tend to grow for a late time in general models with complex Higgs masses, while the sizes are stabilized at some values once triplet masses are introduced for the Higgs fields. We also show that the stationary motion on the moduli space of the domain wall webs represents 1/4 BPS Q-webs of walls.

Minoru Eto; Toshiaki Fujimori; Takayuki Nagashima; Muneto Nitta; Keisuke Ohashi; Norisuke Sakai

2007-07-22T23:59:59.000Z

148

Dynamics of domain wall networks  

SciTech Connect (OSTI)

Networks or webs of domain walls are admitted in Abelian or non-Abelian gauge theory coupled to fundamental Higgs fields with complex masses. We examine the dynamics of the domain wall loops by using the moduli approximation and find a phase rotation induces a repulsive force which can be understood as a Noether charge of Q-solitons. Non-Abelian gauge theory allows different types of loops which can be deformed to each other by changing a modulus. This admits the moduli geometry like a sandglass made by gluing the tips of the two cigar-(cone-)like metrics of a single triangle loop. We conclude that the sizes of all loops tend to grow for a late time in general models with complex Higgs masses, while the sizes are stabilized at some values once triplet masses are introduced for the Higgs fields. We also show that the stationary motion on the moduli space of the domain wall webs represents 1/4 Bogomol'nyi-Prasad-Sommerfield Q-webs of walls.

Eto, Minoru [INFN, Sezione di Pisa, Largo Pontecorvo, 3, Ed. C, 56127 Pisa (Italy); Department of Physics, University of Pisa Largo Pontecorvo, 3, Ed. C, 56127 Pisa (Italy); Fujimori, Toshiaki; Nagashima, Takayuki; Sakai, Norisuke [Department of Physics, Tokyo Institute of Technology, Tokyo 152-8551 (Japan); Nitta, Muneto [Department of Physics, Keio University, Hiyoshi, Yokohama, Kanagawa 223-8521 (Japan); Ohashi, Keisuke [Department of Applied Mathematics and Theoretical Physics, University of Cambridge, CB3 0WA (United Kingdom)

2007-12-15T23:59:59.000Z

149

Performance Assessment Report Domain CHP System  

E-Print Network [OSTI]

Performance Assessment Report for the Domain CHP System November 2005 By Burns & McDonnell Engineering #12;Domain CHP System Performance Assessment Report for the Packaged Cooling, Heating and Power

Oak Ridge National Laboratory

150

15 FUNCTIONAL SERVICE DOMAIN ARCHITECTURE MANAGEMENT  

E-Print Network [OSTI]

. Based on a better understanding of functional domain architecture management approaches, situational, enterprise architecture management, situational method engineering #12;258 Part 5: Design Science 115 FUNCTIONAL SERVICE DOMAIN ARCHITECTURE MANAGEMENT: Building the Foundation for Situational

Paris-Sud XI, Université de

151

Language Modeling for limited-data domains  

E-Print Network [OSTI]

With the increasing focus of speech recognition and natural language processing applications on domains with limited amount of in-domain training data, enhanced system performance often relies on approaches involving model ...

Hsu, Bo-June (Bo-June Paul)

2009-01-01T23:59:59.000Z

152

Frequency domain design of interval controller  

E-Print Network [OSTI]

significant role in the analysis and design of interval systems. Its external properties are also discussed. The image set approach & frequency domain criteria can be used to calculate the IP stability margin. The frequency domain criteria are used...

Park, Wunyong

1993-01-01T23:59:59.000Z

153

Labelling Heuristics for CSP Application Domains  

E-Print Network [OSTI]

Labelling Heuristics for CSP Application Domains Zeynep K#16;z#16;ltan Computer Science Division an application domain as a family of CSP models, so as to exhibit the generic constraint store for all models store and the domain propagation during search is analysed, so as to infer | before modelling any CSP

Rossi, Francesca

154

Topoisomerase II? Binding Domains of Adenomatous Polyposis Coli Influence Cell Cycle Progression and Aneuploidy  

E-Print Network [OSTI]

the original author and source are credited. Funding: This work was funded in part by NIH RO1 CA10922 (Y.W. and K.L.N.), GI Special Program of Research Excellence CA95103 (R.J.C), NCI RO1 CA46413 (R.J.C), GM33944 (N.O.), Higuchi Biosciences Center J.R. & Inez... Jay Award (Y.W. and K.L.N.), and the KUCC Pilot Project Award (Y.W. and K.L.N.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have...

Wang, Yang; Coffey, Robert J.; Osheroff, Neil; Neufeld, Kristi L.

2010-04-02T23:59:59.000Z

155

Distinct domains of antizyme required for binding and proteolysis of ornithine decarboxylase.  

Science Journals Connector (OSTI)

...now to determine the partners with which it interacts and the ambit and conse- quences of those interactions. ACKNOWLEDGMENTS...and M. R. Maurizi. 1992. Regulation by prote- olysis: energy-dependent proteases and their targets. Microbiol. Rev...

X Li; P Coffino

1994-01-01T23:59:59.000Z

156

Cellulose Binding Domains of a Phytophthora Cell Wall Protein Are Novel Pathogen-Associated Molecular Patterns  

Science Journals Connector (OSTI)

...except after heat treatment of the medium (Meindl...and neutralized by dialysis against 100 volumes of water at 4C for 16 h...strain GV3101 by electroporation, and transformed...et al. (1980). Electron Microscopy and Immunogold...

Elodie Gaulin; Nani Dramé; Claude Lafitte; Trudy Torto-Alalibo; Yves Martinez; Carine Ameline-Torregrosa; Moustafa Khatib; Honoré Mazarguil; François Villalba-Mateos; Sophien Kamoun; Christian Mazars; Bernard Dumas; Arnaud Bottin; Marie-Thérèse Esquerré-Tugayé; Martina Rickauer

2006-06-09T23:59:59.000Z

157

Mechanism of membrane binding of the C2 domains of conventional protein kinase C isoforms  

E-Print Network [OSTI]

Kinase Assay for PKC?-WT, PKC?-T250A, and PKC? -T250D -CaCl2+CaCl2 Activity (nmol/minP) Transfected WT Transfected T250A

Scott, Angela Michelle

2006-01-01T23:59:59.000Z

158

Crystallographic and Biochemical Analysis of the Ran-Binding Zinc Finger Domain  

E-Print Network [OSTI]

The nuclear pore complex (NPC) resides in circular openings within the nuclear envelope and serves as the sole conduit to facilitate nucleocytoplasmic transport in eukaryotes. The asymmetric distribution of the small G ...

Partridge, James R.

159

INTRINSIC DISORDER WITHIN AND FLANKING THE DNA-BINDING DOMAINS OF HUMAN TRANSCRIPTION FACTORS  

E-Print Network [OSTI]

disordered. The role these intrinsically disordered regions (IDRs) play in protein function is an area of rigidity. Rather, a protein may sample an ensemble of global conformations; parts of the protein may across the ensemble. These latter regions are sometimes termed `intrinsically disordered regions' (IDRs

Bulyk, Martha L.

160

Crystal structure of mouse coronavirus receptor-binding domain complexed with its murine receptor  

E-Print Network [OSTI]

Lafayette, IN, and approved May 19, 2011 (received for review March 17, 2011) Coronaviruses have evolved

Li, Fang

Note: This page contains sample records for the topic "bind deleted domain" 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

Crystal structure of the ligand-binding domain of the human nuclear receptor RXR-?  

Science Journals Connector (OSTI)

... .5 A were improved by solvent-flattening using the program SQUASH46 and subsequently used for re-refining the heavy-atom parameters. The solvent content in the crystal was calculated as 55% ...

William Bourguet; Marc Ruff; Pierre Chambon; Hinrich Gronemeyer; Dino Moras

1995-06-01T23:59:59.000Z

162

E-Print Network 3.0 - affinity heparin-binding domain Sample...  

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

for Biotechnology and Interdisciplinary Studies & Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute Collection: Biotechnology ; Chemistry 2 Many...

163

Unusual Rel-like architecture in the DNA-binding domain of the transcription factor NFATc  

Science Journals Connector (OSTI)

... based on 1,087 effective non-hydrogen-bond constraints using the program DIANA24 with three REDAC cycles. Structures with target functions below 10 were further refined by simulated annealing using ...

Scot A. Wolfe; Pei Zhou; Volker Dötsch; Lin Chen; Angie You; Steffan N. Ho; Gerald R. Crabtree; Gerhard Wagner; Gregory L. Verdine

1997-01-09T23:59:59.000Z

164

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

E-Print Network [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 ...

Sosa, Brian A.

165

Structural and dynamic characterization of eukaryotic gene regulatory protein domains in solution  

SciTech Connect (OSTI)

Solution NMR was primarily used to characterize structure and dynamics in two different eukaryotic protein systems: the {delta}-Al-{var_epsilon} activation domain from c-jun and the Drosophila RNA-binding protein Sex-lethal. The second system is the Drosophila Sex-lethal (Sxl) protein, an RNA-binding protein which is the ``master switch`` in sex determination. Sxl contains two adjacent RNA-binding domains (RBDs) of the RNP consensus-type. The NMR spectrum of the second RBD (Sxl-RBD2) was assigned using multidimensional heteronuclear NMR, and an intermediate-resolution family of structures was calculated from primarily NOE distance restraints. The overall fold was determined to be similar to other RBDs: a {beta}{alpha}{beta}-{beta}{alpha}{beta} pattern of secondary structure, with the two helices packed against a 4-stranded anti-parallel {beta}-sheet. In addition {sup 15}N T{sub 1}, T{sub 2}, and {sup 15}N/{sup 1}H NOE relaxation measurements were carried out to characterize the backbone dynamics of Sxl-RBD2 in solution. RNA corresponding to the polypyrimidine tract of transformer pre-mRNA was generated and titrated into 3 different Sxl-RBD protein constructs. Combining Sxl-RBD1+2 (bht RBDs) with this RNA formed a specific, high affinity protein/RNA complex that is amenable to further NMR characterization. The backbone {sup 1}H, {sup 13}C, and {sup 15}N resonances of Sxl-RBD1+2 were assigned using a triple-resonance approach, and {sup 15}N relaxation experiments were carried out to characterize the backbone dynamics of this complex. The changes in chemical shift in Sxl-RBD1+2 upon binding RNA are observed using Sxl-RBD2 as a substitute for unbound Sxl-RBD1+2. This allowed the binding interface to be qualitatively mapped for the second domain.

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

1996-05-01T23:59:59.000Z

166

The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 ? resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator  

Science Journals Connector (OSTI)

The crystal structure of the first representative of the Pfam PF07336 (DUF1470) family reveals a two-domain organization that contains a new fold, termed the ABATE domain, at the N-terminus and a treble-clef zinc finger that is likely to bind DNA at the C-terminus.

Bakolitsa, C.

2009-10-27T23:59:59.000Z

167

Crystal Structures of the Tetratricopeptide Repeat Domains of Kinesin Light Chains: Insight into Cargo Recognition Mechanisms  

SciTech Connect (OSTI)

Kinesin-1 transports various cargos along the axon by interacting with the cargos through its light chain subunit. Kinesin light chains (KLC) utilize its tetratricopeptide repeat (TPR) domain to interact with over 10 different cargos. Despite a high sequence identity between their TPR domains (87%), KLC1 and KLC2 isoforms exhibit differential binding properties towards some cargos. We determined the structures of human KLC1 and KLC2 tetratricopeptide repeat (TPR) domains using X-ray crystallography and investigated the different mechanisms by which KLCs interact with their cargos. Using isothermal titration calorimetry, we attributed the specific interaction between KLC1 and JNK-interacting protein 1 (JIP1) cargo to residue N343 in the fourth TRP repeat. Structurally, the N343 residue is adjacent to other asparagines and lysines, creating a positively charged polar patch within the groove of the TPR domain. Whereas, KLC2 with the corresponding residue S328 did not interact with JIP1. Based on these finding, we propose that N343 of KLC1 can form 'a carboxylate clamp' with its neighboring asparagine to interact with JIP1, similar to that of HSP70/HSP90 organizing protein-1's (HOP1) interaction with heat shock proteins. For the binding of cargos shared by KLC1 and KLC2, we propose a different site located within the groove but not involving N343. We further propose a third binding site on KLC1 which involves a stretch of polar residues along the inter-TPR loops that may form a network of hydrogen bonds to JIP3 and JIP4. Together, these results provide structural insights into possible mechanisms of interaction between KLC TPR domains and various cargo proteins.

Zhu, Haizhong; Lee, Han Youl; Tong, Yufeng; Hong, Bum-Soo; Kim, Kyung-Phil; Shen, Yang; Lim, Kyung Jik; Mackenzie, Farrell; Tempel, Wolfram; Park, Hee-Won (SGC-Toronto); (PPCS); (Toronto)

2012-10-23T23:59:59.000Z

168

Word Domain Disambiguation via Word Sense Disambiguation  

SciTech Connect (OSTI)

Word subject domains have been widely used to improve the perform-ance of word sense disambiguation al-gorithms. However, comparatively little effort has been devoted so far to the disambiguation of word subject do-mains. The few existing approaches have focused on the development of al-gorithms specific to word domain dis-ambiguation. In this paper we explore an alternative approach where word domain disambiguation is achieved via word sense disambiguation. Our study shows that this approach yields very strong results, suggesting that word domain disambiguation can be ad-dressed in terms of word sense disam-biguation with no need for special purpose algorithms.

Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.

2006-06-04T23:59:59.000Z

169

Characterization of xylan utilization and discovery of a new endoxylanase in Thermoanaerobacterium saccharolyticum through targeted gene deletions  

SciTech Connect (OSTI)

The economical production of fuels and commodity chemicals from lignocellulose requires the utilization of both the cellulose and hemicellulose fractions. Xylanase enzymes allow greater utilization of hemicellulose while also increasing cellulose hydrolysis. Recent metabolic engineering efforts have resulted in a strain of Thermoanaerobacterium saccharolyticum that can convert C(5) and C(6) sugars, as well as insoluble xylan, into ethanol at high yield. To better understand the process of xylan solubilization in this organism, a series of targeted deletions were constructed in the homoethanologenic T. saccharolyticum strain M0355 to characterize xylan hydrolysis and xylose utilization in this organism. While the deletion of -xylosidase xylD slowed the growth of T. saccharolyticum on birchwood xylan and led to an accumulation of short-chain xylo-oligomers, no other single deletion, including the deletion of the previously characterized endoxylanase XynA, had a phenotype distinct from that of the wild type. This result indicates a multiplicity of xylanase enzymes which facilitate xylan degradation in T. saccharolyticum. Growth on xylan was prevented only when a previously uncharacterized endoxylanase encoded by xynC was also deleted in conjunction with xynA. Sequence analysis of xynC indicates that this enzyme, a low-molecular-weight endoxylanase with homology to glycoside hydrolase family 11 enzymes, is secreted yet untethered to the cell wall. Together, these observations expand our understanding of the enzymatic basis of xylan hydrolysis by T. saccharolyticum.

Podkaminer, Kara K [Thayer School of Engineering at Dartmouth; Guss, Adam M [ORNL; McKenzie, Heather [University of California, Riverside; Hogsett, David [Mascoma Corporation; Lynd, Lee R [Thayer School of Engineering at Dartmouth

2012-01-01T23:59:59.000Z

170

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

171

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

172

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

173

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

174

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

175

NATIONAL PLAN TO ACHIEVE MARITIME DOMAIN AWARENESS  

E-Print Network [OSTI]

infrastructure following attack or similar disruption. · Maritime Transportation System Security Plan responds regarding the maritime domain. · Maritime Commerce Security Plan establishes a comprehensive plan to secure

Acton, Scott

176

Development of Nonlinear SSI Time Domain Methodology  

Broader source: Energy.gov [DOE]

Development of Nonlinear SSI Time Domain Methodology Justin Coleman, P.E. Nuclear Science and Technology Idaho National Laboratory October 22, 2014

177

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

178

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

179

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

180

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 54 kDa subunit (cpSRP54) and a unique 43 kDa 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 Träger; Danja Schünemann

2008-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" 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

New Things For Windows 7 Old icons on the desktop that referenced Office 2007 applications will need to be deleted and  

E-Print Network [OSTI]

New Things For Windows 7 Old icons on the desktop that referenced Office 2007 applications will need to be deleted and replaced with icons for Office 2010. To do this, right click on the non-working icon and select delete or simply drag it to the Recycle Bin. To add the new icon, go to Start, then All

Bogaerts, Steven

182

Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions  

Science Journals Connector (OSTI)

This 22q11 deletion patient was established to have a novel 2.3 Mb deletion with a proximal breakpoint located between genetic markers RH48663 and RH48348 and a distal breakpoint between markers D22S1138 and SHGC

Raihan K Uddin; Yang Zhang; Victoria Mok Siu; Yao-Shan Fan…

2006-03-01T23:59:59.000Z

183

The Abstract Domain of Segmented Ranking Functions  

E-Print Network [OSTI]

function by abstract in- terpretation. We build our work on their proposed general framework, and we designThe Abstract Domain of Segmented Ranking Functions Caterina Urban ´Ecole Normale Sup´erieure - CNRS - INRIA, Paris, France urban@di.ens.fr Abstract. We present a parameterized abstract domain for proving

Paris-Sud XI, Université de

184

Hidden Rotational Symmetries in Magnetic Domain Patterns  

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

Hidden Rotational Symmetries in Magnetic Domain Patterns Print Hidden Rotational Symmetries in Magnetic Domain Patterns Print Magnetic thin films have complicated domain patterns that may or may not repeat with each cycle through a hysteresis loop. A magnetic thin film with perpendicular anisotropy, such as that used in computer hard drives, for example, commonly exhibits labyrinthine domain patterns. These patterns are disordered over a macroscopic length scale, and intuitively we do not expect to observe any symmetry in such systems. Scientists at the ALS, the University of Oregon, and the University of California, San Diego, have recently used coherent soft x-ray scattering with angular Fourier analysis to discover that the disordered domain patterns do, in fact, exhibit rotational symmetries, which can be as small as two-fold or as large as 30-fold. Their study of magnetic symmetries gives scientists a toolbox for discovering hidden symmetries in diverse material systems.

185

Slow Dynamics of Orbital Domains in Manganite  

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

Slow Dynamics of Orbital Domains in Manganite Print Slow Dynamics of Orbital Domains in Manganite Print At the ALS, an international team of researchers has used low-energy coherent x rays to extract new knowledge about the correlated motion of groups of self-assembled, outer-lying electrons in the extremely complex electronic system found in manganites. The manganite family of materials has puzzled physicists for years by defying standard models for the motion of electrons in crystals. By controlling the properties of the incident x rays, the researchers were able to map the complexity of a "half-doped" manganite into a far-field speckle diffraction pattern to study the manganite's domain dynamics. Their results suggest the material undergoes a transition characterized by the competition between a pinned orbital domain topology that remains static and mobile domain boundaries that exhibit slow, temporal fluctuations.

186

Slow Dynamics of Orbital Domains in Manganite  

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

Slow Dynamics of Orbital Domains in Manganite Print Slow Dynamics of Orbital Domains in Manganite Print At the ALS, an international team of researchers has used low-energy coherent x rays to extract new knowledge about the correlated motion of groups of self-assembled, outer-lying electrons in the extremely complex electronic system found in manganites. The manganite family of materials has puzzled physicists for years by defying standard models for the motion of electrons in crystals. By controlling the properties of the incident x rays, the researchers were able to map the complexity of a "half-doped" manganite into a far-field speckle diffraction pattern to study the manganite's domain dynamics. Their results suggest the material undergoes a transition characterized by the competition between a pinned orbital domain topology that remains static and mobile domain boundaries that exhibit slow, temporal fluctuations.

187

Slow Dynamics of Orbital Domains in Manganite  

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

Slow Dynamics of Orbital Domains in Manganite Print Slow Dynamics of Orbital Domains in Manganite Print At the ALS, an international team of researchers has used low-energy coherent x rays to extract new knowledge about the correlated motion of groups of self-assembled, outer-lying electrons in the extremely complex electronic system found in manganites. The manganite family of materials has puzzled physicists for years by defying standard models for the motion of electrons in crystals. By controlling the properties of the incident x rays, the researchers were able to map the complexity of a "half-doped" manganite into a far-field speckle diffraction pattern to study the manganite's domain dynamics. Their results suggest the material undergoes a transition characterized by the competition between a pinned orbital domain topology that remains static and mobile domain boundaries that exhibit slow, temporal fluctuations.

188

Hidden Rotational Symmetries in Magnetic Domain Patterns  

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

Hidden Rotational Symmetries in Hidden Rotational Symmetries in Magnetic Domain Patterns Hidden Rotational Symmetries in Magnetic Domain Patterns Print Wednesday, 27 June 2012 00:00 Magnetic thin films have complicated domain patterns that may or may not repeat with each cycle through a hysteresis loop. A magnetic thin film with perpendicular anisotropy, such as that used in computer hard drives, for example, commonly exhibits labyrinthine domain patterns. These patterns are disordered over a macroscopic length scale, and intuitively we do not expect to observe any symmetry in such systems. Scientists at the ALS, the University of Oregon, and the University of California, San Diego, have recently used coherent soft x-ray scattering with angular Fourier analysis to discover that the disordered domain patterns do, in fact, exhibit rotational symmetries, which can be as small as two-fold or as large as 30-fold. Their study of magnetic symmetries gives scientists a toolbox for discovering hidden symmetries in diverse material systems.

189

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...

190

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

191

Evaluating the Reference and Representation of Domain Concepts in APIs  

E-Print Network [OSTI]

Evaluating the Reference and Representation of Domain Concepts in APIs Daniel Ratiu, Jan Jürjens ICPC 12 June 2008 #12;Domain specific APIs reflect the domain knowledge Programs World c b d API reflection of domain Developed program a Domain knowledge Real World #12;APIs' Quality through

Jurjens, Jan

192

A structural model of anti-anti-[sigma];#963; inhibition by a two-component receiver domain: the PhyR stress response regulator  

SciTech Connect (OSTI)

PhyR is a hybrid stress regulator conserved in {alpha}-proteobacteria that contains an N-terminal {sigma}-like (SL) domain and a C-terminal receiver domain. Phosphorylation of the receiver domain is known to promote binding of the SL domain to an anti-{sigma} factor. PhyR thus functions as an anti-anti-{sigma} factor in its phosphorylated state. We present genetic evidence that Caulobacter crescentus PhyR is a phosphorylation-dependent stress regulator that functions in the same pathway as {sigma}{sup T} and its anti-{sigma} factor, NepR. Additionally, we report the X-ray crystal structure of PhyR at 1.25 {angstrom} resolution, which provides insight into the mechanism of anti-anti-{sigma} regulation. Direct intramolecular contact between the PhyR receiver and SL domains spans regions {sigma}{sub 2} and {sigma}{sub 4}, likely serving to stabilize the SL domain in a closed conformation. The molecular surface of the receiver domain contacting the SL domain is the structural equivalent of {alpha}4-{beta}5-{alpha}5, which is known to undergo dynamic conformational change upon phosphorylation in a diverse range of receiver proteins. We propose a structural model of PhyR regulation in which receiver phosphorylation destabilizes the intramolecular interaction between SL and receiver domains, thereby permitting regions {sigma}{sub 2} and {sigma}{sub 4} in the SL domain to open about a flexible connector loop and bind anti-{sigma} factor.

Herrou, Julien; Foreman, Robert; Fiebig, Aretha; Crosson, Sean (UC)

2012-03-30T23:59:59.000Z

193

A structural model of anti-anti-[sigma] inhibition by a two-component receiver domain: the PhyR stress response regulator  

SciTech Connect (OSTI)

PhyR is a hybrid stress regulator conserved in {alpha}-proteobacteria that contains an N-terminal {sigma}-like (SL) domain and a C-terminal receiver domain. Phosphorylation of the receiver domain is known to promote binding of the SL domain to an anti-{sigma} factor. PhyR thus functions as an anti-anti-{sigma} factor in its phosphorylated state. We present genetic evidence that Caulobacter crescentus PhyR is a phosphorylation-dependent stress regulator that functions in the same pathway as {sigma}{sup T} and its anti-{sigma} factor, NepR. Additionally, we report the X-ray crystal structure of PhyR at 1.25 {angstrom} resolution, which provides insight into the mechanism of anti-anti-{sigma} regulation. Direct intramolecular contact between the PhyR receiver and SL domains spans regions {sigma}{sub 2} and {sigma}{sub 4}, likely serving to stabilize the SL domain in a closed conformation. The molecular surface of the receiver domain contacting the SL domain is the structural equivalent of {alpha}4-{beta}5-{alpha}5, which is known to undergo dynamic conformational change upon phosphorylation in a diverse range of receiver proteins. We propose a structural model of PhyR regulation in which receiver phosphorylation destabilizes the intramolecular interaction between SL and receiver domains, thereby permitting regions {sigma}{sub 2} and {sigma}{sub 4} in the SL domain to open about a flexible connector loop and bind anti-{sigma} factor.

Herrou, Julien; Foreman, Robert; Fiebig, Aretha; Crosson, Sean (UC)

2012-05-09T23:59:59.000Z

194

Time-Domain Electromagnetics | Open Energy Information  

Open Energy Info (EERE)

Time-Domain Electromagnetics Time-Domain Electromagnetics Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Time-Domain Electromagnetics Details Activities (10) Areas (10) Regions (0) NEPA(0) Exploration Technique Information Exploration Group: Geophysical Techniques Exploration Sub Group: Electrical Techniques Parent Exploration Technique: Electromagnetic Sounding Techniques Information Provided by Technique Lithology: Detection of rock units or geological features with contrasting apparent resistivity. Stratigraphic/Structural: Structural information may be inferred from TDEM data. Hydrological: Hydrological information such as depth to groundwater table may be determined. Thermal: Extent of hydrothermal alteration mineralogy may be inferred. Cost Information

195

Skyrmions from Instantons inside Domain Walls  

SciTech Connect (OSTI)

Some years ago, Atiyah and Manton described a method to construct approximate Skyrmion solutions from Yang-Mills instantons. Here we present a dynamical realization of this construction using domain walls in a five-dimensional gauge theory. The non-Abelian gauge symmetry is broken in each vacuum but restored in the core of the domain wall, allowing instantons to nestle inside the wall. We show that the world volume dynamics of the wall is given by the Skyrme model, including the four-derivative term, and the instantons appear as domain wall Skyrmions.

Eto, Minoru; Nitta, Muneto; Ohashi, Keisuke [Department of Physics, Tokyo Institute of Technology, Tokyo, 152-8551 (Japan); Tong, David [Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA (United Kingdom)

2005-12-16T23:59:59.000Z

196

Detecting Networks Employing Algorithmically Generated Domain Names  

E-Print Network [OSTI]

and hence has no com- mon IP address or a common domain name. Let ip = I be the total number of IP-addresses that are present after the F1 stage. and let d = D be total number of domain names that are present after the F1 stage. The vertices of graph G... for the second level domain name of xyz.com. At times a few of the IP addresses would end up in this component class because of a shortage in the 27 analysis period, given enough time ideally all the IP addresses (hosting server) of a single business unit...

Ashwath Kumar Krishna Reddy

2011-10-21T23:59:59.000Z

197

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

198

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

199

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

200

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

Note: This page contains sample records for the topic "bind deleted domain" 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

Dynamic Motion of Helix A in the Amino-terminal Domain of Calmodulin is Stabilized Upon Calcium Activation  

SciTech Connect (OSTI)

Calcium-dependent changes in the internal dynamics and average structures of the opposing globular domains of calmodulin (CaM), as well as their relative spatial arrangement, contribute to the productive association between CaM and a range of different target proteins to affect their functional activation. To identify dynamic structural changes involving individual ?-helical elements and their modulation by calcium activation, we have used site-directed mutagenesis to engineer a tetracysteine binding motif within helix A near the amino-terminus of calmodulin (CaM), permitting the selective and rigid attachment of the fluorescent probe 4?,5?-bis(1,3,2-dithioarsolan-2-yl) fluorescein (FlAsH) with full retention of function. The rigid tetracoordinate linkage of FlAsH to CaM, in conjunction with frequency-domain fluorescence anisotropy measurements, allows assessment of dynamic changes associated with calcium activation without interference from independent probe motion. Taking advantage of the large fluorescent enhancement associated with FlAsH binding to CaM, rates of FlAsH binding to apo- and calcium-activated CaM were 2500 ? 10 M-1 sec-1 and 187 ? 2 M-1 sec-1, respectively. There is no difference in the solvent accessibility of the bound FlAsH irrespective of calcium binding to CaM. Thus, given that FlAsH selectively labels disordered structures, the large difference in rates of FlAsH binding indicates that calcium binding stabilizes helix A. Frequency-domain anisotropy measurements of bound FlAsH indicate that prior to calcium activation, helix A undergoes large amplitude nanosecond motions. Following calcium activation, helix A becomes immobile, and structurally coupled to the overall rotation of CaM. We discuss these results in the context of a model that suggests stabilization of helix A relative to other domain elements in the CaM structure is critical to defining high-affinity binding clefts, and in promoting specific and ordered biding of the opposing lobes of CaM to target proteins.

Chen, Baowei; Mayer, M ULJANA.; Markillie, Lye MENG.; Stenoien, David L.; Squier, Thomas C.

2005-01-01T23:59:59.000Z

202

Dynamic Motion of Helix A in the Amino-terminal Domain of Calmodulin is Stabilized Upon Calcium Activation  

SciTech Connect (OSTI)

Calcium-dependent changes in the internal dynamics and average structures of the opposing globular domains of calmodulin (CaM), as well as their relative spatial arrangement, contribute to the productive association between CaM and a range of different target proteins to affect their functional activation. To identify dynamic structural changes involving individual ?-helical elements and their modulation by calcium activation, we have used site-directed mutagenesis to engineer a tetracysteine binding motif within helix A near the amino-terminus of calmodulin (CaM), permitting the selective and rigid attachment of the fluorescent probe 4?,5?-bis(1,3,2-dithioarsolan-2-yl) fluorescein (FlAsH) with full retention of function. The rigid tetracoordinate linkage of FlAsH to CaM, in conjunction with frequency-domain fluorescence anisotropy measurements, allows assessment of dynamic changes associated with calcium activation without interference from independent probe motion. Taking advantage of the large fluorescent enhancement associated with FlAsH binding to CaM, rates of FlAsH binding to apo- and calcium-activated CaM were 2500 ? 10 M-1 sec-1 and 187 ? 2 M-1 sec-1, respectively. There is no difference in the solvent accessibility of the bound FlAsH irrespective of calcium binding to CaM. Thus, given that FlAsH selectively labels disordered structures, the large difference in rates of FlAsH binding indicates that calcium binding stabilizes helix A. Frequency-domain anisotropy measurements of bound FlAsH indicate that prior to calcium activation, helix A undergoes large amplitude nanosecond motions. Following calcium activation, helix A becomes immobile, and structurally coupled to the overall rotation of CaM. We discuss these results in the context of a model that suggests stabilization of helix A relative to other domain elements in the CaM structure is critical to defining high-affinity binding clefts, and in promoting specific and ordered biding of the opposing lobes of CaM to target proteins.

Chen, Baowei; Mayer, M ULJANA.; Markillie, Lye MENG.; Stenoien, David L.; Squier, Thomas C.

2005-02-01T23:59:59.000Z

203

Open-domain textual question answering techniques  

Science Journals Connector (OSTI)

Textual question answering is a technique of extracting a sentence or text snippet from a document or document collection that responds directly to a query. Open-domain textual question answering presupposes that questions are natural and unrestricted ...

Sanda M. Harabagiu; Steven J. Maiorano; Marius A. Pa?ca

2003-09-01T23:59:59.000Z

204

Antiferromagnetic domain size and exchange bias  

E-Print Network [OSTI]

Using neutron diffraction, we measured the sizes of antiferromagnetic domains in three ferromagnet/antiferromagnet bilayer samples as a function of the magnitude and sign of exchange bias, temperature, and antiferromagnet composition. Neutron...

Fitzsimmons, M. R.; Lederman, D.; Cheon, M.; Shi, H.; Olamit, J.; Roshchin, Igor V.; Schuller, Ivan K.

2008-01-01T23:59:59.000Z

205

A Small Molecule Transcriptional Activation Domain  

Science Journals Connector (OSTI)

1 These activation domains often contain surreptitious repeats of 6?14 amino acids,4,5 and the minimal repeat unit of a natural transcriptional activator can itself function as an activator when attached to a DBD. ...

Aaron R. Minter; Brian B. Brennan; Anna K. Mapp

2004-08-07T23:59:59.000Z

206

Magnetically multiplexed heating of single domain nanoparticles  

E-Print Network [OSTI]

Selective hysteretic heating of multiple collocated types of single domain magnetic nanoparticles (SDMNPs) by alternating magnetic fields (AMFs) may offer a useful tool for biomedical applications. The possibility of ...

Romero, G.

207

Multilevel domain decomposition for electronic structure calculations  

E-Print Network [OSTI]

Multilevel domain decomposition for electronic structure calculations M. Barrault a,b,*, E. Cance method (MDD) for electronic structure calculations within semi- empirical and density functional theory electronic structure calculations A molecular system is composed of N electrons, modelled quantum

Hager, William

208

Crystallization and preliminary X-ray analysis of Ebola VP35 interferon inhibitory domain mutant proteins  

SciTech Connect (OSTI)

VP35 is one of seven structural proteins encoded by the Ebola viral genome and mediates viral replication, nucleocapsid formation and host immune suppression. The C-terminal interferon inhibitory domain (IID) of VP35 is critical for dsRNA binding and interferon inhibition. The wild-type VP35 IID structure revealed several conserved residues that are important for dsRNA binding and interferon antagonism. Here, the expression, purification and crystallization of recombinant Zaire Ebola VP35 IID mutants R312A, K319A/R322A and K339A in space groups P6{sub 1}22, P2{sub 1}2{sub 1}2{sub 1} and P2{sub 1}, respectively, are described. Diffraction data were collected using synchrotron sources at the Advanced Light Source and the Advanced Photon Source.

Leung, Daisy W.; Borek, Dominika; Farahbakhsh, Mina; Ramanan, Parameshwaran; Nix, Jay C.; Wang, Tianjiao; Prins, Kathleen C.; Otwinowski, Zbyszek; Honzatko, Richard B.; Helgeson, Luke A.; Basler, Christopher F.; Amarasinghe, Gaya K. (Texas-HSC); (Sinai); (Iowa State); (LBNL)

2010-06-21T23:59:59.000Z

209

Proteomics Strategy to Identify Substrates of LNX, a PDZ Domain-containing E3 Ubiquitin Ligase  

Science Journals Connector (OSTI)

(18) After that, one or more PDZ domains of LNX1 were reported to interact with several proteins, including CAR,(19) ErbB2,(20) SKIP,(21) JAM4,(22) CAST,(23) c-Src,(24) Claudins,(25) RhoC,(26) KCNA4,(27) PAK6,(27) PLEKHG5,(27) PKC-alpha1,(27) TYK2,(27) PDZ-binding kinase (PBK),(27) LNX2,(28) and itself. ... The PANTHER (Protein ANalysis THrough Evolutionary Relationships) classification system(35) was used for GO category enrichment analysis. ...

Zhengguang Guo; Eli Song; Sucan Ma; Xiaorong Wang; Shijuan Gao; Chen Shao; Siqi Hu; Lulu Jia; Rui Tian; Tao Xu; Youhe Gao

2012-08-13T23:59:59.000Z

210

Solution structure and dynamics of C-terminal regulatory domain of Vibrio vulnificus extracellular metalloprotease  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer We have determined solution structures of vEP C-terminal regulatory domain. Black-Right-Pointing-Pointer vEP C-ter100 has a compact {beta}-barrel structure with eight anti-parallel {beta}-strands. Black-Right-Pointing-Pointer Solution structure of vEP C-ter100 shares its molecular topology with that of the collagen-binding domain of collagenase. Black-Right-Pointing-Pointer Residues in the {beta}3 region of vEP C-ter100 might be important in putative ligand/receptor binding. Black-Right-Pointing-Pointer vEP C-ter100 interacts strongly with iron ion. -- Abstract: An extracellular metalloprotease (vEP) secreted by Vibrio vulnificus ATCC29307 is a 45-kDa proteolytic enzyme that has prothrombin activation and fibrinolytic activities during bacterial infection. The action of vEP could result in clotting that could serve to protect the bacteria from the host defense machinery. Very recently, we showed that the C-terminal propeptide (C-ter100), which is unique to vEP, is involved in regulation of vEP activity. To understand the structural basis of this function of vEP C-ter100, we have determined the solution structure and backbone dynamics using multidimensional nuclear magnetic resonance spectroscopy. The solution structure shows that vEP C-ter100 is composed of eight anti-parallel {beta}-strands with a unique fold that has a compact {beta}-barrel formation which stabilized by hydrophobic and hydrogen bonding networks. Protein dynamics shows that the overall structure, including loops, is very rigid and stabilized. By structural database analysis, we found that vEP C-ter100 shares its topology with that of the collagen-binding domain of collagenase, despite low sequence homology between the two domains. Fluorescence assay reveals that vEP C-ter100 interacts strongly with iron (Fe{sup 3+}). These findings suggest that vEP protease might recruit substrate molecules, such as collagen, by binding at C-ter100 and that vEP participates in iron uptake from iron-withholding proteins of the host cell during infection.

Yun, Ji-Hye; Kim, Heeyoun [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)] [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Park, Jung Eun [Department of Biotechnology, College of Natural Sciences, Chosun University, Gwangju 501-759 (Korea, Republic of)] [Department of Biotechnology, College of Natural Sciences, Chosun University, Gwangju 501-759 (Korea, Republic of); Lee, Jung Sup, E-mail: jsplee@mail.chosun.ac.kr [Department of Biotechnology, College of Natural Sciences, Chosun University, Gwangju 501-759 (Korea, Republic of); Lee, Weontae, E-mail: wlee@spin.yonsei.ac.kr [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)] [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)

2013-01-11T23:59:59.000Z

211

Utilization of I-domain of LFA-1 to Target Drug and Marker Molecules to Leukocytes  

E-Print Network [OSTI]

Theranostics 2011, 1 http://www.thno.org 277 Theranostics 2011; 1:277-289 Research Paper Utilization of I-domain of LFA-1 to Target Drug and Marker Molecules to Leukocytes Prakash Manikwar1, Bimo A. Tejo1,2, Heather Shinogle3, David S... via a unique pathway Theranostics 2011, 1 http://www.thno.org 278 referred to as CAM-mediated endocytosis [10-13]. Ligands that bind to CAM can be used to selectively target drugs for intracellular delivery to immune cells expressing...

Manikwar, Prakash; Tejo, Bimo A.; Shinogle, Heather; Moore, David S.; Zimmerman, Tahl; Blanco, Francisco; Siahaan, Teruna J.

2010-05-10T23:59:59.000Z

212

Category:Time-Domain Electromagnetics | Open Energy Information  

Open Energy Info (EERE)

category "Time-Domain Electromagnetics" This category contains only the following page. T Time-Domain Electromagnetics Retrieved from "http:en.openei.orgw...

213

Time-Domain Electromagnetics At Glass Mountain Area (Cumming...  

Open Energy Info (EERE)

Time-Domain Electromagnetics At Glass Mountain Area (Cumming And Mackie, 2007) Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Activity: Time-Domain...

214

Human Sco1 and Sco2 Function as Copper-binding Proteins* Received for publication, June 22, 2005, and in revised form, July 29, 2005 Published, JBC Papers in Press, August 9, 2005, DOI 10.1074/jbc.M506801200  

E-Print Network [OSTI]

Human Sco1 and Sco2 Function as Copper-binding Proteins* Received for publication, June 22, 2005 on copper ion binding. Expression of soluble domains of human Sco1 and Sco2 either in bacteria or the yeast cytoplasm resulted in the recovery of copper-containing proteins. The metallation of human Sco1, but not Sco

Shoubridge, Eric

215

Interstitial deletion of 8q21{yields}22 associated with minor anomalies, congenital heart defect, and Dandy-Walker variant  

SciTech Connect (OSTI)

We describe an infant with a deletion of 8q21{yields}22 who had distinct clinical manifestations including minor facial anomalies, a congenital heart defect, a Dandy-Walker variant, and mild to moderate developmental delay. Her facial characteristics included small, wide-spaced eyes, asymmetric bilateral epicanthal folds, a broad nasal bridge, a {open_quotes}carp-shaped{close_quotes} mouth, micrognathia, and prominent, apparently low-set ears. Three other reports describe children with larger proximal deletions of 8q that include 8q21 and q22. These four children all have similar facial appearance. Of the others reported, one had a congenital heart defect and one had craniosynostosis. This case, in addition to the previously noted three cases, helps in delineating a recognizable syndrome. 12 refs., 3 figs., 1 tab.

Donahue, M.L. [Medical Univ. of South Carolina, Charleston, SC (United States); Ryan, R.M. [Univ. of Rochester, NY (United States)

1995-03-13T23:59:59.000Z

216

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

217

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; Västermark, Åke; Shlykov, Maksim A; Reddy, Vamsee; Sun, Eric I; Saier, Milton H

2013-01-01T23:59:59.000Z

218

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...

219

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...

220

Final Report for the Account Creation/Deletion Reenginering Task for the Scientific Computing Department  

SciTech Connect (OSTI)

In October 2000, the personnel responsible for administration of the corporate computers managed by the Scientific Computing Department assembled to reengineer the process of creating and deleting users' computer accounts. Using the Carnegie Mellon Software Engineering Institute (SEI) Capability Maturity Model (CMM) for quality improvement process, the team performed the reengineering by way of process modeling, defining and measuring the maturity of the processes, per SEI and CMM practices. The computers residing in the classified environment are bound by security requirements of the Secure Classified Network (SCN) Security Plan. These security requirements delimited the scope of the project, specifically mandating validation of all user accounts on the central corporate computer systems. System administrators, in addition to their assigned responsibilities, were spending valuable hours performing the additional tacit responsibility of tracking user accountability for user-generated data. For example, in cases where the data originator was no longer an employee, the administrators were forced to spend considerable time and effort determining the appropriate management personnel to assume ownership or disposition of the former owner's data files. In order to prevent this sort of problem from occurring and to have a defined procedure in the event of an anomaly, the computer account management procedure was thoroughly reengineered, as detailed in this document. An automated procedure is now in place that is initiated and supplied data by central corporate processes certifying the integrity, timeliness and authentication of account holders and their management. Automated scripts identify when an account is about to expire, to preempt the problem of data becoming ''orphaned'' without a responsible ''owner'' on the system. The automated account-management procedure currently operates on and provides a standard process for all of the computers maintained by the Scientific Computing Department.

JENNINGS, BARBARA J.; MCALLISTER, PAULA L.

2002-04-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" 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

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

222

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

223

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

224

Scott Domain Representability of a Class of Generalized Ordered Spaces  

E-Print Network [OSTI]

-space constructed on a locally compact LOTS, is Scott-domain representable, i.e., is homeomorphic to the space-domain representable (i.e., being homeomorphic to the subspace of maximal elements of a Scott-domain with the ScottScott Domain Representability of a Class of Generalized Ordered Spaces Kevin W. Duke and David

Lutzer, David J.

225

Formal Domain Modeling: From Specification to Atif Mashkoor  

E-Print Network [OSTI]

Formal Domain Modeling: From Specification to Validation Atif Mashkoor LORIA ­ DEDALE Team ­ Nancy with re- finement based approach at domain level. We also introduce a stepwise validation process and their inter-relationships, along with their important static and dynamic properties of the domain. The domain

Paris-Sud XI, Université de

226

Domain-specific abstractions and compiler transformations  

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

Domain-specific abstractions and compiler Domain-specific abstractions and compiler transformations Domain-specific abstractions and compiler transformations March 4, 2013 sadayappan Saday Sadayappan Department of Computer Science and Engineering, Ohio State University Recent trends in architecture are making multicore parallelism as well as heterogeneity ubiquitous. This creates significant chalenges to application developers as well as compiler implementations. Currently it is virtually impossible to achieve performance portability of high-performance applications, i.e., develop a single version of source code for an application that achieves high performance on different parallel computer platforms. Different implementations of compute intensive core functions are generally needed for different target platforms, e.g., for multicore

227

Thermodynamics of free Domain Wall fermions  

E-Print Network [OSTI]

Studying various thermodynamic quantities for the free domain wall fermions for both finite and infinite fifth dimensional extent N_5, we find that the lattice corrections are minimum for $N_T\\geq10$ for both energy density and susceptibility, for its irrelevant parameter M in the range 1.45-1.50. The correction terms are, however, quite large for small lattice sizes of $N_T\\leq8$. We propose modifications of the domain wall operator, as well as the overlap operator, to reduce the finite cut-off effects to within 10% of the continuum results of the thermodynamic quantities for the currently used N_T=6-8 lattices. Incorporating chemical potential, we show that \\mu^2 divergences are absent for a large class of such domain wall fermion actions although the chiral symmetry is broken for $\\mu\

R. V. Gavai; Sayantan Sharma

2008-11-19T23:59:59.000Z

228

Eminent Domain (Indiana) | Department of Energy  

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

(Indiana) (Indiana) Eminent Domain (Indiana) < Back Eligibility Agricultural Commercial Construction Fed. Government Fuel Distributor General Public/Consumer Industrial Installer/Contractor Institutional Investor-Owned Utility Local Government Low-Income Residential Multi-Family Residential Municipal/Public Utility Nonprofit Residential Retail Supplier Rural Electric Cooperative Schools State/Provincial Govt Systems Integrator Transportation Tribal Government Utility Savings Category Alternative Fuel Vehicles Hydrogen & Fuel Cells Buying & Making Electricity Water Home Weatherization Solar Wind Program Info State Indiana Program Type Siting and Permitting Provider Indiana Association of Cities and Towns Utilities, corporations, and gas storage facilities may invoke the law of eminent domain in certain circumstances, as provided for in this

229

Skyrmions from Instantons inside Domain Walls  

E-Print Network [OSTI]

Some years ago, Atiyah and Manton described a method to construct approximate Skyrmion solutions from Yang-Mills instantons. Here we present a dynamical realization of this construction using domain walls in a five-dimensional gauge theory. The non-abelian gauge symmetry is broken in each vacuum but restored in the core of the domain wall, allowing instantons to nestle inside the wall. We show that the worldvolume dynamics of the wall is given by the Skyrme model, including the four-derivative term, and the instantons appear as Skyrmions.

Minoru Eto; Muneto Nitta; Keisuke Ohashi; David Tong

2005-08-18T23:59:59.000Z

230

Magnetic spectral bounds on starlike plane domains  

E-Print Network [OSTI]

We develop sharp upper bounds for energy levels of the magnetic Laplacian on starlike plane domains, under either Dirichlet or Neumann boundary conditions and assuming a constant magnetic field in the transverse direction. Our main result says that $\\sum_{j=1}^n \\Phi \\big( \\lambda_j A/G \\big)$ is maximal for a disk whenever $\\Phi$ is concave increasing, $n \\geq 1$, the domain has area $A$, and $\\lambda_j$ is the $j$-th Dirichlet eigenvalue of the magnetic Laplacian $\\big( i\

R. S. Laugesen; B. A. Siudeja

2014-01-04T23:59:59.000Z

231

The Value of the EU Public Domain  

E-Print Network [OSTI]

is as natural and necessary part of our research efforts as the study of copyright.1 1 Mead Fellow in Economics, Emmanuel College, University of Cambridge 2 Erasmus University Rotterdam and Austrian Society for Cultural Economics and Policy Studies 3 Adjunct... proximate but already public domain works. 30We can add and remove mass because the set of in-print public domain and in copyright books do not necessarily match. 31If one considers this over-generous it is worth considering that the various different Harry...

Pollock, Rufus; Stepan, Paul; Välimäki, Mikko

232

Conserved Distal Loop Residues in the Hsp104 and ClpB Middle Domain Contact Nucleotide-binding Domain 2 and  

E-Print Network [OSTI]

polypeptide handover with Hsp70 to dissolve disordered protein aggre- gates is unknown. Results: Conserved strategies to counter protein-misfolding disorders. The homologous hexameric AAA proteins, Hsp104 from yeast and ClpB from bacteria, collaborate with Hsp70 to dissolve disordered protein aggregates but employ

Shorter, James

233

Kinesin-1 and mitochondrial motility control by discrimination of structurally equivalent but distinct subdomains in Ran-GTP-binding domains of Ran-binding protein 2  

Science Journals Connector (OSTI)

...05). Because none of the parameters examined were normally distributed (data not shown), the non-parametric Kruskal-Wallis test for group analysis and the Mann-Whitney U-test for two group comparisons were used at alpha = 0.001...

2013-01-01T23:59:59.000Z

234

Solution Structure of the B-Myb DNA-Binding Domain:? A Possible Role for Conformational Instability of the Protein in DNA Binding and Control of Gene Expression,  

Science Journals Connector (OSTI)

Initially, a family of 50 structures were calculated for B-MybR2R3 from random starting coordinates using the redundant dihedral angle constraint (REDAC) protocol implemented in the distance geometry program DIANA (38, 39). ... In addition, three cycles of the REDAC procedure were included in the calculations to maximize the number of converged B-MybR2R3 structures obtained. ...

Pauline B. McIntosh; Tom A. Frenkiel; Ute Wollborn; John E. McCormick; Karl-Heinz Klempnauer; James Feeney; Mark D. Carr

1998-06-18T23:59:59.000Z

235

Tree based domain-specific mapping languages  

Science Journals Connector (OSTI)

Model transformation languages have been mainly used by researchers --- the software engineering industry has not yet widely accepted the model driven software development (MDSD). One of the main reasons is the complexity of metamodelling principles ... Keywords: UML, domain-specific languages, mappings, model transformation languages

Elina Kalnina; Audris Kalnins; Agris Sostaks; Edgars Celms; Janis Iraids

2012-01-01T23:59:59.000Z

236

Synthesis for Regular Specifications over Unbounded Domains  

E-Print Network [OSTI]

Synthesis for Regular Specifications over Unbounded Domains Jad Hamza # , Barbara Jobstmann + , Viktor Kuncak # # ENS Cachan, France + CNRS/Verimag, France, # EPFL, Switzerland Abstract---Synthesis that are correct by construction. Previous work includes synthesis of reactive finite­state systems from linear

Kuncak, Viktor

237

Synthesis for Regular Specifications over Unbounded Domains  

E-Print Network [OSTI]

Synthesis for Regular Specifications over Unbounded Domains Jad Hamza, Barbara Jobstmann, Viktor Kuncak ENS Cachan, France CNRS/Verimag, France, EPFL, Switzerland Abstract--Synthesis from specifications is a promising method of obtaining systems that are correct by construction. Previous work includes synthesis

Jobstmann, Barbara

238

Synthesis for Regular Specifications over Unbounded Domains  

E-Print Network [OSTI]

Synthesis for Regular Specifications over Unbounded Domains Jad Hamza, Barbara Jobstmann, Viktor Kuncak ENS Cachan, France CNRS/Verimag, France, EPFL, Switzerland Abstract--Synthesis from declarative. Previous work includes synthesis of reactive finite-state systems from linear temporal logic and its

Kuncak, Viktor

239

Large power grid analysis using domain decomposition  

E-Print Network [OSTI]

Large power grid analysis using domain decomposition Quming Zhou, Kai Sun, Kartik Mohanram, Danny C referred to as the power grid. The power grid for a modern integrated circuit may consist of several grid is traditionally described as a large-scale linear system. Simulation of power grids usually

Mohanram, Kartik

240

Competency Patient Care Sub Domain Procedures  

E-Print Network [OSTI]

Competency Patient Care Sub Domain Procedures Learning Objective Understands informed consent and performs uncomplicated procedures on patients or in simulation Milestones Year I Year II Year III Year IV Mid End Mid End Mid End Mid End · Defines elements of informed consent for procedures · Explains

Leistikow, Bruce N.

Note: This page contains sample records for the topic "bind deleted domain" 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

Magnetic field in a finite toroidal domain  

SciTech Connect (OSTI)

The magnetic field structure in a domain surrounded by a closed toroidal magnetic surface is analyzed. It is shown that ergodization of magnetic field lines is possible even in a regular field configuration (with nonvanishing toroidal component). A unified approach is used to describe magnetic fields with nested toroidal (possibly asymmetric) flux surfaces, magnetic islands, and ergodic field lines.

Ilgisonis, V. I.; Skovoroda, A. A., E-mail: skovorod@nfi.kiae.r [Russian Research Centre Kurchatov Institute (Russian Federation)

2010-05-15T23:59:59.000Z

242

Processing electromagnetic data in the time domain  

Science Journals Connector (OSTI)

......necessary to allot storage for the full...the two impulse response functions A and...functions of frequency) that can be...components over all frequencies but a unique...in either the frequency or the time domain...and there is no energy in the direction...unknown impulse response vector A......

George A. McMechan; Ian Barrodale

1985-04-01T23:59:59.000Z

243

Data challenges of time domain astronomy  

Science Journals Connector (OSTI)

Astronomy has been at the forefront of the development of the techniques and methodologies of data intensive science for over a decade with large sky surveys and distributed efforts such as the Virtual Observatory. However, it faces a new data deluge ... Keywords: Astronomy, Classification, Time domain, Virtual observatory

Matthew J. Graham; S. G. Djorgovski; Ashish Mahabal; Ciro Donalek; Andrew Drake; Giuseppe Longo

2012-10-01T23:59:59.000Z

244

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

245

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

246

Homozygous deletions on the short arm of chromosome 9 in ovarian adenocarcinoma cell lines and loss of heterozygosity in sporadic tumors  

SciTech Connect (OSTI)

Rat ovarian surface epithelial cells transformed spontaneously in vitro have been found to have homozygous deletions of the interferon alpha (IFNA) gene. This suggests that inactivation of a tumor-suppressor gene in this region may be crucial for the development of ovarian cancer. The authors therefore used microsatellite markers and Southern analysis to examine the homologous region in humans - the short arm of chromosome 9 - for deletions in sporadic ovarian adenocarcinomas and ovarian tumor cell lines. Loss of heterozygosity occurred in 34 (37%) of 91 informative sporadic tumors, including some benign, low-malignant-potential and early-stage tumors, suggesting that it is an early event in the development of ovarian adenocarcinoma. Furthermore, homozygous deletions on 9p were found in 2 of 10 independent cell lines. Deletion mapping of the tumors and lines indicates that the candidate suppressor gene inactivated as a consequence lies between D9S171 and the IFNA locus, a region that is also deleted in several other tumors and that contains the melanoma predisposition gene, MLM. 52 refs., 4 figs., 1 tab.

Chenevix-Trench, G.; Kerr, J.; Hurst, T.; Sanderson, B.; Coglan, M.; Ward, B.; Khoo, S.K. (Univ. of Queensland, Brisbane (Australia)); Friedlander, M.; Leary, J.

1994-07-01T23:59:59.000Z

247

Budding of domains in mixed bilayer membranes  

E-Print Network [OSTI]

We propose a model that accounts for budding behavior of domains in lipid bilayers, where each of the bilayer leaflets has a coupling between its local curvature and local lipid composition. The compositional asymmetry between the two monolayers leads to an overall spontaneous curvature. The membrane free-energy contains three contributions: bending energy, line tension, and a Landau free-energy for a lateral phase separation. Within a mean-field treatment, we obtain various phase diagrams which contain fully-budded, dimpled and flat states. In particular, for some range of membrane parameters, the phase diagrams exhibit a tricritical behavior as well as three-phase coexistence region. The global phase diagrams can be divided into three types and are analyzed in terms of the curvature-composition coupling parameter and domain size.

Wolff, Jean; Andelman, David

2014-01-01T23:59:59.000Z

248

Budding of domains in mixed bilayer membranes  

E-Print Network [OSTI]

We propose a model that accounts for budding behavior of domains in lipid bilayers, where each of the bilayer leaflets has a coupling between its local curvature and local lipid composition. The compositional asymmetry between the two monolayers leads to an overall spontaneous curvature. The membrane free-energy contains three contributions: bending energy, line tension, and a Landau free-energy for a lateral phase separation. Within a mean-field treatment, we obtain various phase diagrams which contain fully-budded, dimpled and flat states. In particular, for some range of membrane parameters, the phase diagrams exhibit a tricritical behavior as well as three-phase coexistence region. The global phase diagrams can be divided into three types and are analyzed in terms of the curvature-composition coupling parameter and domain size.

Jean Wolff; Shigeyuki Komura; David Andelman

2014-10-14T23:59:59.000Z

249

Domain walls with non-Abelian clouds  

SciTech Connect (OSTI)

Domain walls in U(N) gauge theories, coupled to Higgs scalar fields with degenerate masses, are shown to possess normalizable non-Abelian Nambu-Goldstone (NG) modes, which we call non-Abelian clouds. We construct the moduli space metric and its Kaehler potential of the effective field theory on the domain walls by focusing on two models: a U(1) gauge theory with several charged Higgs fields, and a U(N) gauge theory with 2N Higgs fields in the fundamental representation. We find that non-Abelian clouds spread between two domain walls and that their rotation induces a long-range repulsive force, in contrast to a U(1) mode in models with fully nondegenerate masses which gives a short-range force. We also construct a bound state of dyonic domain walls by introducing the imaginary part of the Higgs masses. In the latter model we find that when all walls coincide, SU(N){sub L}xSU(N){sub R}xU(1) symmetry is broken down to SU(N){sub V}, and U(N){sub A} NG modes and the same number of quasi-NG modes are localized on the wall. When n walls separate, off-diagonal elements of U(n) NG modes have wave functions spreading between two separated walls (non-Abelian clouds), whereas some quasi-NG modes turn to NG bosons as a result of further symmetry breaking U(n){sub V}{yields}U(1){sub V}{sup n}. In the case of 4+1-dimensional bulk, we can dualize the effective theory to the supersymmetric Freedman-Townsend model of non-Abelian 2-form fields.

Eto, Minoru [INFN, Sezione di Pisa, Largo Pontecorvo, 3, Ed. C, 56127 Pisa (Italy); Department of Physics, University of Pisa Largo Pontecorvo, 3, Ed. C, 56127 Pisa (Italy); Fujimori, Toshiaki; Sakai, Norisuke [Department of Physics, Tokyo Institute of Technology, Tokyo 152-8551 (Japan); Nitta, Muneto [Department of Physics, Keio University, Hiyoshi, Yokohama, Kanagawa 223-8521 (Japan); Ohashi, Keisuke [Department of Applied Mathematics and Theoretical Physics, University of Cambridge, CB3 0WA (United Kingdom)

2008-06-15T23:59:59.000Z

250

Domain growth in the clock model  

Science Journals Connector (OSTI)

The development of order in the clock (ZN) model is studied following a quench from the disordered phase to a low-temperature unstable state below the ferromagnetic critical point. Growth laws for the average size of domains are obtained by computer simulation for N=3, 4, 8, 16, and 26 degenerate states. In disagreement with recent Monte Carlo work, no pinning by vortices is observed.

Kimmo Kaski; Martin Grant; J. D. Gunton

1985-03-01T23:59:59.000Z

251

Conserved currents for Mobius Domain Wall Fermions  

E-Print Network [OSTI]

We derive the exactly conserved vector, and almost conserved axial currents for rational approximations to the overlap operator with a general Mobius kernel. The approach maintains manifest Hermiticity, and allows matrix elements of the currents to be constructed at no extra cost after solution of the usual 5d system of equations, similar to the original approach of Furman and Shamir for domain wall Fermions.

P. A. Boyle

2014-11-20T23:59:59.000Z

252

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

253

HYDRATE DISSOCIATION IN A 1-D DOMAIN  

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

HYDRATE DISSOCIATION IN A 1-D DOMAIN HYDRATE DISSOCIATION IN A 1-D DOMAIN I. Domain Description 1-D Cartesian system, L x W x H = 1.5 m x 1.0 m x 1.0 m Discretization: 30 x 1 x 1 in (x,y,z) Uniform Δx = 0.05 m each; Δy = Δz = 1 m II. Initial Conditions Pressure: P i = 8 MPa Temperature: T i = 2 o C (for thermal stimulation), T i = 6 o C (for depressurization) Saturations: S H = 0.5, S A = 0.5, S G = 0.0 III. Boundary Conditions At x = X max : No mass or heat flow At x = 0: Constant S A = 1.0 (1) Constant P 0 = P i Constant T 0 = 45 o C Thermal stimulation (2) Constant T 0 = T i = 6 o C Constant P 0 = 2.8 MPa Depressurization to a pressure above the Q-point, no ice formation (3) Constant T 0 = T i = 6 o C Constant P 0 = 0.5 MPa Depressurization to a pressure below the Q-point,

254

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

255

The Task Agent Resource Function application in UAV domain  

E-Print Network [OSTI]

The Task Agent Resource Function application in UAV domain Tan Viet Anh Truong Ecole National is to present an application of TARF (Task Agent Resource Function) in UAV domain. This TARF is used to optimize of a generic mission planner for cross domain such as UAV, maritime, automotive and manned aerial vehicle (MAV

Paris-Sud XI, Université de

256

Grammar-Based Testing using Realistic Domains in PHP  

E-Print Network [OSTI]

Grammar-Based Testing using Realistic Domains in PHP Ivan Enderlin, Fr´ed´eric Dadeau, Alain-based testing in PHP. It relies on the notion of realistic domains, that make it possible to assign domains to data, by means of contract assertions written inside the source code of a PHP application. Then a test

Paris-Sud XI, Université de

257

Role of Hepatocyte Nuclear Factor 4 alpha in Hepatocyte Proliferation  

E-Print Network [OSTI]

-binding domain and the ligand-binding domain for proper binding of HNF4? to its response elements. A lack of the ligand-binding domain can reduce the affinity of HNF4? for its response elements by 75-fold (Chandra, Huang et al. 2013). HNF4?’s ligand..., 2013, with permission from American Physiological Society. Hepatology, 57(3): 2480-2490, Hepatocyte Nuclear Factor 4 alpha Deletion Promotes Diethylnitrosamine-induced Hepatocellular Carcinoma in Rodents, 2013, with permission from John Wiley & Sons...

Walesky, Chad Michael

2014-05-31T23:59:59.000Z

258

Three-dimensional structures of the ligand-binding domain of the bacterial aspartate receptor with and without a ligand  

Science Journals Connector (OSTI)

...T. Terwilliger, J. Y. Wang, D. E. Koshland, Jr...Crystallogr. 16, 542 (1983)] on synchroton x-ray at Photon Factory...correct space group. 22. B. C. Wang, Methods Enzymol. 115, 90...pp. 163-168. 29. J. H. Wang et al., Nature 348, 411...

MV Milburn; GG Prive; DL Milligan; WG Scott; J Yeh; J Jancarik; DE Koshland Jr; SH Kim

1991-11-29T23:59:59.000Z

259

The Ligand Binding Domain of GCNF Is Not Required for Repression of Pluripotency Genes in Mouse Fetal Ovarian Germ Cells  

E-Print Network [OSTI]

In mice, successful development and reproduction require that all cells, including germ cells, transition from a pluripotent to a differentiated state. This transition is associated with silencing of the pluripotency genes ...

Okumura, Leah M.

260

An atomic resolution view of ICAM recognition in a complex between the binding domains of ICAM-3  

E-Print Network [OSTI]

Medical School, Boston, MA 02115; and Dana­Farber Cancer Institute, Department of Pediatrics. The mark- edly different off-rates of ICAM-1, -2, and -3 appear to be deter- mined by the hydrophobicity cell adhesion and lowering the activation threshold. In the absence of ICAM- 1 L 2 interaction, 100

Springer, Timothy A.

Note: This page contains sample records for the topic "bind deleted domain" 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

Bluetongue virus coat protein VP2 contains sialic acid-binding domains, and VP5 resembles enveloped virus fusion proteins  

Science Journals Connector (OSTI)

...of the rotavirus VP4 spike (PDB ID code 1KQR) (14). When the ribbon model...expression of nonstructural protein 2 (NS2) at 16 h after BTV infection of HeLa...fusion proteins gp41 of HIV (PDB ID code 1SZT) (24) and HA2 of influenza...

Xing Zhang; Mark Boyce; Bishnupriya Bhattacharya; Xiaokang Zhang; Stan Schein; Polly Roy; Z. Hong Zhou

2010-01-01T23:59:59.000Z

262

Biochem. J. (1998) 331, 775781 (Printed in Great Britain) 775 Pseudomonas cellulose-binding domains mediate their effects by increasing  

E-Print Network [OSTI]

, Geoffrey P. HAZLEWOOD and Harry J. GILBERT*1 *Department of Biological and Nutritional Sciences, University, University of Sheffield, Sheffield S10 2TN, U.K., and RDepartment of Microbiology and Immunology, University

Williamson, Mike P.

263

Petroleum Pipeline Eminent Domain Permit Procedures (Georgia) | Department  

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

Petroleum Pipeline Eminent Domain Permit Procedures (Georgia) Petroleum Pipeline Eminent Domain Permit Procedures (Georgia) Petroleum Pipeline Eminent Domain Permit Procedures (Georgia) < Back Eligibility Commercial Construction Developer Fuel Distributor General Public/Consumer Industrial Investor-Owned Utility Municipal/Public Utility Utility Program Info State Georgia Program Type Environmental Regulations Siting and Permitting Provider Georgia Department of Natural Resources The Petroleum Pipeline Eminent Domain Permit Procedures serve to protect Georgia's natural and environmental resources by requiring permits be issued by the Director of the Environmental Protection Division prior to any petroleum or petroleum product pipe company acquiring property or interests by eminent domain. Monitoring conditions will be issued with

264

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.

265

Melting Instantons, Domain Walls, and Large N  

E-Print Network [OSTI]

Monte Carlo studies of $CP^{N-1}$ sigma models have shown that the structure of topological charge in these models undergoes a sharp transition at $N=N_c\\approx 4$. For $NN_c$ it is dominated by extended, thin, 1-dimensionally coherent membranes of topological charge, which can be interpreted as domain walls between discrete quasi-stable vacua. These vacua differ by a unit of background electric flux. The transition can be identified as the delocalization of topological charge, or "instanton melting," a phenomenon first suggested by Witten to resolve the conflict between instantons and large $N$ behavior. Implications for $QCD$ are discussed.

H. B. Thacker

2008-10-22T23:59:59.000Z

266

Effective Action of Domain Wall Networks  

E-Print Network [OSTI]

U(Nc) gauge theory with Nf fundamental scalars admits BPS junctions of domain walls. When the networks/webs of these walls contain loops, their size moduli give localized massless modes. We construct Kahler potential of their effective action. In the large size limit Kahler metric is well approximated by kinetic energy of walls and junctions, which is understood in terms of tropical geometry. Kahler potential can be expressed in terms of hypergeometric functions which are useful to understand small size behavior. Even when the loop shrinks, the metric is regular with positive curvature. Moduli space of a single triangle loop has a geometry between a cone and a cigar.

Minoru Eto; Toshiaki Fujimori; Takayuki Nagashima; Muneto Nitta; Keisuke Ohashi; Norisuke Sakai

2006-12-01T23:59:59.000Z

267

Stochastic Domain-Wall Depinning in Magnetic Nanowires  

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

Stochastic Domain-Wall Depinning Stochastic Domain-Wall Depinning in Magnetic Nanowires Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Wednesday, 29 July 2009 00:00 Reliably controlling the motion of magnetic domain walls along magnetic nanowires is a key requirement for current technological development of novel classes of logic and storage devices, but understanding the nature of non-deterministic domain-wall motion remains a scientific challenge. A statistical analysis of high-resolution magnetic soft x-ray microscopy images by a Berkeley Lab-University of Hamburg group has now revealed that the stochastic behavior of the domain-wall depinning field in notch-patterned Ni80Fe20 (permalloy) nanowires depends strongly on the wire width and the notch depth. This result both provides valuable insight into the motion of magnetic-domain walls and opens a path to further technological developments in spintronics applications.

268

Domain Walls and Vortices in Chiral Symmetry Breaking  

E-Print Network [OSTI]

We study domain walls and vortices in chiral symmetry breaking in a QCD-like theory with N flavors in the chiral limit. If the axial anomaly is absent, there exist stable Abelian axial vortices winding around the spontaneously broken U(1)_A symmetry and non-Abelian axial vortices winding around both the U(1)_A and non-Abelian SU(N) chiral symmetries. In the presence of the axial anomaly term, metastable domain walls are present and Abelian axial vortices must be attached by N domain walls, forming domain wall junctions. We show that a domain wall junction decays into N non-Abelian vortices attached by domain walls, implying its metastability. We also show that domain walls decay through the quantum tunneling by creating a hole bounded by a closed non-Abelian vortex.

Minoru Eto; Yuji Hirono; Muneto Nitta

2013-09-18T23:59:59.000Z

269

Using Non-Government Domain Names | Department of Energy  

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

Using Non-Government Domain Names Using Non-Government Domain Names Using Non-Government Domain Names There may be occasion where it is necessary to utilize a non-government domain. The OMB Policies for Federal Agency Public Websites states: Your agency must use only .gov, .mil, or Fed.us domains unless the agency head explicitly determines another domain is necessary for the proper performance of an agency function. This requirement recognizes the proper performance of agency functions includes an obligation for clear and unambiguous public notification of the agency's involvement in or sponsorship of its information dissemination products including public websites. It also recognizes in certain limited circumstances other domains may be necessary for the proper performance of an agency function.

270

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

271

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:...

272

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

273

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

274

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

275

Structural basis for membrane targeting by the MVB12-associated [beta]-prism domain of the human ESCRT-I MVB12 subunit  

SciTech Connect (OSTI)

MVB12-associated {beta}-prism (MABP) domains are predicted to occur in a diverse set of membrane-associated bacterial and eukaryotic proteins, but their existence, structure, and biochemical properties have not been characterized experimentally. Here, we find that the MABP domains of the MVB12A and B subunits of ESCRT-I are functional modules that bind in vitro to liposomes containing acidic lipids depending on negative charge density. The MABP domain is capable of autonomously localizing to subcellular puncta and to the plasma membrane. The 1.3-{angstrom} atomic resolution crystal structure of the MVB12B MABP domain reveals a {beta}-prism fold, a hydrophobic membrane-anchoring loop, and an electropositive phosphoinositide-binding patch. The basic patch is open, which explains how it senses negative charge density but lacks stereoselectivity. These observations show how ESCRT-I could act as a coincidence detector for acidic phospholipids and protein ligands, enabling it to function both in protein transport at endosomes and in cytokinesis and viral budding at the plasma membrane.

Boura, Evzen; Hurley, James H. (NIH)

2012-03-15T23:59:59.000Z

276

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.

Anikó Várnai; Miia R. Mäkelä; Demi T. Djajadi; Jenni Rahikainen; Annele Hatakka; Liisa Viikari

2014-01-01T23:59:59.000Z

277

Respiratory Syncytial Virus Modified by Deletions of the NS2 Gene and Amino Acid S1313 of the L Polymerase Protein Is a Temperature-Sensitive, Live-Attenuated Vaccine Candidate That Is Phenotypically Stable at Physiological Temperature  

Science Journals Connector (OSTI)

...previously (38). Animal identification codes and vaccine virus are indicated on the...and (iv) the non-ts deletion of the NS2 gene. This resulted in 5 new cDNA-derived...and (ii) it bears the deletion of the NS2 protein, which is an antagonist of the...

Cindy Luongo; Christine C. Winter; Peter L. Collins; Ursula J. Buchholz

2012-12-12T23:59:59.000Z

278

Deletions of SKY1 or PTK2 in the Saccharomyces cerevisiae trk1Dtrk2D mutant cells exert dual effect on ion homeostasis  

E-Print Network [OSTI]

that regulate ion transport across the plasma membrane of Saccharomyces cerevisiae. We show here that deletion to spermine and salt ions. A model that integrates these results to explain the mechanism of ion transport on ion homeostasis Omri Erez and Chaim Kahana* Department of Molecular Genetics, Weizmann Institute

Kahana, Chaim

279

ANDERSON-TEIXEIRA FINAL PROOF.DOCX (DO NOT DELETE) 3/7/2011 9:29 AM DO BIOFUELS LIFE CYCLE  

E-Print Network [OSTI]

ANDERSON-TEIXEIRA FINAL PROOF.DOCX (DO NOT DELETE) 3/7/2011 9:29 AM 589 DO BIOFUELS LIFE CYCLE ANALYSES ACCURATELY QUANTIFY THE CLIMATE IMPACTS OF BIOFUELS-RELATED LAND USE CHANGE? Kristina J. Anderson in determining the sustainability of biofuels. To ensure that legal standards are effective in limiting climate

DeLucia, Evan H.

280

Identification of a Novel Homozygous Deletion Region at 6q23.1 in Medulloblastomas Using High-Resolution Array Comparative Genomic Hybridization Analysis  

Science Journals Connector (OSTI)

...homozygous deletion at 6q23.1 flanked by markers SHGC-14149 (6q22.33) and SHGC-110551 (6q23.1). Quantitative reverse transcription-PCR...and flanked by the sequence-tagged site markers SHGC-13149 and SHGC-110551. B, quantitative reverse...

Angela B.Y. Hui; Hirokuni Takano; Kwok-Wai Lo; Wen-Lin Kuo; Cleo N.Y. Lam; Carol Y.K. Tong; Qing Chang; Joe W. Gray; Ho-Keung Ng

2005-07-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" 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

Identification of a novel homozygous deletion region at 6q23.1 in medullobalstomas using high-resolution array CGH analysis  

Science Journals Connector (OSTI)

...markers confined a 0.887Mb minimal region of homozygous deletion at 6q23.1 which was flanked by markers SHGC-14149 (6q22.33) and SHGC-110551 (6q23.1). Quantitative RT-PCR analysis showed complete loss of expression of 2 genes located...

Angela Bik-Yu Hui; Hirokuni Takano; Kwok Wai Lo; Wen Lin Kuo; Joe Gray; Ho Keung Ng

2005-05-01T23:59:59.000Z

282

Genetic deletion of Rnd3 results in aqueductal stenosis leading to hydrocephalus through up-regulation of Notch signaling  

Science Journals Connector (OSTI)

...signaling 10.1073/pnas.1219995110 Xi Lin Baohui Liu Xiangsheng Yang Xiaojing Yue...Huh MS Todd MA Picketts DJ ( 2009 ) SCO-ping out the mechanisms underlying the etiology of hydrocephalus...2853 – 2858 . 9 Riento K Guasch RM Garg R Jin B Ridley AJ ( 2003 ) RhoE binds to ROCK...

Xi Lin; Baohui Liu; Xiangsheng Yang; Xiaojing Yue; Lixia Diao; Jing Wang; Jiang Chang

2013-01-01T23:59:59.000Z

283

Stochastic Domain-Wall Depinning in Magnetic Nanowires  

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

Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Reliably controlling the motion of magnetic domain walls along magnetic nanowires is a key requirement for current technological development of novel classes of logic and storage devices, but understanding the nature of non-deterministic domain-wall motion remains a scientific challenge. A statistical analysis of high-resolution magnetic soft x-ray microscopy images by a Berkeley Lab-University of Hamburg group has now revealed that the stochastic behavior of the domain-wall depinning field in notch-patterned Ni80Fe20 (permalloy) nanowires depends strongly on the wire width and the notch depth. This result both provides valuable insight into the motion of magnetic-domain walls and opens a path to further technological developments in spintronics applications.

284

Stochastic Domain-Wall Depinning in Magnetic Nanowires  

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

Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Reliably controlling the motion of magnetic domain walls along magnetic nanowires is a key requirement for current technological development of novel classes of logic and storage devices, but understanding the nature of non-deterministic domain-wall motion remains a scientific challenge. A statistical analysis of high-resolution magnetic soft x-ray microscopy images by a Berkeley Lab-University of Hamburg group has now revealed that the stochastic behavior of the domain-wall depinning field in notch-patterned Ni80Fe20 (permalloy) nanowires depends strongly on the wire width and the notch depth. This result both provides valuable insight into the motion of magnetic-domain walls and opens a path to further technological developments in spintronics applications.

285

Stochastic Domain-Wall Depinning in Magnetic Nanowires  

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

Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Reliably controlling the motion of magnetic domain walls along magnetic nanowires is a key requirement for current technological development of novel classes of logic and storage devices, but understanding the nature of non-deterministic domain-wall motion remains a scientific challenge. A statistical analysis of high-resolution magnetic soft x-ray microscopy images by a Berkeley Lab-University of Hamburg group has now revealed that the stochastic behavior of the domain-wall depinning field in notch-patterned Ni80Fe20 (permalloy) nanowires depends strongly on the wire width and the notch depth. This result both provides valuable insight into the motion of magnetic-domain walls and opens a path to further technological developments in spintronics applications.

286

Stochastic Domain-Wall Depinning in Magnetic Nanowires  

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

Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Reliably controlling the motion of magnetic domain walls along magnetic nanowires is a key requirement for current technological development of novel classes of logic and storage devices, but understanding the nature of non-deterministic domain-wall motion remains a scientific challenge. A statistical analysis of high-resolution magnetic soft x-ray microscopy images by a Berkeley Lab-University of Hamburg group has now revealed that the stochastic behavior of the domain-wall depinning field in notch-patterned Ni80Fe20 (permalloy) nanowires depends strongly on the wire width and the notch depth. This result both provides valuable insight into the motion of magnetic-domain walls and opens a path to further technological developments in spintronics applications.

287

Stochastic Domain-Wall Depinning in Magnetic Nanowires  

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

Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Reliably controlling the motion of magnetic domain walls along magnetic nanowires is a key requirement for current technological development of novel classes of logic and storage devices, but understanding the nature of non-deterministic domain-wall motion remains a scientific challenge. A statistical analysis of high-resolution magnetic soft x-ray microscopy images by a Berkeley Lab-University of Hamburg group has now revealed that the stochastic behavior of the domain-wall depinning field in notch-patterned Ni80Fe20 (permalloy) nanowires depends strongly on the wire width and the notch depth. This result both provides valuable insight into the motion of magnetic-domain walls and opens a path to further technological developments in spintronics applications.

288

Effective action of domain wall networks  

SciTech Connect (OSTI)

U(N{sub C}) gauge theory with N{sub F} fundamental scalars admits BPS junctions of domain walls. When the networks/webs of these walls contain loops, their size moduli give localized massless modes. We construct Kaehler potential of their effective action. In the large size limit Kaehler metric is well approximated by kinetic energy of walls and junctions, which is understood in terms of tropical geometry. Kaehler potential can be expressed in terms of hypergeometric functions that are useful to understand small size behavior. Even when the loop shrinks, the metric is regular with positive curvature. Moduli space of a single triangle loop has a geometry between a cone and a cigar.

Eto, Minoru [Institute of Physics, University of Tokyo, Komaba 3-8-1, Tokyo 153-8902 (Japan); Fujimori, Toshiaki; Nagashima, Takayuki; Ohashi, Keisuke; Sakai, Norisuke [Department of Physics, Tokyo Institute of Technology, Tokyo 152-8551 (Japan); Nitta, Muneto [Department of Physics, Keio University, Hiyoshi, Yokohama, Kanagawa 223-8521 (Japan)

2007-02-15T23:59:59.000Z

289

Birefringence insensitive optical coherence domain reflectometry system  

DOE Patents [OSTI]

A birefringence insensitive fiber optic optical coherence domain reflectometry (OCDR) system is provided containing non-polarization maintaining (non-PM) fiber in the sample arm and the reference arm without suffering from signal degradation caused by birefringence. The use of non-PM fiber significantly reduces the cost of the OCDR system and provides a disposable or multiplexed section of the sample arm. The dispersion in the reference arm and sample arm of the OCDR system are matched to achieve high resolution imaging. This system is useful in medical applications or for non-medical in situ probes. The disposable section of non-PM fiber in the sample arm can be conveniently replaced when contaminated by a sample or a patient.

Everett, Matthew J. (Livermore, CA); Davis, Joseph G. (Lafayette, CA)

2002-01-01T23:59:59.000Z

290

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

291

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

292

D-brane Configurations for Domain Walls and Their Webs  

SciTech Connect (OSTI)

Supersymmetric U(NC) gauge theory with NF massive hypermultiplets in the fundamental representation admits various BPS solitons like domain walls and their webs. In the first part we show as a review of the previous paper that domain walls are realized as kinky fractional D3-branes interpolating between separated D7-branes. In the second part we discuss brane configurations for domain wall webs. This is a contribution to the conference based on the talk given by MN.

Eto, Minoru; Isozumi, Youichi; Nitta, Muneto; Ohashi, Keisuke; Sakai, Norisuke [Department of Physics, Tokyo Institute of Technology, Tokyo 152-8551 (Japan); Ohta, Kazutoshi [Theoretical Physics Laboratory, Institute of Physical and Chemical Research (RIKEN), 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

2005-12-02T23:59:59.000Z

293

Definition: Time-Domain Electromagnetics | Open Energy Information  

Open Energy Info (EERE)

Definition Definition Edit with form History Facebook icon Twitter icon » Definition: Time-Domain Electromagnetics Jump to: navigation, search Dictionary.png Time-Domain Electromagnetics Time-domain electromagnetic (TDEM) surveys are active-source soundings which provide information about the electrical structure of the shallow subsurface.[1] View on Wikipedia Wikipedia Definition Transient electromagnetics, (also time-domain electromagnetics / TDEM), is a geophysical exploration technique in which electric and magnetic fields are induced by transient pulses of electric current and the subsequent decay response measured. TEM / TDEM methods are generally able to determine subsurface electrical properties, but are also sensitive to subsurface magnetic properties in applications like UXO detection and

294

Semantic technology in the oil and gas drilling domain.  

E-Print Network [OSTI]

??Data integration and knowledge representation in the oil and gas drilling domain are two challenges much work is focused upon. They are important real-world challenges… (more)

Overå, Lars

2010-01-01T23:59:59.000Z

295

Nuclear morphology measurements using Fourier domain low coherence interferometry  

Science Journals Connector (OSTI)

We present a new common path configuration Fourier domain low coherence interferometry (fLCI) optical system and demonstrate its capabilities by presenting results which determine the...

Graf, Robert; Wax, Adam

2005-01-01T23:59:59.000Z

296

National Geothermal Data System (NGDS) Geothermal Data Domain...  

Open Energy Info (EERE)

Data System (NGDS) Geothermal Data Domain: Assessment of Geothermal Community Data Needs Abstract To satisfy the critical need for geothermal data to advance geothermal energy as...

297

WHERE MULTIFUNCTIONAL DNA REPAIR PROTEINS MEET: MAPPING THE INTERACTION DOMAINS BETWEEN XPG AND WRN  

SciTech Connect (OSTI)

The rapid recognition and repair of DNA damage is essential for the maintenance of genomic integrity and cellular survival. Multiple complex and interconnected DNA damage responses exist within cells to preserve the human genome, and these repair pathways are carried out by a specifi c interplay of protein-protein interactions. Thus a failure in the coordination of these processes, perhaps brought about by a breakdown in any one multifunctional repair protein, can lead to genomic instability, developmental and immunological abnormalities, cancer and premature aging. This study demonstrates a novel interaction between two such repair proteins, Xeroderma pigmentosum group G protein (XPG) and Werner syndrome helicase (WRN), that are both highly pleiotropic and associated with inherited genetic disorders when mutated. XPG is a structure-specifi c endonuclease required for the repair of UV-damaged DNA by nucleotide excision repair (NER), and mutations in XPG result in the diseases Xeroderma pigmentosum (XP) and Cockayne syndrome (CS). A loss of XPG incision activity results in XP, whereas a loss of non-enzymatic function(s) of XPG causes CS. WRN is a multifunctional protein involved in double-strand break repair (DSBR), and consists of 3’–5’ DNA-dependent helicase, 3’–5’ exonuclease, and single-strand DNA annealing activities. Nonfunctional WRN protein leads to Werner syndrome, a premature aging disorder with increased cancer incidence. Far Western analysis was used to map the interacting domains between XPG and WRN by denaturing gel electrophoresis, which separated purifi ed full length and recombinant XPG and WRN deletion constructs, based primarily upon the length of each polypeptide. Specifi c interacting domains were visualized when probed with the secondary protein of interest which was then detected by traditional Western analysis using the antibody of the secondary protein. The interaction between XPG and WRN was mapped to the C-terminal region of XPG as well as the C-terminal region of WRN. The physical interaction between XPG and WRN links NER, (made evident by the disease XP) with DSBR, which imparts additional knowledge of the overlapping nature of these two proteins and the previously distinct DNA repair pathways they are associated with. Since genomic integrity is constantly threatened by both endogenous and exogenous (internal and external) damage, understanding the roles of these proteins in coordinating DNA repair processes with replication will signifi cantly further understanding how defects instigate physiological consequences in response to various DNA damaging sources. This ultimately contributes to our understanding of cancer and premature aging.

Rangaraj, K.; Cooper, P.K.; Trego, K.S.

2009-01-01T23:59:59.000Z

298

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

299

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

300

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

Note: This page contains sample records for the topic "bind deleted domain" 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

Structure and Mutagenesis of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Stalk Domain Reveals a Four-Helix Bundle and the Role of the Stalk in Fusion Promotion  

SciTech Connect (OSTI)

Paramyxovirus entry into cells requires the fusion protein (F) and a receptor binding protein (hemagglutinin-neuraminidase [HN], H, or G). The multifunctional HN protein of some paramyxoviruses, besides functioning as the receptor (sialic acid) binding protein (hemagglutinin activity) and the receptor-destroying protein (neuraminidase activity), enhances F activity, presumably by lowering the activation energy required for F to mediate fusion of viral and cellular membranes. Before or upon receptor binding by the HN globular head, F is believed to interact with the HN stalk. Unfortunately, until recently none of the receptor binding protein crystal structures have shown electron density for the stalk domain. Parainfluenza virus 5 (PIV5) HN exists as a noncovalent dimer-of-dimers on the surface of cells, linked by a single disulfide bond in the stalk. Here we present the crystal structure of the PIV5-HN stalk domain at a resolution of 2.65 {angstrom}, revealing a four-helix bundle (4HB) with an upper (N-terminal) straight region and a lower (C-terminal) supercoiled part. The hydrophobic core residues are a mix of an 11-mer repeat and a 3- to 4-heptad repeat. To functionally characterize the role of the HN stalk in F interactions and fusion, we designed mutants along the PIV5-HN stalk that are N-glycosylated to physically disrupt F-HN interactions. By extensive study of receptor binding, neuraminidase activity, oligomerization, and fusion-promoting functions of the mutant proteins, we found a correlation between the position of the N-glycosylation mutants on the stalk structure and their neuraminidase activities as well as their abilities to promote fusion.

Bose, Sayantan; Welch, Brett D.; Kors, Christopher A.; Yuan, Ping; Jardetzky, Theodore S.; Lamb, Robert A. (NWU); (Stanford-MED)

2014-10-02T23:59:59.000Z

302

Stripe Domain-Structures in a Thin Ferromagnetic Film  

E-Print Network [OSTI]

We present a theory of the stripe domain structure in a thin ferromagnetic film with single-ion easy-axis magnetic anisotropy and long-range dipole interactions, for a wide range of temperatures and applied magnetic field. The domains exist...

KASHUBA, AB; Pokrovsky, Valery L.

1993-01-01T23:59:59.000Z

303

LNG FEM: Graded Meshes on Domains of Polygonal Structures  

E-Print Network [OSTI]

LNG FEM: Graded Meshes on Domains of Polygonal Structures Hengguang Li and Victor Nistor Abstract. We develop LNG FEM, a software package for graded mesh generation and for solving elliptic equations. LNG FEM gen- erates user-specified graded meshes on arbitrary 2D domains with straight edges

Nistor, Victor

304

ORIGINAL ARTICLE Single ferroelectric-domain photovoltaic switch based  

E-Print Network [OSTI]

ORIGINAL ARTICLE Single ferroelectric-domain photovoltaic switch based on lateral BiFeO3 cells Ji serves as a basis for solid-state memory. This phenomenon can also yield an interesting photovoltaic imposed by the ferroelectric polarization vectors. Here, we demonstrate a single-domain photovoltaic

Jo, Moon-Ho

305

Important Cognitive Components of Domain-Specific Search Knowledge  

E-Print Network [OSTI]

the subject-specific terms to enter in a query. For example, many university students often buy electronicImportant Cognitive Components of Domain-Specific Search Knowledge Suresh K. Bhavnani School Many users have acquired a sophisticated understanding of searching the Web in specific domains

Bhavnani, Suresh K.

306

Interactive situation modelling in knowledge-intensive domains  

Science Journals Connector (OSTI)

This paper shows how knowledge from various sources in a knowledge intensive domain can be modelled using principles of ethnography. This is achieved by bridging the symmetry of ignorance gap that exists between process owners and system developers. ... Keywords: ethnography, knowledge intensive domains, requirement engineering, situation modelling, systems modelling

Kiran Jude Fernandes

2008-11-01T23:59:59.000Z

307

Building DomainSpecific Search Engines with Machine Learning Techniques  

E-Print Network [OSTI]

.netpart.com lets the user search over company pages by hostname, company name, and location. ffl wwwBuilding Domain­Specific Search Engines with Machine Learning Techniques Andrew McCallum zy Science Carnegie Mellon University Pittsburgh, PA 15213 Abstract Domain­specific search engines

McCallum, Andrew

308

First Elements on Knowledge Discovery Guided by Domain Knowledge (KDDK)  

E-Print Network [OSTI]

First Elements on Knowledge Discovery Guided by Domain Knowledge (KDDK) Jean Lieber, Amedeo Napoli how knowledge discovery and knowl- edge processing may be combined. The knowledge discovery knowledge units. From a knowledge representa- tion perspective, the kdd process may take advantage of domain

Boyer, Edmond

309

Complexity of Dependencies in Bounded Domains, Armstrong Codes, and Generalizations  

E-Print Network [OSTI]

Complexity of Dependencies in Bounded Domains, Armstrong Codes, and Generalizations Yeow Meng Chee University, Singapore email: {ymchee, huizhang, xiandezhang}@ntu.edu.sg Abstract--The study of Armstrong systems, where attributes have bounded domains. A (q, k, n)-Armstrong code is a q-ary code of length n

Chee, Yeow Meng

310

Partially compressed-encrypted domain robust JPEG image watermarking  

Science Journals Connector (OSTI)

Digital media is often handled in a compressed and encrypted form in Digital Asset Management Systems. And watermarking of the compressed encrypted media items in the compressed-encrypted domain itself is required sometimes for copyright violation detection ... Keywords: Compressed-encrypted domain watermarking, JPEG watermarking

A. V. Subramanyam, Sabu Emmanuel

2014-08-01T23:59:59.000Z

311

Determinants of the Src Homology Domain 3-Like Fold  

Science Journals Connector (OSTI)

...alignment of an ensemble of such domains from unrelated proteins shows a common...flexible and disordered (35, 36, 41...conservation within the ensemble. RESULTS Structure...density for the protein model is continuous...alignment of an ensemble of such domains from unrelated proteins shows a common...

J. Alejandro D'Aquino; Dagmar Ringe

2003-07-01T23:59:59.000Z

312

Structure of the phylogenetically most conserved domain of SRP RNA  

E-Print Network [OSTI]

Structure of the phylogenetically most conserved domain of SRP RNA ULI SCHMITZ,1 STEFAN BEHRENS,1, San Francisco, California 94143-0448, USA ABSTRACT The signal recognition particle (SRP of the endoplasmic reticulum of the bacterial plasma membrane. Domain IV of SRP RNA consists of a short stem

Walter, Peter

313

Overcoming Dataset Bias: An Unsupervised Domain Adaptation Approach  

E-Print Network [OSTI]

Overcoming Dataset Bias: An Unsupervised Domain Adaptation Approach Boqing Gong Dept. of Computer that recognition datasets are biased. Paying no heed to those biases, learning algorithms often result in classifiers with poor cross- dataset generalization. We are developing domain adaptation techniques to over

Grauman, Kristen

314

A certifying frontend for (sub)polyhedral abstract domains  

E-Print Network [OSTI]

of the overall abstract domain. The main contribution of the work described here is the design of the linkA certifying frontend for (sub)polyhedral abstract domains Alexis Fouilhe and Sylvain Boulmé Univ. Grenoble-Alpes, VERIMAG, F-38000 Grenoble, France {alexis.fouilhe,sylvain.boulme}@imag.fr Abstract. Convex

Paris-Sud XI, Université de

315

Domain-theoretic models of parametric polymorphism L. Birkedal  

E-Print Network [OSTI]

gives formal proof of solutions to a large class of recursive domain equations, which we explicate Copenhagen S, DENMARK, birkedal@itu.dk This work is sponsored by Danish Research Agency stipend no. 272 that such a calculus could serve as a very powerful metalanguage for domain theory in which one could also encode

Birkedal, Lars

316

Audio signal representations for indexing in the transform domain  

E-Print Network [OSTI]

1 Audio signal representations for indexing in the transform domain Emmanuel Ravelli, Student--Indexing audio signals directly in the transform domain can potentially save a significant amount of computation to fully decode the signals. Here, we show that the representations used in standard transform-based audio

Paris 7 - Denis Diderot, Université

317

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....

318

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...

319

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...

320

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...

Note: This page contains sample records for the topic "bind deleted domain" 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

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

322

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...

323

Domain wall QCD with physical quark masses  

E-Print Network [OSTI]

We present results for several light hadronic quantities ($f_\\pi$, $f_K$, $B_K$, $m_{ud}$, $m_s$, $t_0^{1/2}$, $w_0$) obtained from simulations of 2+1 flavor domain wall lattice QCD with large physical volumes and nearly-physical pion masses at two lattice spacings. We perform a short, O(3)%, extrapolation in pion mass to the physical values by combining our new data in a simultaneous chiral/continuum `global fit' with a number of other ensembles with heavier pion masses. We use the physical values of $m_\\pi$, $m_K$ and $m_\\Omega$ to determine the two quark masses and the scale - all other quantities are outputs from our simulations. We obtain results with sub-percent statistical errors and negligible chiral and finite-volume systematics for these light hadronic quantities, including: $f_\\pi$ = 130.2(9) MeV; $f_K$ = 155.5(8) MeV; the average up/down quark mass and strange quark mass in the $\\overline {\\rm MS}$ scheme at 3 GeV, 2.997(49) and 81.64(1.17) MeV respectively; and the neutral kaon mixing parameter, $B_K$, in the RGI scheme, 0.750(15) and the $\\overline{\\rm MS}$ scheme at 3 GeV, 0.530(11).

RBC; UKQCD collaborations; :; T. Blum; P. A. Boyle; N. H. Christ; J. Frison; N. Garron; R. J. Hudspith; T. Izubuchi; T. Janowski; C. Jung; A. Juettner; C. Kelly; R. D. Kenway; C. Lehner; M. Marinkovic; R. D. Mawhinney; G. McGlynn; D. J. Murphy; S. Ohta; A. Portelli; C. T. Sachrajda; A. Soni

2014-11-25T23:59:59.000Z

324

Dynamics of domain wall networks with junctions  

SciTech Connect (OSTI)

We use a combination of analytic tools and an extensive set of the largest and most accurate three-dimensional field theory numerical simulations to study the dynamics of domain wall networks with junctions. We build upon our previous work and consider a class of models which, in the limit of large number N of coupled scalar fields, approaches the so-called ''ideal'' model (in terms of its potential to lead to network frustration). We consider values of N between N=2 and N=20, and a range of cosmological epochs, and we also compare this class of models with other toy models used in the past. In all cases we find compelling evidence for a gradual approach to scaling, strongly supporting our no-frustration conjecture. We also discuss the various possible types of junctions (including cases where there is a hierarchy of them) and their roles in the dynamics of the network. Finally, we provide a cosmological Zel'dovich-type bound on the energy scale of this kind of defect network: it must be lower than 10 keV.

Avelino, P. P.; Oliveira, J. C. R. E. [Centro de Fisica do Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); Departamento de Fisica da Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); Martins, C. J. A. P. [Centro de Astrofisica da Universidade do Porto, Rua das Estrelas s/n, 4150-762 Porto (Portugal); DAMTP, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA (United Kingdom); Menezes, J. [Centro de Fisica do Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); Centro de Astrofisica da Universidade do Porto, Rua das Estrelas s/n, 4150-762 Porto (Portugal); Departamento de Fisica, Universidade Federal da Paraiba, Caixa Postal 5008, 58051-970 Joao Pessoa, Paraiba (Brazil); Menezes, R. [Departamento de Fisica, Universidade Federal da Paraiba, Caixa Postal 5008, 58051-970 Joao Pessoa, Paraiba (Brazil)

2008-11-15T23:59:59.000Z

325

A Cleavable N-Terminal Membrane Anchor is Involved in Membrane Binding of the Escherichia coli SRP Receptor  

Science Journals Connector (OSTI)

Different from eukaryotes, the bacterial signal recognition particle (SRP) receptor lacks a membrane-tethering SRP receptor (SR) ? subunit and is composed of only the SR? homologue FtsY. FtsY is a modular protein composed of three domains. The N- and G-domains of FtsY are highly similar to the corresponding domains of Ffh/SRP54 and SR? and constitute the essential core of FtsY. In contrast, the weakly conserved N-terminal A-domain does not seem to be essential, and its exact function is unknown. Our data show that a 14-amino-acid-long positively charged region at the N-terminus of the A-domain is involved in stabilizing the FtsY–SecYEG interaction. Mutant analyses reveal that the positively charged residues are crucial for this function, and we propose that the 14-amino-acid region serves as a transient lipid anchor. In its absence, the activity of FtsY to support cotranslational integration is reduced to about 50%. Strikingly, in vivo, a truncated isoform of FtsY that lacks exactly these first 14 amino acids exists. Different from full-length FtsY, which primarily cofractionates with the membrane, the N-terminally truncated isoform is primarily present in the soluble fraction. Mutating the conserved glycine residue at position 14 prevents the formation of the truncated isoform and impairs the activity of FtsY in cotranslational targeting. These data suggest that membrane binding and function of FtsY are in part regulated by proteolytic cleavage of the conserved 14-amino-acid motif.

Benjamin Weiche; Jonas Bürk; Sandra Angelini; Emile Schiltz; Jörg Oliver Thumfart; Hans-Georg Koch

2008-01-01T23:59:59.000Z

326

Definition: Controlled Source Frequency-Domain Magnetics | Open Energy  

Open Energy Info (EERE)

Frequency-Domain Magnetics Frequency-Domain Magnetics Jump to: navigation, search Dictionary.png Controlled Source Frequency-Domain Magnetics AquaTrackTM, a controlled-source frequency domain magnetics tool (CS-FDM), is a patented invention by Willowstick Technologies. This technique is meant to characterize groundwater conditions and flow patterns up to 1,000 m depth.[1] References ↑ http://pangea.stanford.edu/ERE/pdf/IGAstandard/SGW/2006/kofoed.pdf Ret LikeLike UnlikeLike You like this.Sign Up to see what your friends like. rieved from "http://en.openei.org/w/index.php?title=Definition:Controlled_Source_Frequency-Domain_Magnetics&oldid=590084" Category: Definitions What links here Related changes Special pages Printable version Permanent link Browse properties 429 Throttled (bot load)

327

Controlled Source Frequency-Domain Magnetics At Salt Wells Area  

Open Energy Info (EERE)

Controlled Source Frequency-Domain Magnetics At Salt Wells Area Controlled Source Frequency-Domain Magnetics At Salt Wells Area (Montgomery, Et Al., 2005) Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Activity: Controlled Source Frequency-Domain Magnetics At Salt Wells Area (Montgomery, Et Al., 2005) Exploration Activity Details Location Salt Wells Area Exploration Technique Controlled Source Frequency-Domain Magnetics Activity Date 2004 - 2004 Usefulness useful DOE-funding Unknown Exploration Basis AMP Resource contracted Willowstick Technologies, LLC to conduct a Controlled Source-Frequency Domain Magnetics (CS-FDM) geophysical investigation at Salt Wells in order to characterize and delineate areas showing the greatest concentrations and highest temperatures of geothermal groundwater. The investigation also sought to map blind faults beneath the

328

Boojums and the Shapes of Domains in Monolayer Films  

E-Print Network [OSTI]

Domains in Langmuir monolayers support a texture that is the two-dimensional version of the feature known as a boojum. Such a texture has a quantifiable effect on the shape of the domain with which it is associated. The most noticeable consequence is a cusp-like feature on the domain boundary. We report the results of an experimental and theoretical investigation of the shape of a domain in a Langmuir monolayer. A further aspect of the investigation is the study of the shape of a ``bubble'' of gas-like phase in such a monolayer. This structure supports a texture having the form of an inverse boojum. The distortion of a bubble resulting from this texture is also studied. The correspondence between theory and experiment, while not perfect, indicates that a qualitative understanding of the relationship between textures and domain shapes has been achieved.

Jiyu Fang; Ellis Teer; Charles M. Knobler; Kok-Kiong Loh; Joseph Rudnick

1997-01-08T23:59:59.000Z

329

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

330

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

331

Distal 8p deletion (8) (p23.1): An easily missed chromosomal abnormality that may be associated with congenital heart defect and mental retardation  

SciTech Connect (OSTI)

We describe the clinical manifestations and molecular cytogenetic analyses of three patients with a similar distal deletion of chromosome 8. Each child had mild developmental delay and subtle minor anomalies. Two had cardiac anomalies but no other major congenital anomalies were present. High resolution G and R banding showed in all three patients del(8)(p23.1), but the breakpoint in case 1 was distal to 8p23.1, in case 2 was in the middle of 8p23.1, and in case 3 proximal to 8p23.1. Fluorescence in situ hybridization (FISH) studies with a chromosome 8 paint probe confirmed that no other rearrangement had occurred. FISH with a chromosome 8-specific telomere probe indicated that two patients had terminal deletions. Chromosome analysis of the parents of case 1 and mother of case 2 were normal; the remaining parents were not available for study. Thirteen individual patients including the three in this study, and three relatives in one family with del(8)(p23.1), have been reported in the past 5 years. Major congenital anomalies, especially congenital heart defects, are most often associated with a breakpoint proximal to 8p23.1. Three patients were found within a 3-year period in this study and five cases were found within 4 years by another group, indicating that distal 8p deletion might be a relatively common chromosomal abnormality. This small deletion is easily overlooked (i.e., cases 1 and 2 were reported as normal at amniocentesis) and can be associated with few or no major congenital anomalies. 31 refs., 4 figs., 2 tabs.

Wu, Bai-Lin; Schneider, G.H.; Sabatino, D.E. [Harvard Medical School, Boston, MA (United States)] [and others] [Harvard Medical School, Boston, MA (United States); and others

1996-03-01T23:59:59.000Z

332

Deletion of the COOH-Terminal Domain of CXC Chemokine Receptor 4 Leads to the Down-regulation of Cell-to-Cell Contact, Enhanced Motility and Proliferation in Breast Carcinoma Cells  

Science Journals Connector (OSTI)

...pSV-psi-envMLV (pSV-pol/gag) provided by Dr. Jane Burns (University of California, San Diego, CA). Virus-containing...Perrais D, Zenisek D. Coupling between clathrin-coated-pit invagination, cortactin recruitment, and membrane scission...

Yukiko Ueda; Nicole F. Neel; Evemie Schutyser; Dayanidhi Raman; and Ann Richmond

2006-06-01T23:59:59.000Z

333

Modulation of Pseudomonas aeruginosa Biofilm Dispersal by a Cyclic-Di-GMP Phosphodiesterase with a Putative Hypoxia-Sensing Domain  

Science Journals Connector (OSTI)

...was confirmed by PCR and DNA sequencing analysis. Single-deletion bifA, pelD, and pslF mutants, double-deletion rbdA pelD, rbdA pslF, and pelD pslF mutants, and the triple-deletion rbdA pelD pslF mutant were generated by the same procedure...

Shuwen An; Ji'en Wu; Lian-Hui Zhang

2010-10-22T23:59:59.000Z

334

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

335

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

336

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

337

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.

338

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

339

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

340

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)-1×1 . Unexpected Nondissociative Binding of N2O on Oxygen Vacancies on a Rutile TiO2(110)-1×1 ....

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
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341

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

342

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

343

Definition: Frequency-Domain Electromagnetics Survey | Open Energy  

Open Energy Info (EERE)

Frequency-Domain Electromagnetics Survey Frequency-Domain Electromagnetics Survey Jump to: navigation, search Dictionary.png Frequency-Domain Electromagnetics Survey Frequency-domain electromagnetic techniques are continuous wave field methods which enable the mapping of the electrical conductivity of the subsurface through electromagnetic induction.[1] View on Wikipedia Wikipedia Definition Electromagnetic induction is the production of a potential difference (voltage) across a conductor when it is exposed to a varying magnetic field. Michael Faraday is generally credited with the discovery of induction in 1831 though it may have been anticipated by the work of Francesco Zantedeschi in 1829. Around 1830 to 1832, Joseph Henry made a similar discovery, but did not publish his findings until later. Faraday's

344

Time-Domain Electromagnetics At Haleakala Volcano Area (Thomas, 1986) |  

Open Energy Info (EERE)

Time-Domain Electromagnetics At Haleakala Volcano Time-Domain Electromagnetics At Haleakala Volcano Area (Thomas, 1986) Exploration Activity Details Location Haleakala Volcano Area Exploration Technique Time-Domain Electromagnetics Activity Date Usefulness useful DOE-funding Unknown Notes Controlled-source electromagnetic soundings were found to be substantially more successful in the southwest rift than either the Schlumberger or the self-potential studies. This was largely due to the ability of time-domain methods to penetrate high-resistivity surface layers and thus to define lower-resistivity sections at depth. The results of this sounding study, which was conducted at elevations ranging from 75 to 497 m a.s.l., generally indicated moderate- to lowresistivity (6 - 7 ohm.m) sections to depths of 1 km on the lower rift zone and higher resistivities (12-16

345

Domain area planning utility (DAPU) for planning wireless battlefield networks  

Science Journals Connector (OSTI)

We describe the key design concepts of Domain Area Planning Utility (DAPU) developed by the PILSNER program to perform high-speed automated planning of Future Battlefield Networks (FBNs). DAPU processes multiple inputs from Resource Planning such as ...

Mariusz A. Fecko; John Unger; Sunil Samtani; Douglas Davey; Andrzej Cichocki; Bill Biagini; Paul Rego; Rick Stewart; Aristides Staikos

2009-10-01T23:59:59.000Z

346

Scaling reinforcement learning to the unconstrained multi-agent domain  

E-Print Network [OSTI]

policies over continuous action spaces, which can reduce problem complexity for domains that require continuous action spaces (analog controllers) by eliminating the need to finely discretize the action space. Finally, we look at ways to perform...

Palmer, Victor

2009-06-02T23:59:59.000Z

347

Understanding Domain Registration Abuses Scott E. Coull1  

E-Print Network [OSTI]

Understanding Domain Registration Abuses Scott E. Coull1 , Andrew M. White1 , Ting-Fang Yen2. Varadharajan, and C. Weber (Eds.): SEC 2010, IFIP AICT 330, pp. 68­79, 2010. c IFIP International Federation

Reiter, Michael

348

Understanding Domain Registration Abuses Scott E. Coull1  

E-Print Network [OSTI]

Understanding Domain Registration Abuses Scott E. Coull1 , Andrew M. White1 , Ting-Fang Yen2 (Ed.) (2012) 68-79" DOI : 10.1007/978-3-642-15257-3_7 #12;security problem underlying these behaviors

Boyer, Edmond

349

Domain wall induced magnetoresistance in a superconductor/ferromagnet nanowire  

E-Print Network [OSTI]

In a nanowire consisting of a ferromagnet/insulator/superconductor multilayer structure, the superconductivity is shown to depend strongly on the configuration of the magnetic domain walls in the neighboring ferromagnetic ...

Miao, G. X.

350

The Observation of Highly Ordered Domains in Membranes with Cholesterol  

SciTech Connect (OSTI)

Rafts, or functional domains, are transient nano- or mesoscopic structures in the exoplasmic leaflet of the plasma membrane, and are thought to be essential for many cellular processes. Using neutron diffraction and computer modelling, we present evidence for the existence of highly ordered lipid domains in the cholesterol-rich (32.5 mol%) liquid-ordered (lo) phase of dipalmitoylphosphatidylcholine membranes. The liquid ordered phase in one-component lipid membranes has previously been thought to be a homogeneous phase. The presence of highly ordered lipid domains embedded in a disordered lipid matrix implies non-uniform distribution of cholesterol between the two phases. The experimental results are in excellent agreement with recent computer simulations of DPPC/cholesterol complexes [Meinhardt, Vink and Schmid (2013). Proc Natl Acad Sci USA 110(12): 4476 4481], which reported the existence of nanometer size lo domains in a liquid disordered lipid environment.

Armstrong, Clare L [McMaster University; Marquardt, Drew [Brock University, St. Catharines, ON, Canada; Dies, Hannah [McMaster University; Kucerka, Norbert [Canadian Neutron Beam Centre and Comelius University (Slovakia); Yamani, Zahra [Canadian Neutron Beam Centre, National Research Council, Chalk River Laboratorie; Harroun, Thad [Brock University, St. Catharines, ON, Canada; Katsaras, John [ORNL; Shi, A-C [McMaster University; Rheinstadter, Maikel C [McMaster University

2013-01-01T23:59:59.000Z

351

Domain-specific Web Service Discovery with Service Class Descriptions  

SciTech Connect (OSTI)

This paper presents DynaBot, a domain-specific web service discovery system. The core idea of the DynaBot service discovery system is to use domain-specific service class descriptions powered by an intelligent Deep Web crawler. In contrast to current registry-based service discovery systems--like the several available UDDI registries--DynaBot promotes focused crawling of the Deep Web of services and discovers candidate services that are relevant to the domain of interest. It uses intelligent filtering algorithms to match services found by focused crawling with the domain-specific service class descriptions. We demonstrate the capability of DynaBot through the BLAST service discovery scenario and describe our initial experience with DynaBot.

Rocco, D; Caverlee, J; Liu, L; Critchlow, T J

2005-02-14T23:59:59.000Z

352

Domain growth in the random-field Ising model  

Science Journals Connector (OSTI)

We study a continuum random-field model of domain growth in quenched nonequilibrium systems. We derive an equation of motion for the interfaces separating domains and find approximate solutions for the growth laws in two and three dimensions. We find what may be a dynamical mechanism for the theoretical prediction that the lower critical dimension of this model is d1=2. Our theoretical predictions can be tested experimentally or by computer simulation.

Martin Grant and J. D. Gunton

1984-02-01T23:59:59.000Z

353

Antigen-specific blocking of immunological synapse formation using bifunctional peptide, Utilization of I-domain of LFA-1 to Target Drug and Marker Molecules to Leukocytes  

E-Print Network [OSTI]

Theranostics 2011, 1 http://www.thno.org 277 Theranostics 2011; 1:277-289 Research Paper Utilization of I-domain of LFA-1 to Target Drug and Marker Molecules to Leukocytes Prakash Manikwar1, Bimo A. Tejo1,2, Heather Shinogle3, David S... via a unique pathway Theranostics 2011, 1 http://www.thno.org 278 referred to as CAM-mediated endocytosis [10-13]. Ligands that bind to CAM can be used to selectively target drugs for intracellular delivery to immune cells expressing...

Manikwar, Prakash; Tejo, Bimo A.; Shinogle, Heather; Moore, David S.; Zimmerman, Tahl; Blanco, Francisco; Siahaan, Teruna J.

2011-05-01T23:59:59.000Z

354

E-Print Network 3.0 - associating transmembrane domains Sample...  

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

transmembrane domains Search Powered by Explorit Topic List Advanced Search Sample search results for: associating transmembrane domains Page: << < 1 2 3 4 5 > >> 1 SUPPLEMENTARY...

355

Magnetic soft x-ray microscopy of the domain wall depinning process in permalloy magnetic nanowires  

E-Print Network [OSTI]

R P 2002 Magnetic domain-wall logic Science 296 1688 [2]magnetic domain»wall nanowire shift register Science 320

Im, Mi-Young

2014-01-01T23:59:59.000Z

356

Ferroelectric stripe domains in PbTiO{sub 3} thin films: Depolarization field and domain randomness  

SciTech Connect (OSTI)

Observation of stripe domains in PbTiO{sub 3} thin films using standard x-ray diffraction analysis at room temperature is discussed. High-quality c-axis oriented thin films of varying thickness, from 6 to 210 unit cells, were grown on buffered NH{sub 4}-HF etched SrTiO{sub 3}(001) and Nb:SrTiO{sub 3}(001) substrates using off-axis radio frequency magnetron sputtering. High-resolution linear Q{sub x} scans reveal a superstructure around the specular Bragg peaks, consistent with the presence of ferroelectric stripe domains. For thin samples, the stripe width is found to be proportional to the square root of the film thickness, with random in-plane orientation of domains. For films with a thickness of more than {approx}100 unit cells, both monodomain samples and stripe domains were observed. We present evidence for the presence of a threshold depolarization field, above which there is a monotonically decreasing relationship between the domain width and the depolarization field. Furthermore, simulations show that random variations in size of the domains affect the separation of the diffuse scattering peaks from that of the specular reflection.

Takahashi, R.; Dahl, O.; Eberg, E.; Grepstad, J. K.; Tybell, T. [Department of Electronics and Telecommunications, Norwegian University of Science and Technology, O. S. Bragstads plass 2a, 7491 Trondheim (Norway)

2008-09-15T23:59:59.000Z

357

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

358

The distal 8p deletion (8)(p23.1): A common syndrome associated with cogenital heart defect and mental retardation?  

SciTech Connect (OSTI)

We describe the clinical manifestations and molecular cytogenetic analysis of three patients with a similar distal deletion: del(8)(p23.1). Case 1: A nine-year-old girl who was the product of a normal pregnancy, with family history of recurrent miscarriages. She has an ASD, development delay and dysmorphic features. Case 2: A three-month-old female who died with a hypoplastic left heart and dysmorphic features. Her non-identical twin sister is healthy. No further family history is available. Case 3: A four-year-old boy who was the product of a normal pregnancy with family history of mental retardation. He has bifid uvula, delayed speech and language, and no major malformations or dysmorphic features. High resolution G and R banding revealed in all three patients del(8)(p23.1), but the breakpoint for case 1 and 2 was proximal to 8p23.1 and for case 3 distal to 8p23.1. FISH studies with a chromosome 8 paint probe confirmed that no other rearrangement was involved. Chromosome analysis of the parents of case 3 and mother of case 1 were normal; the remaining parents were not available for study. Eight individual patients and three members in one family with del(8)(p23.1) have been reported in the past five years. Major congenital anomalies, especially congenital heart defect, is most often associated with a breakpoint proximal to 8p23.1 Three patients were detected within a three year period in this study and five cases were found within a four year period by another group, suggesting that the distal 8p deletion may be a relatively common syndrome. This small deletion is easily overlooked (i.e. case 1 and 3 were reported as normal at amniocentesis) and can be associated with few or no major congenital anomalies.

Wu, B.L.; Schneider, G.H.; Sabatino, D.E. [Harvard Medical School, Boston, MA (United States)] [and others

1994-09-01T23:59:59.000Z

359

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...

360

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

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


361

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...

362

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...

363

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...

364

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...

365

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

366

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

367

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 Ceria–Titania and its Synthesis Dependent Core Level Binding Energy Shift in the Oxidation State ofPlatinum Coated...

368

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

369

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

370

Disordered binding regions of Ewing’s 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 Ewing’s sarcoma protein (EWS) and oncogenic EWS f...

R. Todorova

2014-01-01T23:59:59.000Z

371

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

372

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

373

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

374

Sampling Approaches for Multi-Domain Internet Performance Measurement Infrastructures  

SciTech Connect (OSTI)

The next-generation of high-performance networks being developed in DOE communities are critical for supporting current and emerging data-intensive science applications. The goal of this project is to investigate multi-domain network status sampling techniques and tools to measure/analyze performance, and thereby provide “network awareness” to end-users and network operators in DOE communities. We leverage the infrastructure and datasets available through perfSONAR, which is a multi-domain measurement framework that has been widely deployed in high-performance computing and networking communities; the DOE community is a core developer and the largest adopter of perfSONAR. Our investigations include development of semantic scheduling algorithms, measurement federation policies, and tools to sample multi-domain and multi-layer network status within perfSONAR deployments. We validate our algorithms and policies with end-to-end measurement analysis tools for various monitoring objectives such as network weather forecasting, anomaly detection, and fault-diagnosis. In addition, we develop a multi-domain architecture for an enterprise-specific perfSONAR deployment that can implement monitoring-objective based sampling and that adheres to any domain-specific measurement policies.

Calyam, Prasad

2014-09-15T23:59:59.000Z

375

Frequency-domain multiscale quantum mechanics/electromagnetics simulation method  

SciTech Connect (OSTI)

A frequency-domain quantum mechanics and electromagnetics (QM/EM) method is developed. Compared with the time-domain QM/EM method [Meng et al., J. Chem. Theory Comput. 8, 1190–1199 (2012)], the newly developed frequency-domain QM/EM method could effectively capture the dynamic properties of electronic devices over a broader range of operating frequencies. The system is divided into QM and EM regions and solved in a self-consistent manner via updating the boundary conditions at the QM and EM interface. The calculated potential distributions and current densities at the interface are taken as the boundary conditions for the QM and EM calculations, respectively, which facilitate the information exchange between the QM and EM calculations and ensure that the potential, charge, and current distributions are continuous across the QM/EM interface. Via Fourier transformation, the dynamic admittance calculated from the time-domain and frequency-domain QM/EM methods is compared for a carbon nanotube based molecular device.

Meng, Lingyi; Yin, Zhenyu; Yam, ChiYung, E-mail: yamcy@yangtze.hku.hk, E-mail: ghc@everest.hku.hk; Koo, SiuKong; Chen, GuanHua, E-mail: yamcy@yangtze.hku.hk, E-mail: ghc@everest.hku.hk [Department of Chemistry, The University of Hong Kong, Pokfulam Road (Hong Kong)] [Department of Chemistry, The University of Hong Kong, Pokfulam Road (Hong Kong); Chen, Quan; Wong, Ngai [Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road (Hong Kong)] [Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road (Hong Kong)

2013-12-28T23:59:59.000Z

376

Automatically structuring domain knowledge from text: An overview of current research  

Science Journals Connector (OSTI)

This paper presents an overview of automatic methods for building domain knowledge structures (domain models) from text collections. Applications of domain models have a long history within knowledge engineering and artificial intelligence. In the last ... Keywords: Artificial intelligence, Domain models, Information retrieval, Natural language processing

Malcolm Clark; Yunhyong Kim; Udo Kruschwitz; Dawei Song; Dyaa Albakour; Stephen Dignum; Ulises Cerviño Beresi; Maria Fasli; Anne De Roeck

2012-05-01T23:59:59.000Z

377

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.

378

Frequency-Domain Electromagnetic Survey | Open Energy Information  

Open Energy Info (EERE)

Frequency-Domain Electromagnetic Survey Frequency-Domain Electromagnetic Survey Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Frequency-Domain Electromagnetic Survey Details Activities (0) Areas (0) Regions (0) NEPA(0) Exploration Technique Information Exploration Group: Geophysical Techniques Exploration Sub Group: Electrical Techniques Parent Exploration Technique: Electromagnetic Profiling Techniques Information Provided by Technique Lithology: Detection of high-conductivity bodies in the subsurface. Stratigraphic/Structural: Hydrological: Thermal: Detection of the presence of a thermal anomaly through its resistivity signature. Cost Information Low-End Estimate (USD): 2,928.38292,838 centUSD 2.928 kUSD 0.00293 MUSD 2.92838e-6 TUSD / mile Median Estimate (USD): 4,505.20450,520 centUSD

379

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

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

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from hydrolysing ATP into a series of small conformational changes that allow them to literally "walk" along microscopic tracks. Motor proteins (in the kinesin and myosin families) have been extensively studied by x-ray crystallography, but until recently there was little molecular structural information for dyneins, another type of motor protein. A group from the University of California, San Francisco, working at ALS Beamline 8.3.1 has reported the 6-Å-resolution structure of the motor domain of dynein in yeast. It reveals details of the ring-shaped motor as well as a new, unanticipated feature called the buttress that may play an important role in dynein's mechanical cycle.

380

National Geothermal Data System (NGDS) Geothermal Data Domain: Assessment  

Open Energy Info (EERE)

National Geothermal Data System (NGDS) Geothermal Data Domain: Assessment National Geothermal Data System (NGDS) Geothermal Data Domain: Assessment of Geothermal Community Data Needs Jump to: navigation, search OpenEI Reference LibraryAdd to library Conference Paper: National Geothermal Data System (NGDS) Geothermal Data Domain: Assessment of Geothermal Community Data Needs Abstract To satisfy the critical need for geothermal data to advance geothermal energy as a viable renewable energy contender, the U.S. Department of Energy is in-vesting in the development of the National Geothermal Data System (NGDS). This paper outlines efforts among geothermal data providers nationwide to sup-ply cutting edge geoinformatics. NGDS geothermal data acquisition, delivery, and methodology are dis-cussed. In particular, this paper addresses the various types of data required to effectively assess

Note: This page contains sample records for the topic "bind deleted domain" 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

Controlled Source Frequency-Domain Magnetics | Open Energy Information  

Open Energy Info (EERE)

Controlled Source Frequency-Domain Magnetics Controlled Source Frequency-Domain Magnetics Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Controlled Source Frequency-Domain Magnetics Details Activities (2) Areas (2) Regions (0) NEPA(0) Exploration Technique Information Exploration Group: Geophysical Techniques Exploration Sub Group: Magnetic Techniques Parent Exploration Technique: Magnetic Techniques Information Provided by Technique Lithology: Stratigraphic/Structural: Hydrological: Locate geothermal groundwater and flow patterns. Thermal: Cost Information Low-End Estimate (USD): 12,000.001,200,000 centUSD 12 kUSD 0.012 MUSD 1.2e-5 TUSD / mile Median Estimate (USD): 18,000.001,800,000 centUSD 18 kUSD 0.018 MUSD 1.8e-5 TUSD / mile High-End Estimate (USD): 25,000.002,500,000 centUSD

382

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

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

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from hydrolysing ATP into a series of small conformational changes that allow them to literally "walk" along microscopic tracks. Motor proteins (in the kinesin and myosin families) have been extensively studied by x-ray crystallography, but until recently there was little molecular structural information for dyneins, another type of motor protein. A group from the University of California, San Francisco, working at ALS Beamline 8.3.1 has reported the 6-Å-resolution structure of the motor domain of dynein in yeast. It reveals details of the ring-shaped motor as well as a new, unanticipated feature called the buttress that may play an important role in dynein's mechanical cycle.

383

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

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

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from hydrolysing ATP into a series of small conformational changes that allow them to literally "walk" along microscopic tracks. Motor proteins (in the kinesin and myosin families) have been extensively studied by x-ray crystallography, but until recently there was little molecular structural information for dyneins, another type of motor protein. A group from the University of California, San Francisco, working at ALS Beamline 8.3.1 has reported the 6-Å-resolution structure of the motor domain of dynein in yeast. It reveals details of the ring-shaped motor as well as a new, unanticipated feature called the buttress that may play an important role in dynein's mechanical cycle.

384

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

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

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from hydrolysing ATP into a series of small conformational changes that allow them to literally "walk" along microscopic tracks. Motor proteins (in the kinesin and myosin families) have been extensively studied by x-ray crystallography, but until recently there was little molecular structural information for dyneins, another type of motor protein. A group from the University of California, San Francisco, working at ALS Beamline 8.3.1 has reported the 6-Å-resolution structure of the motor domain of dynein in yeast. It reveals details of the ring-shaped motor as well as a new, unanticipated feature called the buttress that may play an important role in dynein's mechanical cycle.

385

Definition: Frequency-Domain Electromagnetic Survey | Open Energy  

Open Energy Info (EERE)

Electromagnetic Survey Electromagnetic Survey Jump to: navigation, search Dictionary.png Frequency-Domain Electromagnetic Survey Frequency-domain electromagnetic techniques are continuous wave field methods which enable the mapping of the electrical conductivity of the subsurface through electromagnetic induction.[1] Also Known As Controlled-Source EM References ↑ http://library.seg.org/doi/pdf/10.1190/1.1441531 Ret LikeLike UnlikeLike You like this.Sign Up to see what your friends like. rieved from "http://en.openei.org/w/index.php?title=Definition:Frequency-Domain_Electromagnetic_Survey&oldid=591411" Category: Definitions What links here Related changes Special pages Printable version Permanent link Browse properties About us Disclaimers Energy blogs Linked Data Developer services

386

RAPID: A Reachable Anytime Planner for Imprecisely-sensed Domains  

E-Print Network [OSTI]

Despite the intractability of generic optimal partially observable Markov decision process planning, there exist important problems that have highly structured models. Previous researchers have used this insight to construct more efficient algorithms for factored domains, and for domains with topological structure in the flat state dynamics model. In our work, motivated by findings from the education community relevant to automated tutoring, we consider problems that exhibit a form of topological structure in the factored dynamics model. Our Reachable Anytime Planner for Imprecisely-sensed Domains (RAPID) leverages this structure to efficiently compute a good initial envelope of reachable states under the optimal MDP policy in time linear in the number of state variables. RAPID performs partially-observable planning over the limited envelope of states, and slowly expands the state space considered as time allows. RAPID performs well on a large tutoring-inspired problem simulation with 122 state variables, cor...

Brunskill, Emma

2012-01-01T23:59:59.000Z

387

Dissection and Manipulation of LRR Domains in Plant Disease Resistance Gene Products.  

SciTech Connect (OSTI)

Leucine-rich repeat (LRR) protein domains offer a readily diversifiable platform - literally, an extended protein surface - for specific binding of very diverse ligands. The project addressed the following overlapping research questions: - How do leucine-rich repeat proteins recognize their cognate ligands? - What are the intra- and inter-molecular transitions that occur that cause transmembrane LRR proteins to switch between �off� and �on� states? - How do plants use LRR receptor proteins to activate disease resistance? - Can we synthetically evolve new LRR proteins that have acquired new ligand specificities? The following peer-reviewed primary research papers were published as part of the DOE-funded research: Sun*, W., Y. Cao*, K.L. Jansen, P. Bittel, T. Boller and A.F. Bent (*co-first authors), 2012. Probing the Arabidopsis flagellin receptor: FLS2-FLS2 association and the contributions of specific domains to signaling function. Plant Cell 24:1096-1113. DOI 10.1105/tpc.112.095919. Sun, W., L. Liu and A.F. Bent, 2011. Type III secretion�dependent host defense elicitation and Type III secretion�independent growth within leaves by Xanthomonas campestris pv.campestris. Mol. Plant Pathol. 12:731-745. DOI: 10.1111/J.1364-3703.2011.00707.X Helft, L., V. Reddy, X. Chen, T. Koller, L. Federici, J. Fernandez-Recio, R. Gupta and A. Bent, 2011. LRR Conservation Mapping to predict functional sites within protein leucine-rich repeat domains. PLoS ONE 6(7): e21614. doi:10.1371/journal.pone.0021614 Danna, C.H., Y.A. Millet, T. Koller, S.-W. Han, A.F. Bent, P.C. Ronald and F.M. Ausubel, 2011. The Arabidopsis flagellin receptor FLS2 mediates the perception of Xanthomonas Ax21 secreted peptides. Proc. Natl. Acad. Sci. (USA) 108:9286-9291. Two additional manuscripts are currently complete, one is submitted and is now being revised according to referee suggestions, and the other is not yet submitted. The provisional titles of those papers are: �FLS2/BIK1/BAK1 Association and Dissociation are Not Sufficient to Activate Arabidopsis Immunity but FLS2 Phosphorylation Site Ser-938 is Required.� and �Directed Evolution of FLS2 towards Novel Flagellin Peptide Recognition.� An additional tangible outcome of the work is the public availability of a bioinformatics website that we developed, www.plantpath.wisc.edu/RCM, where researchers can enter primary amino acid sequences for two or more related leucine-rich repeat proteins and use the program to identify sites on the predicted surface of the LRR that have been most conserved or most diversified across the proteins. These sites are typically the key functional sites on the protein, such as ligand binding sites. Despite a shift of DOE priorities away from support of research on plant immune system function, we are continuing our work on the engineering or in vitro evolution of LRR proteins toward novel ligand specificities.

Bent, Andrew

2012-11-28T23:59:59.000Z

388

Impact on the steam electric power industry of deleting Section 316(a) of the Clean Water Act: Energy and environmental impacts  

SciTech Connect (OSTI)

Many power plants discharge large volumes of cooling water. In some cases, the temperature of the discharge exceeds state thermal requirements. Section 316(a) of the Clean Water Act (CWA) allows a thermal discharger to demonstrate that less stringent thermal effluent limitations would still protect aquatic life. About 32% of the total steam electric generating capacity in the United States operates under Section 316(a) variances. In 1991, the US Senate proposed legislation that would delete Section 316(a) from the CWA. This study, presented in two companion reports, examines how this legislation would affect the steam electric power industry. This report quantitatively and qualitatively evaluates the energy and environmental impacts of deleting the variance. No evidence exists that Section 316(a) variances have caused any widespread environmental problems. Conversion from once-through cooling to cooling towers would result in a loss of plant output of 14.7-23.7 billion kilowatt-hours. The cost to make up the lost energy is estimated at $12.8-$23.7 billion (in 1992 dollars). Conversion to cooling towers would increase emission of pollutants to the atmosphere and water loss through evaporation. The second report describes alternatives available to plants that currently operate under the variance and estimates the national cost of implementing such alternatives. Little justification has been found for removing the 316(a) variance from the CWA.

Veil, J.A.; VanKuiken, J.C.; Folga, S.; Gillette, J.L.

1993-01-01T23:59:59.000Z

389

A novel inactivated gE/gI deleted pseudorabies virus (PRV) vaccine completely protects pigs from an emerged variant PRV challenge  

Science Journals Connector (OSTI)

Abstract A highly virulent and antigenic variant of pseudorabies virus (PRV) broke out in China at the end of 2011 and caused great economic loss in the pig industry. In this study, an infectious bacterial artificial chromosome (BAC) clone containing the full-length genome of the emerged variant PRV ZJ01 strain was generated. The BAC-derived viruses, vZJ01-GFP?gE/gI (gE/gI deleted strain, and exhibiting green autofluorescence), vZJ01?gE/gI (gE/gI deleted strain), and vZJ01gE/gI-R (gE/gI revertant strain), showed similar in vitro growth to their parent strain. In pigs, inactivated vZJ01?gE/gI vaccine generated significantly high levels of neutralizing antibodies against ZJ01 compared with Bartha-K61 live vaccine (p < 0.05). After fatal ZJ01 challenge, all five animals in the inactivated vZJ01?gE/gI vaccine group survived without exhibiting any clinical sings, but two of five animals exhibited central nervous signs in the Bartha-K61 group. Meanwhile, all the non-vaccinated control animals died at 7 days post-challenge. This indicates that the inactivated vZJ01?gE/gI vaccine is a promising vaccine candidate for controlling the variant strains of PRV now circulating in China.

Zhenqing Gu; Jing Dong; Jichun Wang; Chengcai Hou; Haifeng Sun; Wenping Yang; Juan Bai; Ping Jiang

2015-01-01T23:59:59.000Z

390

SUBCRITICAL BUBBLES NEAR THE PHASE SPACE DOMAIN WALL  

E-Print Network [OSTI]

We study the subcritical bubble formation near the phase space domain wall. We take into account that the phase of the scalar field can vary using complex U(1) symmetric field and a phenomenological potential with cubic term responsible to symmetry breaking. We show that the presence of the domain wall induces subcritical bubbles so that their formation rate near the wall is considerably larger than far of it. The allowed deviations of the phases of new bubbles are so large that they prevent the system from induced nucleation.

J. Sirkka; I. Vilja

1995-03-31T23:59:59.000Z

391

Domain-growth kinetics of systems with soft walls  

Science Journals Connector (OSTI)

It has recently been suggested by Mouritsen on the basis of computer simulations that systems with soft domain walls exhibit slower domain growth than the R?t1/2 growth law predicted by Lifshitz and Allen and Cahn. We underscore the reasons to believe this interpretation of the data to be incorrect and draw attention to an experiment by Pindak, Young, Meyer, and Clark, whose results are in complete agreement with the predictions of Allen and Cahn. The reason for the unexpected growth dynamics observed in Mouritsen’s simulations is suggested.

Wim van Saarloos and Martin Grant

1988-02-01T23:59:59.000Z

392

Targeted Gene Deletion Demonstrates that Cell Adhesion MoleculeICAM-4 is Critical for Erythroblastic Island Formation  

SciTech Connect (OSTI)

Erythroid progenitors differentiate in erythroblastic islands, bone marrow niches composed of erythroblasts surrounding a central macrophage. Evidence suggests that within islands adhesive interactions regulate erythropoiesis and apoptosis. We are exploring whether erythroid intercellular adhesion molecule-4 (ICAM-4), animmunoglobulin superfamily member, participates in island formation. Earlier, we identified alpha V integrins as ICAM-4 counter receptors. Since macrophages express alpha V, ICAM-4 potentially mediates island attachments. To test this, we generated ICAM-4 knockout mice and developed quantitative, live cell techniques for harvesting intact islands and for reforming islands in vitro. We observed a 47 percent decrease in islands reconstituted from ICAM-4 null marrow compared to wild type. We also found a striking decrease in islands formed in vivo in knockout mice. Further, peptides that block ICAM-4 alpha V adhesion produced a 53-57 percent decrease in reconstituted islands, strongly suggesting that ICAM-4 binding to macrophage alpha V functions in island integrity. Importantly, we documented that alpha V integrin is expressed in macrophages isolated from erythro blastic islands. Collectively, these data provide convincing evidence that ICAM-4 is critical in erythroblastic island formation via ICAM-4/alpha V adhesion and also demonstrate that the novel experimental strategies we developed will be valuable in exploring molecular mechanisms of erythroblastic island formation and their functional role in regulating erythropoiesis.

Lee, Gloria; Lo, Annie; Short, Sarah A.; Mankelow, Tosti J.; Spring, Frances; Parsons, Stephen F.; Mohandas, Narla; Anstee, David J.; Chasis, Joel Anne

2006-02-15T23:59:59.000Z

393

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

394

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 Ã? Brent C

Christner, Brent C.

395

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

396

On the Oberbeck-Boussinesq approximation on unbounded domains  

E-Print Network [OSTI]

On the Oberbeck-Boussinesq approximation on unbounded domains Eduard Feireisl and Maria E. Schonbek Abstract We study the Oberbeck-Boussinesq approximation describing the mo- tion of an incompressible, heat that the total energy of any solution of the resulting Oberbeck-Boussinesq system tends to zero with growing time

Schonbek, Maria

397

10 DOMAIN-APPROPRIATE DEVICES * For a video example, see  

E-Print Network [OSTI]

of drawing as its application area, and a process control system in a power plant has the domain of that power plant and its functions as its application area. However, most interactive systems use a lot of work into creating "meta- phors" in which the virtual, on-screen world resembles items

Borchers, Jan

398

Multi-agent Cooperative Cleaning of Expanding Domains  

Science Journals Connector (OSTI)

Several recent works considered multi-a(ge)nt robotics in static environments. In this work we examine ways of operating in dynamic environments, where changes take place independently of the agentsâ?? activity. The work focuses on a dynamic ... Keywords: Collaborative cleaning, collaborative search, decentralized robots, expanding domains, grid search

Yaniv Altshuler; Vladimir Yanovski; Israel A Wagner; Alfred M Bruckstein

2011-07-01T23:59:59.000Z

399

Interpreting Performance Data Across Intuitive Domains Martin Schulz1  

E-Print Network [OSTI]

performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National LaboratoryInterpreting Performance Data Across Intuitive Domains Martin Schulz1 , Joshua A. Levine2 , Peer, USA 2 Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT {schulzm

Utah, University of

400

Hybrid Powertrain Design Using a Domain-Specific Modeling Environment  

E-Print Network [OSTI]

tools for automotive engineering. A face-off with modeling and simulation tools in the electronicsHybrid Powertrain Design Using a Domain- Specific Modeling Environment Wenzhong Gao1 , Sandeep--State of the art design tools in automotive engineering still lack the power, sophistication, and automation

Gray, Jeffrey G.

Note: This page contains sample records for the topic "bind deleted domain" 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

Catalytic Domain of Phosphoinositide-specific Phospholipase C (PLC)  

E-Print Network [OSTI]

Catalytic Domain of Phosphoinositide-specific Phospholipase C (PLC) MUTATIONAL ANALYSIS OF RESIDUES WITHIN THE ACTIVE SITE AND HYDROPHOBIC RIDGE OF PLC 1* (Received for publication, November 20, 1997 Institute, University of Dundee, Dundee DD1 4HN, United Kingdom Structural studies of phospholipase C 1 (PLC

Williams, Roger L.

402

WHEELS: A CONVERSATIONAL SYSTEM IN THE AUTOMOBILE CLASSIFIEDS DOMAIN  

E-Print Network [OSTI]

WHEELS: A CONVERSATIONAL SYSTEM IN THE AUTOMOBILE CLASSIFIEDS DOMAIN Helen Meng, Senis WHEELS is a conversational system which provides access to a database of eletronic automobile classified users to search through a database of 5,000 automobile classifieds. The current end-to-end system can re

403

TIME DOMAIN REFLECTOMETRY MEASUREMENT AND HIGHLY PLASTIC CLAYS  

E-Print Network [OSTI]

1 TIME DOMAIN REFLECTOMETRY MEASUREMENT AND HIGHLY PLASTIC CLAYS By: J. A. Kuhn1 and J. G. Zornberg for use in highly plastic clay. The clay used for experimentation was taken locally from the Eagle Ford Ford Clay is determined. INTRODUCTION The progression of wetting and drying fronts in highly plastic

Zornberg, Jorge G.

404

Cognitive Domain: K=Knowledge S=Skill  

E-Print Network [OSTI]

Cognitive Domain: K=Knowledge S=Skill AB=Attitude/Behavior Institutional Learning Objectives: K1 Knowledge of the normal structure of the human body (cell tissues and organs). K2 Knowledge of the normal function of the human body (cell tissues and organs). K3 Knowledge of the nature of agents and mechanisms

Finley Jr., Russell L.

405

BAYESIAN WAVELET-DOMAIN IMAGE MODELING USING HIDDEN MARKOV TREES  

E-Print Network [OSTI]

to be approximately decorrelated. Energy Compaction: The wavelet transforms of real-world images-1892, USA ABSTRACT Wavelet-domain hidden Markov models have proven to be useful tools.for statistical signal and image processing. The hidden Markov tree (HMT) model captures the key features of the joint statistics

406

Multiferroic Domain Dynamics in Strained Strontium Titanate A. Vasudevarao,1  

E-Print Network [OSTI]

Multiferroic Domain Dynamics in Strained Strontium Titanate A. Vasudevarao,1 A. Kumar,1 L. Tian,1 J (Received 19 June 2006; published 21 December 2006) Multiferroicity can be induced in strontium titanate to the ferroelectric mm2 phase, followed by a transition to a ferroelastic-ferroelectric mm2 phase in a strontium

Gopalan, Venkatraman

407

FACTS about threat Possible INTERVENTIONS Strong domain identification  

E-Print Network [OSTI]

FACTS about threat Possible INTERVENTIONS Strong domain identification heightens the effect are able to self affirm in difficult situations can lessen the effects of threat. Encourage students to use to students not under threat. Educate students on self talk! Teach them to pay close attention

Chisholm, Rex L.

408

Applying electronic contracting to the aerospace aftercare domain Felipe Meneguzzia,  

E-Print Network [OSTI]

Applying electronic contracting to the aerospace aftercare domain Felipe Meneguzzia, , Sanjay The contract project was a European Commission project whose aim was to develop frame- works, components contracts. In this context, an electronic contract provides a specifi- cation of the expected behaviours

Luck, Michael

409

Time-domain Dynamics and Stability Analysis of Optoelectronic Oscillators  

E-Print Network [OSTI]

Time-domain Dynamics and Stability Analysis of Optoelectronic Oscillators based on Whispering and Yanne K. Chembo Optoelectronic oscillators (OEOs) are microwave photonics systems in- tended to generate in "" #12;1 Introduction The optoelectronic oscillator (OEO) is nowadays considered as one of the most

Paris-Sud XI, Université de

410

Projective lines over one-dimensional semilocal domains  

E-Print Network [OSTI]

ian domain A, we have dim(B) ? 2 so dim(B) = 2. At most finitely many of the height-one maximals ..... f = r0 + r1(y/x) + ... + (y/x)n, then N is the unique height-

2013-01-21T23:59:59.000Z

411

Familiarity Breeds Trust: Collective Action in a Policy Domain  

E-Print Network [OSTI]

Familiarity Breeds Trust: Collective Action in a Policy Domain Mark Lubell University of California), a variety of public policy settings like taxpaying (Levi 1988; Scholz and Lubell 1998a, 1998b) and environmental policy (Lubell 2003; Ostrom 1990; Scheberle 1997), and more fundamen- tally for citizens engaged

Lubell, Mark

412

An Energy Efficient Asynchronous Time-Domain Comparator  

E-Print Network [OSTI]

/falling), asynchronous comparison and 2-bit/step comparison. With these features, power consumption of the comparator can be effectively reduced. For verification, the proposed time-domain comparator is fabricated in IBM 0.18um CMOS technology in comparison with other...

Gao, Yang

2013-04-26T23:59:59.000Z

413

BLINK: Pixel-Domain Encryption for Secure Document Idris Atakli  

E-Print Network [OSTI]

be a video cable with an integrated decoder box; its interface is a single switch by which the user canBLINK: Pixel-Domain Encryption for Secure Document Management Idris Atakli Department of Electrical. The primary application is delivery of confidential documents that can only be viewed by a specific machine

Chen, Yu

414

ROO: Involving Domain Experts in Authoring OWL Ronald Denaux  

E-Print Network [OSTI]

Authoring, Controlled Natural Language Interfaces, Evaluation of Ontology Building Tools, Geographical process and improve the quality of the resultant ontologies. Recently, controlled language (CL) interfaces domain experts' definition of ontologies in OWL by allowing them to author the ontology in a controlled

Dimitrova, Vania

415

IDENTIFICATION OF MATERIAL DAMAGE IN TWO DIMENSIONAL DOMAINS  

E-Print Network [OSTI]

IDENTIFICATION OF MATERIAL DAMAGE IN TWO DIMENSIONAL DOMAINS USING SQUID BASED NDE SYSTEM H on such problems entails quantitative nondestructive evaluation methods in SQUID-based NDE system [1]. It is well, SQUID based nondestructive evaluation (NDE) systems using injection current methods have been recently

416

IDENTIFICATION OF MATERIAL DAMAGE IN TWO DIMENSIONAL DOMAINS  

E-Print Network [OSTI]

IDENTIFICATION OF MATERIAL DAMAGE IN TWO DIMENSIONAL DOMAINS USING SQUID BASED NDE SYSTEM H#ort on such problems entails quantitative nondestructive evaluation methods in SQUID­based NDE system [1]. It is well nondestructive evaluation (NDE) systems using injection current methods have been recently developed [3, 4

417

Audio signal representations for indexing in the transform domain  

E-Print Network [OSTI]

1 Audio signal representations for indexing in the transform domain Emmanuel Ravelli, Ga¨el Richard, Senior Member, IEEE, and Laurent Daudet, Member, IEEE Abstract--Indexing audio signals directly that the representations used in standard transform-based audio codecs (e.g. MDCT for AAC, or hybrid PQF/MDCT for MP3) have

Richard, Gaël

418

Databases on the Web: national web domain survey Denis Shestakov  

E-Print Network [OSTI]

, Aalto University Konemiehentie 2, Espoo, 02150 Finland denis.shestakov@aalto.fi ABSTRACT The deep Web of the deep Web by sampling one national web domain. We report some of our results ob- tained when surveying the Russian Web. The survey find- ings, namely the size estimates of the deep Web, could be useful for further

Hammerton, James

419

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

420

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

Note: This page contains sample records for the topic "bind deleted domain" 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

Structure of the Full-Length Human RPA14/32 Complex Gives Insights Into the Mechanism of DNA Binding And Complex Formation  

SciTech Connect (OSTI)

Replication protein A (RPA) is the ubiquitous, eukaryotic single-stranded DNA (ssDNA) binding protein and is essential for DNA replication, recombination, and repair. Here, crystal structures of the soluble RPA heterodimer, composed of the RPA14 and RPA32 subunits, have been determined for the full-length protein in multiple crystal forms. In all crystals, the electron density for the N-terminal (residues 1--42) and C-terminal (residues 175--270) regions of RPA32 is weak and of poor quality indicating that these regions are disordered and/or assume multiple positions in the crystals. Hence, the RPA32 N terminus, that is hyperphosphorylated in a cell-cycle-dependent manner and in response to DNA damaging agents, appears to be inherently disordered in the unphosphorylated state. The C-terminal, winged helix-loop-helix, protein-protein interaction domain adopts several conformations perhaps to facilitate its interaction with various proteins. Although the ordered regions of RPA14/32 resemble the previously solved protease-resistant core crystal structure, the quaternary structures between the heterodimers are quite different. Thus, the four-helix bundle quaternary assembly noted in the original core structure is unlikely to be related to the quaternary structure of the intact heterotrimer. An organic ligand binding site between subunits RPA14 and RPA32 was identified to bind dioxane. Comparison of the ssDNA binding surfaces of RPA70 with RPA14/32 showed that the lower affinity of RPA14/32 can be attributed to a shallower binding crevice with reduced positive electrostatic charge.

Deng, X.; Habel, J.E.; Kabaleeswaran, V.; Snell, E.H.; Wold, M.S.; Borgstahl, G.E.O.

2009-06-03T23:59:59.000Z

422

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

423

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

424

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

425

Molecular Modeling of the Extracellular Domain of the RET Receptor Tyrosine Kinase Reveals Multiple Cadherin-like Domains  

E-Print Network [OSTI]

induce constitutive activation of the RET tyrosine kinase and lead to congenital and sporadic cancers-directed mutagenesis studies aimed at identifying residues in- volved in ligand binding and receptor activation transducing receptor subunit, with specificity being deter- mined by cooperation between RET and different

Ibáñez, Carlos

426

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

427

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 0.9 M?. 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. Köhler

1964-10-12T23:59:59.000Z

428

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

429

Calculation of HVDC-converter harmonics in frequency domain with regard to asymmetries and comparison with time domain simulations  

SciTech Connect (OSTI)

In order to study the effects of large HVDC converters to the feeding ac networks, it is of importance to explain and to calculate harmonic phenomena which are a result of converter operation. During commissioning of real HVDC converters it could be seen, that harmonics resulting from unsymmetries in the system voltages or from unsymmetries in converter operation led to significant difficulties concerning the system design. For this reason, not only the effects of characteristic but also the effects of noncharacteristic converter harmonics must be taken into account. The aim is to describe the steady state harmonic behavior of the converter. The harmonic spectra are not determined by time domain analysis but instead the solution is found by frequency domain calculations. This can result in reduced calculation time in comparison to conventional fourier analysis of the time functions. The converter is interpreted as an amplitude modulator with voltage and current converter functions which describe the coupling of the dc circuit and the ac network through the converter. To verify the theory, comparison of frequency domain with time domain calculations were carried out.

Rittiger, J. [Siemens AG, Erlangen (Germany)] [Siemens AG, Erlangen (Germany); Kulicke, B. [Technische Univ. Berlin (Germany)] [Technische Univ. Berlin (Germany)

1995-10-01T23:59:59.000Z

430

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

431

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

432

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

433

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

434

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

435

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

436

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.

437

Workshop on Time Domain Science Using X-ray Techniques  

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

Time-Resolved Beamlines Time-Resolved Beamlines Advisory Committee Workshop Home Workshop Chairs: Lin Chen (Argonne National Laboratory) Steve Milton (Advanced Photon Source) David Reis (University of Michigan) Linda Young (Argonne National Laboratory) Workshop on Time Domain Science Using X-ray Techniques August 29 September 1, 2004, The Abbey, Fontana, Lake Geneva Area, Wisconsin A workshop on "Time Domain Science Using X-ray Techniques" was held from August 29 September 1, 2004 , welcoming both experts and beginners in the field. This is one of the concurrently held workshops in the series on "Future Scientific Directions for the Advanced Photon Source." The goal of the workshop was to identify future directions in scientific research using time resolved x-ray techniques and to address possiblities to produce ps

438

Investigation of Unusual Albedos in the SGP Domain  

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

Investigation of Unusual Albedos in the SGP Domain Investigation of Unusual Albedos in the SGP Domain Groff, David ARM SGP Duchon, Claude University Of Oklahoma Category: Atmospheric State and Surface We investigate the cause of unusually high albedos at an Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) extended facility near Morris, OK. In a previous study, daily albedos were calculated at several SGP extended facilities for 1998 and 1999 using broadband (.28 to 3 microns) pyranometers. The average daily albedo during this period was calculated to be at least about 5% higher at Morris than at any of the other SGP extended facilities. Surface based measurements of daily albedos at Morris and two nearby SGP extended facilities during 2004 and 2005 suggest the unusually high albedo measurements at Morris are real.

439

Stopbands in the existence domains of acoustic solitons  

SciTech Connect (OSTI)

A fully nonlinear Sagdeev pseudopotential approach is used to study the existence domain of fast mode ion-acoustic solitons in a three-species plasma composed of cold and warm adiabatic positive ion species and Boltzmann electrons. It is shown that for appropriate values of the cold-to-warm ion charge-to-mass ratio, ?, and the effective warm ion-to-electron temperature ratio, ?, there is a range in cold to warm ion charge density ratio, f, over which a stopband in soliton speed exists. Solitons do not propagate in the stopband, although they can occur for both higher and lower speeds. The stopbands are associated with a limiting curve of the existence domain that is double-valued in speed for a range of values of f. Analytical estimates of the upper and lower limits of ? and ? that support stopbands are found. It is suggested that, inter alia, the analysis should be applicable to the solar wind plasma.

Nsengiyumva, F., E-mail: franco.nseng@gmail.com; Hellberg, M. A., E-mail: hellberg@ukzn.ac.za; Mace, R. L., E-mail: macer@ukzn.ac.za [School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4000 (South Africa); Verheest, F., E-mail: frank.verheest@ugent.be [School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4000 (South Africa); Sterrenkundig Observatorium, Universiteit Gent, Krijgslaan 281, B–9000 Gent (Belgium)

2014-10-15T23:59:59.000Z

440

Time Domain Partitioning of Electricity Production Cost Simulations  

SciTech Connect (OSTI)

Production cost models are often used for planning by simulating power system operations over long time horizons. The simulation of a day-ahead energy market can take several weeks to compute. Tractability improvements are often made through model simplifications, such as: reductions in transmission modeling detail, relaxation of commitment variable integrality, reductions in cost modeling detail, etc. One common simplification is to partition the simulation horizon so that weekly or monthly horizons can be simulated in parallel. However, horizon partitions are often executed with overlap periods of arbitrary and sometimes zero length. We calculate the time domain persistence of historical unit commitment decisions to inform time domain partitioning of production cost models. The results are implemented using PLEXOS production cost modeling software in an HPC environment to improve the computation time of simulations while maintaining solution integrity.

Barrows, C.; Hummon, M.; Jones, W.; Hale, E.

2014-01-01T23:59:59.000Z

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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

Understanding domain registration abuses Scott E. Coull a,  

E-Print Network [OSTI]

Understanding domain registration abuses Scott E. Coull a, *, Andrew M. White b , Ting-Fang Yen c Carolina, Chapel Hill, NC 27599, USA c RSA Laboratories, Cambridge, MA 02140, USA a r t i c l e i n f o author. E-mail addresses: scott.coull@redjack.com (S.E. Coull), amw@cs.unc.edu (A.M. White), tingfang

Reiter, Michael

442

Simulating Acoustic Emission: the Noise of Collapsing Domains  

E-Print Network [OSTI]

,26 , magnetization measurements 27 , calorimetry 15,28 , resistivity 29,30 and capacitance measurements 31 , and optical observations 24,32 . In comparison with these techniques, AE appears to be the most popular method for the observation of intense jerks... to the same energy change. We will now analyze the elementary movements of the twinning and de-twinning processes and compare the energies with those of the yield event. A. Collapse of spanning needle domains in the horizontal direction The formation...

Salje, E.K.H.; Wang, X; Ding, X; Sun, J

2014-08-07T23:59:59.000Z

443

Domain wall network evolution in (N+1)-dimensional FRW universes  

SciTech Connect (OSTI)

We develop a velocity-dependent one-scale model for the evolution of domain wall networks in flat expanding or collapsing homogeneous and isotropic universes with an arbitrary number of spatial dimensions, finding the corresponding scaling laws in frictionless and friction dominated regimes. We also determine the allowed range of values of the curvature parameter and the expansion exponent for which a linear scaling solution is possible in the frictionless regime.

Avelino, P. P. [Centro de Fisica do Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); Departamento de Fisica da Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); Departamento de Fisica, Universidade Federal da Paraiba 58051-970 Joao Pessoa, Paraiba (Brazil); Sousa, L. [Centro de Fisica do Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); Departamento de Fisica da Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal)

2011-02-15T23:59:59.000Z

444

Computer Forensics: you can hide but you canComputer Forensics: you can hide but you can''t deletet delete Dr. Nazli Hardy, 2009Reference: Computer Forensics: Principles and Practice  

E-Print Network [OSTI]

1 Computer Forensics: you can hide but you canComputer Forensics: you can hide but you can''t deletet delete Dr. Nazli Hardy, 2009Reference: Computer Forensics: Principles and Practice Volonino Anzaldua Godwin Computer Forensics April 10, 2009 Presentation for Dr. Maria Schiza's Forensics class

Hardy, Christopher R.

445

E-Print Network 3.0 - adam22 pro domain Sample Search Results  

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

2 pro domain Search Powered by Explorit Topic List Advanced Search Sample search results for: adam22 pro domain Page: << < 1 2 3 4 5 > >> 1 Role of Leucine-Rich Repeat Proteins in...

446

E-Print Network 3.0 - atp catalytic 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 catalytic domain Page: << < 1 2 3 4 5 > >> 1 Encyclopedia of Molecular Biology Thomas E....

447

Structure of the DUF2233 Domain in Bacteria and the Stuttering...  

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

the DUF2233 Domain in Bacteria and the Stuttering-associated UCE Glycoprotein Wednesday, July 31, 2013 UCE figure DUF2233, a Domain of Unknown Function (DUF), is present in 1200...

448

A Thesaurus and Online Encyclopedia Merging Method for Large Scale Domain-Ontology Automatic Construction  

Science Journals Connector (OSTI)

While building the large-scale domain ontology, the traditional manually-based construction method is low efficient and not feasible. In order to construct the large scale domain-ontology automatically; therefore...

Ting Wang; Jicheng Song; Ruihua Di; Yi Liang

2013-01-01T23:59:59.000Z

449

Phenomenological theory of a single domain wall in uniaxial trigonal ferroelectrics: Lithium niobate and lithium tantalate  

E-Print Network [OSTI]

Phenomenological theory of a single domain wall in uniaxial trigonal ferroelectrics: Lithium niobate and lithium tantalate David A. Scrymgeour and Venkatraman Gopalan Department of Materials Science, lithium niobate and lithium tantalate. The contributions to the domain- wall energy from polarization

Gopalan, Venkatraman

450

A New Methodology for Frequency Domain Analysis of Wave Energy Converters with Periodically Varying Physical Parameters  

E-Print Network [OSTI]

A New Methodology for Frequency Domain Analysis of Wave Energy Converters with Periodically Varying Methodology for Frequency Domain Analysis of Wave Energy Converters with Periodically Varying Physical of Mechanical Engineering) ABSTRACT Within a wave energy converter's operational bandwidth, device operation

Victoria, University of

451

One Work Analysis, Two Domains: A Display Information Requirements Case Study  

E-Print Network [OSTI]

Work domain analyses can be time consuming, requiring extensive interviews, documentation review, and observations, among other techniques. Given the time and resources required, we examine how to generalize a work domain ...

Cummings, M. L.

452

One Work Analysis, Two Domains: A Display Information Requirements Case Study  

E-Print Network [OSTI]

d observations, among other techniques. Given the time and resources required, we examine how to generalize a work domain analysis technique, namely the hybrid Cognitive Task Analysis (hCTA) method across two domains in ...

Cummings, M. L.

2012-01-01T23:59:59.000Z

453

Hierarchical Mixed-Domain Circuit Simulation, Synthesis and Extraction Methodology for MEMS  

Science Journals Connector (OSTI)

Emerging results for mixed-domain circuit simulation, a component-level synthesis strategy, and a layout extractor is presented for use in design of microelectromechanical systems (MEMS). The mixed-domain circuit representation is based on Kirchhoffian ...

Tamal Mukherjee; Gary K. Fedder

1999-07-01T23:59:59.000Z

454

Stability analysis of polarized domains Jos'e A. Miranda and Michael Widom  

E-Print Network [OSTI]

is the magnetization and fl the line tension (essentially h times the surface tension). Jackson, Goldstein Stability analysis of polarized domains Jos'e A. Miranda and Michael Polarized ferrofluids, lipid monolayers and magnetic bubbles form domains with deformable boundaries

Widom, Michael

455

E-Print Network 3.0 - ankyrin repeat domain-containing Sample...  

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

domain-containing Search Powered by Explorit Topic List Advanced Search Sample search results for: ankyrin repeat domain-containing Page: << < 1 2 3 4 5 > >> 1 Ankyrin-B...

456

Cross-domain comparison of quantitative technology improvement using patent derived characteristics  

E-Print Network [OSTI]

This thesis compares the performance improvement rates of 28 technological domains with characteristics derived from the patents of the domains, seeking to objectively test theories of how and why technologies change over ...

Benson, Christopher Lee

2014-01-01T23:59:59.000Z

457

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

458

E-Print Network 3.0 - apiai domain se Sample Search Results  

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

- Matematiska institutionen, Uppsala Universitet Collection: Mathematics 42 Service Oriented Architecture Introduction and Research Issues Summary: Domain Area Context Business...

459

Crystallization of the regulatory and effector domains of the key sporulation response regulator Spo0A  

Science Journals Connector (OSTI)

Crystals of both the effector and regulatory domains of Spo0A from Bacillus stearothermophilus have been grown.

Muchov?, K.

1999-03-01T23:59:59.000Z

460

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

Note: This page contains sample records for the topic "bind deleted domain" 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

An Optimized, Synthetic DNA Vaccine Encoding the Toxin A and Toxin B Receptor Binding Domains of Clostridium difficile Induces Protective Antibody Responses In Vivo  

Science Journals Connector (OSTI)

...Immunity and Vaccines An Optimized, Synthetic DNA Vaccine Encoding the Toxin A and...these advantages make newer, synthetic DNA-based immunizations a desirable...our work demonstrates that a synthetic DNA vaccine encoding the toxin RBDs...

Scott M. Baliban; Amanda Michael; Berje Shammassian; Shikata Mudakha; Amir S. Khan; Simon Cocklin; Isaac Zentner; Brian P. Latimer; Laurent Bouillaut; Meredith Hunter; Preston Marx; Niranjan Y. Sardesai; Seth L. Welles; Jeffrey M. Jacobson; David B. Weiner; Michele A. Kutzler

2014-07-14T23:59:59.000Z

462

Tethering a Type IB Topoisomerase to a DNA Site by Enzyme Fusion to a Heterologous Site-selective DNA-binding Protein Domain  

Science Journals Connector (OSTI)

...Therapeutics Tethering a Type IB Topoisomerase to a DNA Site by Enzyme Fusion to a Heterologous...viral DNA mediated by fusion proteins consisting...immunodeficiency virus type 1 integrase and Escherichia...1990. Tethering a type IB topoisomerase to a DNA site by enzyme fusion to a heterologous...

Giovanni Luca Beretta; Monica Binaschi; Emanuela Zagni; Luisa Capuani; and Giovanni Capranico

1999-08-01T23:59:59.000Z

463

Engagement of Nucleotide-Binding Oligomerization Domain-Containing Protein 1 (NOD1) by Receptor Interacting Protein 2 (RIP2) is Insufficient for Signal Transduction.  

E-Print Network [OSTI]

) according to the manufacturer’s instructions. After 24 h, cells were fixed with 3% paraformaldehyde (Roth) in PBS for 10min and permeabilized with 0.5% Triton X-100 (Roth) in cold PBS for 5min. Cells were blocked in 3% BSA (Roth) in PBS for 20 min... interaction. To overcome this prob- lem, we modified the recently reported co-expression system used to study interaction between NOD2 and RIP2 (33). We expressed either GST-NOD1 or His-MBP-NOD1 fusions and GB1-RIP2 fusion CARDs in separate cultures...

Mayle, Sophie; Boyle, Joseph P.; Sekine, Eiki; Zurek, Birte; Kufer, Thomas A.; Monie, Tom P.

2014-06-23T23:59:59.000Z

464

I:EBS 16060 FEBS Letters 372 (1995) 215-221 Classification of multi-helical DNA-binding domains and application to  

E-Print Network [OSTI]

recognition; DNA-protein interaction; Protein folding Resemblance between individual multi-helical DBDs has

465

TP53 and long-term prognosis in colorectal cancer: mutations in the L3 zinc-binding domain predict poor survival.  

Science Journals Connector (OSTI)

...of cyclin E in 139 suboptimally debulked AOC specimens. MATERIALS AND METHODS Tissue...were provided from 139 cases of primary AOC from women who participated on GOG experimental...cyclin E expression in the 139 cases of AOC from women with suboptimal disease revealed...

A L Børresen-Dale; R A Lothe; G I Meling; P Hainaut; T O Rognum; E Skovlund

1998-01-01T23:59:59.000Z

466

Architectural Accommodation in the Complex of Four p53 DNA Binding Domain Peptides with the p21/waf1/cip1  

E-Print Network [OSTI]

1/cip1 DNA Response Element* (Received for publication, January 10, 1997, and in revised form, March acids 98­ 309) and the p21/waf1/cip1 DNA response element impli- cated in the G1/S phase cell cycle, gadd45, and p21/waf1/cip1, the last being involved in the G1/S phase checkpoint (5­8). When ex- pressed

Clore, G. Marius

467

Binding STAT2 by the Acidic Domain of Human Cytomegalovirus IE1 Promotes Viral Growth and Is Negatively Regulated by SUMO  

Science Journals Connector (OSTI)

...Promotes Viral Growth and Is Negatively Regulated by SUMO Published ahead of print on 13 August 2008. Yong Ho Huh 1 Young Eui Kim 1 Eui Tae Kim 1 Jung Jin Park 1 Moon Jung Song 2 Hua Zhu 3 Gary S. Hayward 4 Jin-Hyun Ahn 1 Corresponding author. Mailing...

Yong Ho Huh; Young Eui Kim; Eui Tae Kim; Jung Jin Park; Moon Jung Song; Hua Zhu; Gary S. Hayward; Jin-Hyun Ahn

2008-08-13T23:59:59.000Z

468

MATERNALLY EXPRESSED PAB C-TERMINAL, a Novel Imprinted Gene in Arabidopsis, Encodes the Conserved C-Terminal Domain of Polyadenylate Binding Proteins  

Science Journals Connector (OSTI)

...27 and 16.0 mug 1.05 (n 5 plants for each). There were significant differences among the seed weights (Kruskal-Wallis test, P 0.003). Compared with developing seeds from wild-type siliques, MPC RNAi seeds showed a range of...

Sushma Tiwari; Reiner Schulz; Yoko Ikeda; Lindsay Dytham; Jaime Bravo; Lucille Mathers; Melissa Spielman; Plinio Guzmán; Rebecca J. Oakey; Tetsu Kinoshita; Rod J. Scott

2008-09-16T23:59:59.000Z

469

The Laminin 511/521 Binding Site on the Lutheran Blood Group Glycoprotein is Located at theFlexible Junction of Ig Domains 2 and 3  

E-Print Network [OSTI]

The receptor critical for sickle cell adhesion to laminin. JML, Hines PC et al. Sickle cell adhesion to laminin:glycoprotein / Laminin / sickle cell disease / X- ray

Mankelow, Tosti J.

2009-01-01T23:59:59.000Z

470

Role of the E1A Rb-binding domain in repression of the NF-?B-dependent defense against tumor necrosis factor-?  

Science Journals Connector (OSTI)

...Hung M C Yu D Crispens M A van Golen K L Price J E ( 1997 ) Clin Cancer Res 3 : 2017 – 2024...Herrmann J L Estrov Z Shao R Andreeff M Price J Paul R W Anklesaria P Yu D Hung M C...649 – 683 , 8717528 . 45 Smits P H de Wit L van der Eb A J Zantema A ( 1996 ) Oncogene...

James L. Cook; Thomas A. Walker; G. Scott Worthen; Jay R. Radke

2002-01-01T23:59:59.000Z

471

Effect of Single-Site Charge-Reversal Mutations on the Catalytic Properties of Yeast Cytochrome c Peroxidase: Evidence for a Single, Catalytically Active, Cytochrome c Binding Domain  

Science Journals Connector (OSTI)

Coordinates are from PCB ID 2pcc. ... Teske, J. G., Savenkova, M. I., Mauro, J. M., Erman, J. E., and Satterlee, J. D. ( 2000) Yeast cytochrome c peroxidase expression in Escherichia coli and rapid isolation of various highly purified holoenzymes Protein Expression Purif. ...

Naw May Pearl; Timothy Jacobson; Cassandra Meyen; Anthony G. Clementz; Esther Y. Ok; Eric Choi; Kyle Wilson; Lidia B. Vitello; James E. Erman

2008-01-31T23:59:59.000Z

472

Arabidopsis WD REPEAT DOMAIN55 Interacts with DNA DAMAGED BINDING PROTEIN1 and Is Required for Apical Patterning in the Embryo  

Science Journals Connector (OSTI)

...University of Oslo, N-0316 Oslo, Norway b Institut de Biologie Moleculaire des...we performed fluorescence resonance energy transfer (FRET) assays (Levitt et al...University of Oslo, N-0316 Oslo, Norway. | Journal Article Research Support...

Katrine N. Bjerkan; Sabrina Jung-Roméo; Gerd Jürgens; Pascal Genschik; Paul E. Grini

2012-03-23T23:59:59.000Z

473

The Essential Role of the N-Terminal Domain of the Orange Carotenoid Protein in Cyanobacterial Photoprotection: Importance of a Positive Charge for Phycobilisome Binding  

Science Journals Connector (OSTI)

...Mutated OCPs in Water after Illumination with a Blue Light-Emitting Diode in the Carbonyl Region between 1750 and 1550 cm1...software. The photoreaction was induced by a blue light-emitting diode. The temperature was set to 293K using a cryostat...

Adjélé Wilson; Michal Gwizdala; Alberto Mezzetti; Maxime Alexandre; Cheryl A. Kerfeld; Diana Kirilovsky

2012-05-25T23:59:59.000Z

474

Arabidopsis WD REPEAT DOMAIN55 Interacts with DNA DAMAGED BINDING PROTEIN1 and Is Required for Apical Patterning in the Embryo  

Science Journals Connector (OSTI)

...AdvanceTM v.10 software (Invitrogen) and using the BLAST engine provided by the National Center for Biotechnology Information...dynamic auxin activities during reproductive development. Cold Spring Harb. Perspect. Biol. 1 : a001628. Tan, X.Y. , Liu...

Katrine N. Bjerkan; Sabrina Jung-Roméo; Gerd Jürgens; Pascal Genschik; Paul E. Grini

2012-03-23T23:59:59.000Z

475

CP(Graph): Introducing a Graph Computation Domain in Constraint Programming  

E-Print Network [OSTI]

CP(Graph): Introducing a Graph Computation Domain in Constraint Programming Gregoire Dooms, Yves constraint programming by introducing CP(Graph), a new computation domain focused on graphs including a new and its associated propagator are sketched. CP(Graph) is in- tegrated with finite domain and finite sets

Deville, Yves

476

WHEN Cp(X) IS DOMAIN REPRESENTABLE WILLIAM FLEISSNER AND LYNNE YENGULALP  

E-Print Network [OSTI]

WHEN Cp(X) IS DOMAIN REPRESENTABLE WILLIAM FLEISSNER AND LYNNE YENGULALP ABSTRACT. Let M corollaries answer open questions. If X is completely regular and Cp(X) is domain representable, then X is discrete. If X is zero-dimensional, T2 , and Cp(X, D) is subcompact, then X is discrete. keywords: Domain

Yengulalp, Lynne

477

Three-dimensional finite difference time domain modeling of the Earth-ionosphere cavity resonances  

E-Print Network [OSTI]

domain (FDTD) model of Schumann resonances (SR) with a set of classical eigenfrequency and quality factorThree-dimensional finite difference time domain modeling of the Earth-ionosphere cavity resonances-dimensional finite difference time domain modeling of the Earth-ionosphere cavity resonances, Geophys. Res. Lett., 32

Pasko, Victor

478

Reflexive Scott domains are not complete for the extensional lambda calculus Alberto Carraro  

E-Print Network [OSTI]

for the -calculus, i.e., there are equations not in which hold in all extensional reflexive Scott domains. (ii). The following are the main results of the paper: (i) Extensional reflexive Scott domains are not complete, Reflexive Scott domains, Filter models. I. INTRODUCTION Lambda theories are congruences on the set of -terms

Salibra, Antonino

479

Propagating and reflecting of spin wave in permalloy nanostrip with 360° domain wall  

SciTech Connect (OSTI)

By micromagnetic simulation, we investigated the interaction between propagating spin wave (or magnonic) and a 360° domain wall in a nanostrip. It is found that propagating spin wave can drive a 360° domain wall motion, and the velocity and direction are closely related to the transmission coefficient of the spin wave of the domain wall. When the spin wave passes through the domain wall completely, the 360° domain wall moves toward the spin wave source. When the spin wave is reflected by the domain wall, the 360° domain wall moves along the spin wave propagation direction. Moreover, when the frequency of the spin wave is coincident with that of the 360° domain wall normal mode, the 360° domain wall velocity will be resonantly enhanced no matter which direction the 360 DW moves along. On the other hand, when the spin wave is reflected from the moving 360° domain wall, we observed the Doppler effect clearly. After passing through a 360° domain wall, the phase of the spin wave is changed, and the phase shift is related to the frequency. Nevertheless, phase shift could be manipulated by the number of 360° domain walls that spin wave passing through.

Zhang, Senfu; Mu, Congpu; Zhu, Qiyuan; Zheng, Qi; Liu, Xianyin; Wang, Jianbo; Liu, Qingfang, E-mail: liuqf@lzu.edu.cn [Key Laboratory for Magnetism and Magnetic Materials of Ministry of Education, Lanzhou University, Lanzhou 730000 (China)

2014-01-07T23:59:59.000Z

480

Phase-field simulation of strain-induced domain switching in magnetic thin films  

E-Print Network [OSTI]

Phase-field simulation of strain-induced domain switching in magnetic thin films Jia-Mian Hu, G of the Bloch point in a magnetic film with strong uniaxial magnetic anisotropy Low Temp. Phys. 37, 690 (2011) Evolution of magnetic bubble domains in manganite films Appl. Phys. Lett. 99, 042503 (2011) 360° domain wall

Chen, Long-Qing

Note: This page contains sample records for the topic "bind deleted domain" 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

In-medium effects for nuclear matter in the Fermi energy domain D. Durand,1  

E-Print Network [OSTI]

In-medium effects for nuclear matter in the Fermi energy domain O. Lopez,1 D. Durand,1 G. Lehaut,1 of nuclear reactions in the Fermi energy domain. I. INTRODUCTION Transport properties in nuclear matter energy domain, transport features should exhibit the in- terplay between mean-field (nuclear degrees

Boyer, Edmond

482

Domain-specific textual meta-modelling languages for model driven engineering  

Science Journals Connector (OSTI)

Domain-specific modelling languages are normally defined through general-purpose meta-modelling languages like the MOF. While this is satisfactory for many Model-Driven Engineering (MDE) projects, several researchers have identified the need for domain-specific ... Keywords: deep languages, domain-specific meta-modelling, model-driven engineering, multi-Level transformations, textual concrete syntax

Juan de Lara; Esther Guerra

2012-07-01T23:59:59.000Z

483

Numerical methods for extracting edge stress intensity functions in anisotropic three-dimensional domains  

E-Print Network [OSTI]

) depending on the given body forces and tractions on the other hand. The eigen-pairs (eigen-values and eigen domains is provided in many prior publications [21,12,9,2]. A semi-analytic approach for the eigen domains in the vicinity of an edge is represented by a family of eigen-functions (similar to 2-D domains

Yosibash, Zohar

484

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

485

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 -...

486

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,...

487

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...

488

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...

489

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...

490

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...4 M?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

491

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 Dosztányi; Bálint Mészáros; István Simon

2009-10-15T23:59:59.000Z

492

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...

493

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...

494

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

495

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...

496

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...

497

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

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

498

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...

499

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...

500

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. Yukawa’s mesontheory of the nucleon–nucleon 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