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  • Models, Molecular  (49)
  • American Association for the Advancement of Science (AAAS)  (49)
  • 2015-2019
  • 1995-1999  (49)
  • 1995  (49)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (49)
Years
  • 2015-2019
  • 1995-1999  (49)
Year
  • 1
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    Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-04-28
    Description: DCoH, the dimerization cofactor of hepatocyte nuclear factor-1, stimulates gene expression by associating with specific DNA binding proteins and also catalyzes the dehydration of the biopterin cofactor of phenylalanine hydroxylase. The x-ray crystal structure determined at 3 angstrom resolution reveals that DCoH forms a tetramer containing two saddle-shaped grooves that comprise likely macromolecule binding sites. Two equivalent enzyme active sites flank each saddle, suggesting that there is a spatial connection between the catalytic and binding activities. Structural similarities between the DCoH fold and nucleic acid-binding proteins argue that the saddle motif has evolved to bind diverse ligands or that DCoH unexpectedly may bind nucleic acids.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Endrizzi, J A -- Cronk, J D -- Wang, W -- Crabtree, G R -- Alber, T -- New York, N.Y. -- Science. 1995 Apr 28;268(5210):556-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley 94720-3206, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7725101" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Gene Expression Regulation ; Hydro-Lyases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Rats ; Recombinant Fusion Proteins/chemistry/metabolism ; Transcription Factors/*chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-03-10
    Description: The crystal structure of the tungsten-containing aldehyde ferredoxin oxidoreductase (AOR) from Pyrococcus furiosus, a hyperthermophilic archaeon (formerly archaebacterium) that grows optimally at 100 degrees C, has been determined at 2.3 angstrom resolution by means of multiple isomorphous replacement and multiple crystal form averaging. AOR consists of two identical subunits, each containing an Fe4S4 cluster and a molybdopterin-based tungsten cofactor that is analogous to the molybdenum cofactor found in a large class of oxotransferases. Whereas the general features of the tungsten coordination in this cofactor were consistent with a previously proposed structure, each AOR subunit unexpectedly contained two molybdopterin molecules that coordinate a tungsten by a total of four sulfur ligands, and the pterin system was modified by an intramolecular cyclization that generated a three-ringed structure. In comparison to other proteins, the hyperthermophilic enzyme AOR has a relatively small solvent-exposed surface area, and a relatively large number of both ion pairs and buried atoms. These properties may contribute to the extreme thermostability of this enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chan, M K -- Mukund, S -- Kletzin, A -- Adams, M W -- Rees, D C -- 1F32 GM15006/GM/NIGMS NIH HHS/ -- GM50775/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Mar 10;267(5203):1463-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, Pasadena, CA 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7878465" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Oxidoreductases/*chemistry/metabolism ; Amino Acid Sequence ; Archaea/*enzymology ; Binding Sites ; *Coenzymes ; Computer Graphics ; Crystallography, X-Ray ; Enzyme Stability ; Ferrous Compounds ; Metalloproteins/analysis/chemistry ; Models, Molecular ; Molecular Sequence Data ; Organometallic Compounds/analysis/*chemistry ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Secondary ; Pteridines/analysis/chemistry ; Pterins/analysis/*chemistry ; Surface Properties ; Temperature ; Tungsten/analysis/*chemistry
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  • 3
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    Structure of a complex of two plasma proteins: transthyretin and retinol-binding protein (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-05-19
    Description: The three-dimensional structure of the complex formed by two plasma proteins, transthyretin and retinol-binding protein, was determined from x-ray diffraction data to a nominal resolution of 3.1 angstroms. One tetramer of transthyretin was bound to two molecules of retinol-binding protein. The two retinol-binding protein molecules established molecular interactions with the same transthyretin dimer, and each also made contacts with one of the other two monomers. Thus, the other two potential binding sites in a transthyretin tetramer were blocked. The amino acid residues of the retinol-binding protein that were involved in the contacts were close to the retinol-binding site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Monaco, H L -- Rizzi, M -- Coda, A -- New York, N.Y. -- Science. 1995 May 19;268(5213):1039-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, University of Pavia, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7754382" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Biopolymers ; Chickens ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Molecular Sequence Data ; Prealbumin/*chemistry ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Retinol-Binding Proteins/*chemistry ; Retinol-Binding Proteins, Plasma ; Sequence Homology, Amino Acid
    Print ISSN: 0036-8075
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  • 4
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    Crystal structure of the V alpha domain of a T cell antigen receptor (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-15
    Description: The crystal structure of the V alpha domain of a T cell antigen receptor (TCR) was determined at a resolution of 2.2 angstroms. This structure represents an immunoglobulin topology set different from those previously described. A switch in a polypeptide strand from one beta sheet to the other enables a pair of V alpha homodimers to pack together to form a tetramer, such that the homodimers are parallel to each other and all hypervariable loops face in one direction. On the basis of the observed mode of V alpha association, a model of an (alpha beta)2 TCR tetramer can be positioned relative to the major histocompatibility complex class II (alpha beta)2 tetramer with the third hypervariable loop of V alpha over the amino-terminal portion of the antigenic peptide and the corresponding loop of V beta over its carboxyl-terminal residues. TCR dimerization that is mediated by the alpha chain may contribute to the coupling of antigen recognition to signal transduction during T cell activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fields, B A -- Ober, B -- Malchiodi, E L -- Lebedeva, M I -- Braden, B C -- Ysern, X -- Kim, J K -- Shao, X -- Ward, E S -- Mariuzza, R A -- AI31592/AI/NIAID NIH HHS/ -- GM52801/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Dec 15;270(5243):1821-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8525376" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallography, X-Ray ; Humans ; Mice ; Models, Molecular ; Protein Conformation ; Protein Folding ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/immunology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Solution structure of a cisplatin-induced DNA interstrand cross-link (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-15
    Description: The widely used antitumor drug cis-diamminedichloroplatinum(II) (cisplatin or cis-DDP) reacts with DNA, cross-linking two purine residues through the N7 atoms, which reside in the major groove in B-form DNA. The solution structure of the short duplex [d(CAT-AGCTATG)]2 cross-linked at the GC:GC site was determined by nuclear magnetic resonance (NMR). The deoxyguanosine-bridging cis-diammineplatinum(II) lies in the minor groove, and the complementary deoxycytidines are extrahelical. The double helix is locally reversed to a left-handed form, and the helix is unwound and bent toward the minor groove. These findings were independently confirmed by results from a phase-sensitive gel electrophoresis bending assay. The NMR structure differs markedly from previously proposed models but accounts for the chemical reactivity, the unwinding, and the bending of cis-DDP interstrand cross-linked DNA and may be important in the formation and repair of these cross-links in chromatin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, H -- Zhu, L -- Reid, B R -- Drobny, G P -- Hopkins, P B -- GM32681/GM/NIGMS NIH HHS/ -- GM45804/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Dec 15;270(5243):1842-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Washington, Seattle 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8525382" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/*pharmacology ; Base Sequence ; Cisplatin/*pharmacology ; DNA/*chemistry/drug effects ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Solutions
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  • 6
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    Crystal structure of a purple acid phosphatase containing a dinuclear Fe(III)-Zn(II) active site (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-06-09
    Description: Kidney bean purple acid phosphatase (KBPAP) is an Fe(III)-Zn(II) metalloenzyme resembling the mammalian Fe(III)-Fe(II) purple acid phosphatases. The structure of the homodimeric 111-kilodalton KBPAP was determined at a resolution of 2.9 angstroms. The enzyme contains two domains in each subunit. The active site is located in the carboxyl-terminal domain at the carboxy end of two sandwiched beta alpha beta alpha beta motifs. The two metal ions are 3.1 angstroms apart and bridged monodentately by Asp164. The iron is further coordinated by Tyr167, His325, and Asp135, and the zinc by His286, His323, and Asn201. The active-site structure is consistent with previous proposals regarding the mechanism of phosphate ester hydrolysis involving nucleophilic attack on the phosphate group by an Fe(III)-coordinated hydroxide ion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strater, N -- Klabunde, T -- Tucker, P -- Witzel, H -- Krebs, B -- New York, N.Y. -- Science. 1995 Jun 9;268(5216):1489-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Anorganisch-Chemisches Institut, Universitat Munster, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7770774" target="_blank"〉PubMed〈/a〉
    Keywords: Acid Phosphatase/*chemistry/metabolism ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Fabaceae/enzymology ; Ferric Compounds/chemistry/metabolism ; Glycoproteins/*chemistry/metabolism ; Ligands ; Models, Molecular ; Plants, Medicinal ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Zinc/chemistry/metabolism
    Print ISSN: 0036-8075
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  • 7
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    Regulatory subunit of protein kinase A: structure of deletion mutant with cAMP binding domains (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-08-11
    Description: In the molecular scheme of living organisms, adenosine 3',5'-monophosphate (cyclic AMP or cAMP) has been a universal second messenger. In eukaryotic cells, the primary receptors for cAMP are the regulatory subunits of cAMP-dependent protein kinase. The crystal structure of a 1-91 deletion mutant of the type I alpha regulatory subunit was refined to 2.8 A resolution. Each of the two tandem cAMP binding domains provides an extensive network of hydrogen bonds that buries the cyclic phosphate and the ribose between two beta strands that are linked by a short alpha helix. Each adenine base stacks against an aromatic ring that lies outside the beta barrel. This structure provides a molecular basis for understanding how cAMP binds cooperatively to its receptor protein, thus mediating activation of the kinase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Su, Y -- Dostmann, W R -- Herberg, F W -- Durick, K -- Xuong, N H -- Ten Eyck, L -- Taylor, S S -- Varughese, K I -- GM07313/GM/NIGMS NIH HHS/ -- GM34921/GM/NIGMS NIH HHS/ -- RR01644/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1995 Aug 11;269(5225):807-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0654, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7638597" target="_blank"〉PubMed〈/a〉
    Keywords: Affinity Labels ; Amino Acid Sequence ; Binding Sites ; Carrier Proteins/*chemistry/genetics/metabolism ; Computer Graphics ; Crystallization ; Crystallography, X-Ray ; Cyclic AMP/analogs & derivatives/*metabolism ; Cyclic AMP-Dependent Protein Kinases/*chemistry ; Enzyme Activation ; Hydrogen Bonding ; *Intracellular Signaling Peptides and Proteins ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
    Print ISSN: 0036-8075
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  • 8
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    Crystal structure of Pseudomonas mevalonii HMG-CoA reductase at 3.0 angstrom resolution (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-06-23
    Description: The rate-limiting step in cholesterol biosynthesis in mammals is catalyzed by 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase, a four-electron oxidoreductase that converts HMG-CoA to mevalonate. The crystal structure of HMG-CoA reductase from Pseudomonas mevalonii was determined at 3.0 angstrom resolution by multiple isomorphous replacement. The structure reveals a tightly bound dimer that brings together at the subunit interface the conserved residues implicated in substrate binding and catalysis. These dimers are packed about a threefold crystallographic axis, forming a hexamer with 23 point group symmetry. Difference Fourier studies reveal the binding sites for the substrates HMG-CoA and reduced or oxidized nicotinamide adenine dinucleotide [NAD(H)] and demonstrate that the active sites are at the dimer interfaces. The HMG-CoA is bound by a domain with an unusual fold, consisting of a central alpha helix surrounded by a triangular set of walls of beta sheets and alpha helices. The NAD(H) is bound by a domain characterized by an antiparallel beta structure that defines a class of dinucleotide-binding domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lawrence, C M -- Rodwell, V W -- Stauffacher, C V -- AI 127713/AI/NIAID NIH HHS/ -- HL 47113/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1995 Jun 23;268(5218):1758-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7792601" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Coenzyme A/metabolism ; Amino Acid Sequence ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Fourier Analysis ; Hydroxymethylglutaryl CoA Reductases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; NAD/metabolism ; Protein Folding ; Protein Structure, Secondary ; Pseudomonas/*enzymology
    Print ISSN: 0036-8075
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  • 9
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    Crystal structure of lac repressor core tetramer and its implications for DNA looping (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-06-23
    Description: The crystal structure of the tryptic core fragment of the lac repressor of Escherichia coli (LacR) complexed with the inducer isopropyl-beta-D-thiogalactoside was determined at 2.6 A resolution. The quaternary structure consists of two dyad-symmetric dimers that are nearly parallel to each other. This structure places all four DNA binding domains of intact LacR on the same side of the tetramer, and results in a deep, V-shaped cleft between the two dimers. Each monomer contributes a carboxyl-terminal helix to an antiparallel four-helix bundle that functions as a tetramerization domain. Some of the side chains whose mutation reduce DNA binding form clusters on a surface near the amino terminus. Placing the structure of the DNA binding domain complexed with operator previously determined by nuclear magnetic resonance onto this surface results in two operators being adjacent and nearly parallel to each other. Structural considerations suggest that the two dimers of LacR may flexibly alter their relative orientation in order to bind to the known varied spacings between two operators.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Friedman, A M -- Fischmann, T O -- Steitz, T A -- GM22778/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Jun 23;268(5218):1721-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7792597" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; DNA, Bacterial/*chemistry/metabolism ; Isopropyl Thiogalactoside/metabolism ; Models, Molecular ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/metabolism
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  • 10
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    Crystal structure of the tetramerization domain of the p53 tumor suppressor at 1.7 angstroms (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-03-10
    Description: The p53 protein is a tetrameric transcription factor that plays a central role in the prevention of neoplastic transformation. Oligomerization appears to be essential for the tumor suppressing activity of p53 because oligomerization-deficient p53 mutants cannot suppress the growth of carcinoma cell lines. The crystal structure of the tetramerization domain of p53 (residues 325 to 356) was determined at 1.7 angstrom resolution and refined to a crystallographic R factor of 19.2 percent. The monomer, which consists of a beta strand and an alpha helix, associates with a second monomer across an antiparallel beta sheet and an antiparallel helix-helix interface to form a dimer. Two of these dimers associate across a second and distinct parallel helix-helix interface to form the tetramer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jeffrey, P D -- Gorina, S -- Pavletich, N P -- CA08748-29/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1995 Mar 10;267(5203):1498-502.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7878469" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Graphics ; Crystallography, X-Ray ; DNA/metabolism ; Hydrogen Bonding ; Macromolecular Substances ; Models, Molecular ; *Protein Conformation ; Protein Structure, Secondary ; Tumor Suppressor Protein p53/*chemistry/metabolism
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  • 11
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    Interhelical angles in the solution structure of the oligomerization domain of p53: correction (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-03-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clore, G M -- Omichinski, J G -- Sakaguchi, K -- Zambrano, N -- Sakamoto, H -- Appella, E -- Gronenborn, A M -- New York, N.Y. -- Science. 1995 Mar 10;267(5203):1515-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7878474" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Macromolecular Substances ; Magnetic Resonance Spectroscopy ; Models, Molecular ; *Protein Conformation ; Protein Structure, Secondary ; Tumor Suppressor Protein p53/*chemistry
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  • 12
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    A new face for the glutamate receptor (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-01-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barinaga, M -- New York, N.Y. -- Science. 1995 Jan 13;267(5195):177-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7809622" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/*chemistry ; Cloning, Molecular ; Glycosylation ; Models, Molecular ; Phosphorylation ; Receptors, Glutamate/*chemistry/genetics
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  • 13
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    Structures of metal sites of oxidized bovine heart cytochrome c oxidase at 2.8 A (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-08-25
    Description: The high resolution three-dimensional x-ray structure of the metal sites of bovine heart cytochrome c oxidase is reported. Cytochrome c oxidase is the largest membrane protein yet crystallized and analyzed at atomic resolution. Electron density distribution of the oxidized bovine cytochrome c oxidase at 2.8 A resolution indicates a dinuclear copper center with an unexpected structure similar to a [2Fe-2S]-type iron-sulfur center. Previously predicted zinc and magnesium sites have been located, the former bound by a nuclear encoded subunit on the matrix side of the membrane, and the latter situated between heme a3 and CuA, at the interface of subunits I and II. The O2 binding site contains heme a3 iron and copper atoms (CuB) with an interatomic distance of 4.5 A; there is no detectable bridging ligand between iron and copper atoms in spite of a strong antiferromagnetic coupling between them. A hydrogen bond is present between a hydroxyl group of the hydroxyfarnesylethyl side chain of heme a3 and an OH of a tyrosine. The tyrosine phenol plane is immediately adjacent and perpendicular to an imidazole group bonded to CuB, suggesting a possible role in intramolecular electron transfer or conformational control, the latter of which could induce the redox-coupled proton pumping. A phenyl group located halfway between a pyrrole plane of the heme a3 and an imidazole plane liganded to the other heme (heme a) could also influence electron transfer or conformational control.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsukihara, T -- Aoyama, H -- Yamashita, E -- Tomizaki, T -- Yamaguchi, H -- Shinzawa-Itoh, K -- Nakashima, R -- Yaono, R -- Yoshikawa, S -- New York, N.Y. -- Science. 1995 Aug 25;269(5227):1069-74.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Protein Research, Osaka University, Suita, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7652554" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cattle ; Copper/*analysis ; Crystallization ; Crystallography, X-Ray ; Electron Transport ; Electron Transport Complex IV/*chemistry/metabolism ; Fourier Analysis ; Heme/*analogs & derivatives/analysis ; Hydrogen Bonding ; Magnesium/*analysis ; Mitochondria, Heart/enzymology ; Models, Molecular ; Oxidation-Reduction ; Oxygen/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Proton Pumps ; Zinc/*analysis
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  • 14
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    Crystal structure of the mammalian Grb2 adaptor (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-04-14
    Description: The mammalian growth factor receptor-binding protein Grb2 is an adaptor that mediates activation of guanine nucleotide exchange on Ras. Grb2 binds to the receptor through its SH2 domain and to the carboxyl-terminal domain of Son of sevenless through its two SH3 domains. It is thus a key element in the signal transduction pathway. The crystal structure of Grb2 was determined to 3.1 angstrom resolution. The asymmetric unit is composed of an embedded dimer. The interlaced junctions between the SH2 and SH3 domains bring the two adjacent faces of the SH3 domains in van der Waals contact but leave room for the binding of proline-rich peptides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maignan, S -- Guilloteau, J P -- Fromage, N -- Arnoux, B -- Becquart, J -- Ducruix, A -- New York, N.Y. -- Science. 1995 Apr 14;268(5208):291-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire de Biologie Structurale, Unite Mixte de Recherche CNRS-Universite de Paris-Sud, Gif sur Yvette, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7716522" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptor Proteins, Signal Transducing ; Amino Acid Sequence ; Binding Sites ; Computer Graphics ; Crystallization ; Crystallography, X-Ray ; GRB2 Adaptor Protein ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Proteins/*chemistry/metabolism ; *Receptor, Epidermal Growth Factor/metabolism
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  • 15
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    Architectures of class-defining and specific domains of glutamyl-tRNA synthetase (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-03-31
    Description: The crystal structure of a class I aminoacyl-transfer RNA synthetase, glutamyl-tRNA synthetase (GluRS) from Thermus thermophilus, was solved and refined at 2.5 A resolution. The amino-terminal half of GluRS shows a geometrical similarity with that of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) of the same subclass in class I, comprising the class I-specific Rossmann fold domain and the intervening subclass-specific alpha/beta domain. These domains were found to have two GluRS-specific, secondary-structure insertions, which then participated in the specific recognition of the D and acceptor stems of tRNA(Glu) as indicated by mutagenesis analyses based on the docking properties of GluRS and tRNA. In striking contrast to the beta-barrel structure of the GlnRS carboxyl-terminal half, the GluRS carboxyl-terminal half displayed an all-alpha-helix architecture, an alpha-helix cage, and mutagenesis analyses indicated that it had a role in the anticodon recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nureki, O -- Vassylyev, D G -- Katayanagi, K -- Shimizu, T -- Sekine, S -- Kigawa, T -- Miyazawa, T -- Yokoyama, S -- Morikawa, K -- New York, N.Y. -- Science. 1995 Mar 31;267(5206):1958-65.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biochemistry, School of Science, University of Tokyo, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7701318" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/chemistry ; Anticodon ; Biological Evolution ; Computer Graphics ; Crystallography, X-Ray ; Escherichia coli/enzymology ; Glutamate-tRNA Ligase/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Transfer, Glu/chemistry/metabolism ; Sequence Alignment ; Thermus thermophilus/*enzymology
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  • 16
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    Navigating the folding routes (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-03-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wolynes, P G -- Onuchic, J N -- Thirumalai, D -- New York, N.Y. -- Science. 1995 Mar 17;267(5204):1619-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemical Sciences, University of Illinois, Urbana 61801.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7886447" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Simulation ; Models, Chemical ; Models, Molecular ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; Temperature ; Thermodynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 17
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    Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-11-10
    Description: Polychlorinated biphenyls (PCBs) typify a class of stable aromatic pollutants that are targeted by bioremediation strategies. In the aerobic degradation of biphenyl by bacteria, the key step of ring cleavage is catalyzed by an Fe(II)-dependent extradiol dioxygenase. The crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase from a PCB-degrading strain of Pseudomonas cepacia has been determined at 1.9 angstrom resolution. The monomer comprises amino- and carboxyl-terminal domains. Structural homology between and within the domains reveals evolutionary relationships within the extradiol dioxygenase family. The iron atom has five ligands in square pyramidal geometry: one glutamate and two histidine side chains, and two water molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Han, S -- Eltis, L D -- Timmis, K N -- Muchmore, S W -- Bolin, J T -- GM 52831/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Nov 10;270(5238):976-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7481800" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Biodegradation, Environmental ; Crystallography, X-Ray ; *Dioxygenases ; Evolution, Molecular ; Ferrous Compounds/chemistry/metabolism ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Oxygen/chemistry/metabolism ; Oxygenases/*chemistry/metabolism ; Polychlorinated Biphenyls/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Pseudomonas/*enzymology ; Sequence Alignment
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  • 18
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    Structure-based design of transcription factors (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-01-06
    Description: Computer modeling suggested that transcription factors with novel sequence specificities could be designed by combining known DNA binding domains. This structure-based strategy was tested by construction of a fusion protein, ZFHD1, that contained zinc fingers 1 and 2 from Zif268, a short polypeptide linker, and the homeodomain from Oct-1. The fusion protein bound optimally to a sequence containing adjacent homeodomain (TAATTA) and zinc finger (NGGGNG) subsites. When fused to an activation domain, ZFHD1 regulated promoter activity in vivo in a sequence-specific manner. Analysis of known protein-DNA complexes suggests that many other DNA binding proteins could be designed in a similar fashion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pomerantz, J L -- Sharp, P A -- Pabo, C O -- P01-CA42063/CA/NCI NIH HHS/ -- P30-CA14051/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1995 Jan 6;267(5194):93-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7809612" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Cloning, Molecular ; Computer Simulation ; DNA-Binding Proteins/*chemistry/genetics/metabolism ; Gene Expression Regulation ; Homeodomain Proteins/chemistry ; Host Cell Factor C1 ; Models, Molecular ; Molecular Sequence Data ; Octamer Transcription Factor-1 ; Promoter Regions, Genetic ; Protein Engineering ; Recombinant Fusion Proteins/*chemistry/metabolism ; Transcription Factors/*chemistry/genetics/metabolism ; Transfection ; *Zinc Fingers
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  • 19
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    Revealing the architecture of a K+ channel pore through mutant cycles with a peptide inhibitor (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-04-14
    Description: Thermodynamic mutant cycles provide a formalism for studying energetic coupling between amino acids on the interaction surface in a protein-protein complex. This approach was applied to the Shaker potassium channel and to a high-affinity peptide inhibitor (scorpion toxin) that binds to its pore entryway. The assignment of pairwise interactions defined the spatial arrangement of channel amino acids with respect to the known inhibitor structure. A strong constraint was placed on the Shaker channel pore-forming region by requiring its amino-terminal border to be 12 to 15 angstroms from the central axis. This method is directly applicable to sodium, calcium, and other ion channels where inhibitor or modulatory proteins bind with high affinity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hidalgo, P -- MacKinnon, R -- GM43949/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Apr 14;268(5208):307-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7716527" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Oocytes ; Potassium Channels/*chemistry/genetics/metabolism ; Scorpion Venoms/*metabolism ; Shaker Superfamily of Potassium Channels ; Thermodynamics ; Toxins, Biological/*metabolism ; Xenopus laevis
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  • 20
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    Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-03-24
    Description: The presence and location of water of hydration (that is, bound water) in the solution structure of human interleukin-1 beta (hIL-1 beta) was investigated with water-selective two-dimensional heteronuclear magnetic resonance spectroscopy. It is shown here that in addition to water at the surface of the protein and ordered internal water molecules involved in bridging hydrogen bonds, positionally disordered water is present within a large, naturally occurring hydrophobic cavity located at the center of the molecule. These water molecules of hydration have residency times in the range of 1 to 2 nanoseconds to 100 to 200 microseconds and can be readily detected by nuclear magnetic resonance (NMR). Thus, large hydrophobic cavities in proteins may not be truly empty, as analysis of crystal structures appears to show, but may contain mobile water molecules that are crystallographically invisible but detectable by NMR.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ernst, J A -- Clubb, R T -- Zhou, H X -- Gronenborn, A M -- Clore, G M -- New York, N.Y. -- Science. 1995 Mar 24;267(5205):1813-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7892604" target="_blank"〉PubMed〈/a〉
    Keywords: Electrochemistry ; Humans ; Hydrogen Bonding ; Interleukin-1/*chemistry ; Magnetic Resonance Spectroscopy ; Models, Chemical ; Models, Molecular ; Protein Conformation ; Protons ; Water/*analysis/*chemistry
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  • 21
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    Tertiary and quaternary structural changes in Gi alpha 1 induced by GTP hydrolysis (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-11-10
    Description: Crystallographic analysis of 2.2 angstrom resolution shows that guanosine triphosphate (GTP) hydrolysis triggers conformational changes in the heterotrimeric G-protein alpha subunit, Gi alpha 1. The switch II and switch III segments become disordered, and linker II connecting the Ras and alpha helical domains moves, thus altering the structures of potential effector and beta gamma binding regions. Contacts between the alpha-helical and Ras domains are weakened, possibly facilitating the release of guanosine diphosphate (GDP). The amino and carboxyl termini, which contain receptor and beta gamma binding determinants, are disordered in the complex with GTP, but are organized into a compact microdomain on GDP hydrolysis. The amino terminus also forms extensive quaternary contacts with neighboring alpha subunits in the lattice, suggesting that multimers of alpha subunits or heterotrimers may play a role in signal transduction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mixon, M B -- Lee, E -- Coleman, D E -- Berghuis, A M -- Gilman, A G -- Sprang, S R -- DK 46371/DK/NIDDK NIH HHS/ -- GM34497/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Nov 10;270(5238):954-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235-9050, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7481799" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; GTP-Binding Proteins/*chemistry/metabolism ; Guanosine 5'-O-(3-Thiotriphosphate)/metabolism ; Guanosine Diphosphate/*metabolism ; Guanosine Triphosphate/*metabolism ; Hydrogen Bonding ; Hydrolysis ; Magnesium/metabolism ; Models, Molecular ; *Protein Conformation ; Protein Structure, Secondary ; *Protein Structure, Tertiary
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  • 22
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    Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-10-13
    Description: The Saccharomyces cerevisiae MATa1 and MAT alpha 2 homeodomain proteins, which play a role in determining yeast cell type, form a heterodimer that binds DNA and represses transcription in a cell type-specific manner. Whereas the alpha 2 and a1 proteins on their own have only modest affinity for DNA, the a1/alpha 2 heterodimer binds DNA with high specificity and affinity. The three-dimensional crystal structure of the a1/alpha 2 homeodomain heterodimer bound to DNA was determined at a resolution of 2.5 A. The a1 and alpha 2 homeodomains bind in a head-to-tail orientation, with heterodimer contacts mediated by a 16-residue tail located carboxyl-terminal to the alpha 2 homeodomain. This tail becomes ordered in the presence of a1, part of it forming a short amphipathic helix that packs against the a1 homeodomain between helices 1 and 2. A pronounced 60 degree bend is induced in the DNA, which makes possible protein-protein and protein-DNA contacts that could not take place in a straight DNA fragment. Complex formation mediated by flexible protein-recognition peptides attached to stably folded DNA binding domains may prove to be a general feature of the architecture of other classes of eukaryotic transcriptional regulators.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, T -- Stark, M R -- Johnson, A D -- Wolberger, C -- GM-37049/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Oct 13;270(5234):262-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7569974" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; DNA, Fungal/*chemistry/metabolism ; Fungal Proteins/*chemistry/metabolism ; Homeodomain Proteins/*chemistry/metabolism ; Hydrogen Bonding ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Operator Regions, Genetic ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/metabolism ; Saccharomyces cerevisiae/*chemistry/genetics ; *Saccharomyces cerevisiae Proteins ; Transcription, Genetic
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  • 23
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    Minimization of a polypeptide hormone (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-12-08
    Description: A stepwise approach for reducing the size of a polypeptide hormone, atrial natriuretic peptide (ANP), from 28 residues to 15 while retaining high biopotency is described. Systematic structural and functional analysis identified a discontinuous functional epitope for receptor binding and activation, most of which was placed onto a smaller ring (Cys6 to Cys17) that was created by repositioning the ANP native disulfide bond (Cys7 to Cys23). High affinity was subsequently restored by optimizing the remaining noncritical residues by means of phage display. Residues that flanked the mini-ring structure were then deleted in stages, and affinity losses were rectified by additional phage-sorting experiments. Thus, structural and functional data on hormones, coupled with phage display methods, can be used to shrink the hormones to moieties more amendable to small-molecule design.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, B -- Tom, J Y -- Oare, D -- Yen, R -- Fairbrother, W J -- Wells, J A -- Cunningham, B C -- New York, N.Y. -- Science. 1995 Dec 8;270(5242):1657-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Protein Engineering, Genenteeh, South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7502074" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Atrial Natriuretic Factor/*chemistry/genetics/immunology/metabolism ; Base Sequence ; Cell Line ; Cyclic GMP/metabolism ; Epitopes ; Guanylate Cyclase/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Conformation ; *Protein Engineering ; Receptors, Atrial Natriuretic Factor/metabolism
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  • 24
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    At last--the crystal structure of urease (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-05-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lippard, S J -- New York, N.Y. -- Science. 1995 May 19;268(5213):996-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7754394" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Models, Molecular ; Urease/*chemistry/metabolism
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  • 25
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    Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-08-04
    Description: The crystal structure of restriction endonuclease Bam HI complexed to DNA has been determined at 2.2 angstrom resolution. The DNA binds in the cleft and retains a B-DNA type of conformation. The enzyme, however, undergoes a series of conformational changes, including rotation of subunits and folding of disordered regions. The most striking conformational change is the unraveling of carboxyl-terminal alpha helices to form partially disordered "arms." The arm from one subunit fits into the minor groove while the arm from the symmetry related subunit follows the DNA sugar-phosphate backbone. Recognition of DNA base pairs occurs primarily in the major groove, with a few interactions occurring in the minor groove. Tightly bound water molecules play an equally important role as side chain and main chain atoms in the recognition of base pairs. The complex also provides new insights into the mechanism by which the enzyme catalyzes the hydrolysis of DNA phosphodiester groups.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Newman, M -- Strzelecka, T -- Dorner, L F -- Schildkraut, I -- Aggarwal, A K -- GM-44006/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Aug 4;269(5224):656-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7624794" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Binding Sites ; Catalysis ; Computer Graphics ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; Deoxyribonuclease BamHI/*chemistry/*metabolism ; Deoxyribonuclease EcoRI/chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary
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  • 26
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    Bent helix formation between RNA hairpins with complementary loops (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-06-09
    Description: The initial interaction between the ColE1 plasmid specific transcripts RNA I and RNA II, which function as antisense regulators of plasmid replication, comprises a transient complex between complementary loops found within the RNA secondary structures. Multidimensional heteronuclear magnetic resonance spectroscopy was used to characterize complexes formed between model RNA hairpins having seven nucleotide complementary loops. Seven base pairs are formed in the loop-loop helix, with continuous helical stacking of the loop residues on the 3' side of their helical stems. A sharp bend in the loop-loop helix, documented by gel electrophoresis, narrows the major groove and allows bridging of the phosphodiester backbones across the major groove in order to close the hairpin loops at their 5'-ends. The bend is further enhanced by the binding of Rom, a ColE1 encoded protein that regulates replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marino, J P -- Gregorian, R S Jr -- Csankovszki, G -- Crothers, D M -- GM 21966/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Jun 9;268(5216):1448-54.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Yale University, New Haven, CT 06511, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7539549" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Bacteriocin Plasmids/*genetics ; Base Composition ; Base Sequence ; Computer Graphics ; Electrophoresis, Polyacrylamide Gel ; Helix-Loop-Helix Motifs ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Protein Structure, Secondary ; RNA/*chemistry/metabolism ; RNA, Bacterial/*chemistry/metabolism
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    Solution structure of the epithelial cadherin domain responsible for selective cell adhesion (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-01-20
    Description: Cadherins are calcium-dependent cell adhesion molecules containing extracellular repeats of approximately 110 amino acids. The three-dimensional structure of the amino-terminal repeat of mouse epithelial cadherin was determined by multidimensional heteronuclear magnetic resonance spectroscopy. The calcium ion was bound by a short alpha helix and by loops at one end of the seven-stranded beta-barrel structure. An exposed concave face is in a position to provide homophilic binding specificity and was also sensitive to calcium ligation. Unexpected structural similarities with the immunoglobulin fold suggest an evolutionary relation between calcium-dependent and calcium-independent cell adhesion molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Overduin, M -- Harvey, T S -- Bagby, S -- Tong, K I -- Yau, P -- Takeichi, M -- Ikura, M -- New York, N.Y. -- Science. 1995 Jan 20;267(5196):386-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular and Structural Biology, Ontario Cancer Institute, Toronto, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7824937" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antigens, CD2/chemistry ; Binding Sites ; Cadherins/*chemistry/metabolism/physiology ; Calcium/*metabolism ; *Cell Adhesion ; Hydrogen Bonding ; Immunoglobulins/chemistry ; Mice ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary
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    Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-11-17
    Description: The Tat protein of bovine immunodeficiency virus (BIV) binds to its target RNA, TAR, and activates transcription. A 14-amino acid arginine-rich peptide corresponding to the RNA-binding domain of BIV Tat binds specifically to BIV TAR, and biochemical and in vivo experiments have identified the amino acids and nucleotides required for binding. The solution structure of the RNA-peptide complex has now been determined by nuclear magnetic resonance spectroscopy. TAR forms a virtually continuous A-form helix with two unstacked bulged nucleotides. The peptide adopts a beta-turn conformation and sits in the major groove of the RNA. Specific contacts are apparent between critical amino acids in the peptide and bases and phosphates in the RNA. The structure is consistent with all biochemical data and demonstrates ways in which proteins can recognize the major groove of RNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Puglisi, J D -- Chen, L -- Blanchard, S -- Frankel, A D -- AI08591/AI/NIAID NIH HHS/ -- AI29135/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1995 Nov 17;270(5239):1200-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7502045" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Composition ; Base Sequence ; Gene Products, tat/*chemistry/metabolism ; Hydrogen Bonding ; Immunodeficiency Virus, Bovine/*chemistry ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; RNA, Viral/*chemistry/metabolism
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    First-principles calculation of the folding free energy of a three-helix bundle protein (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-07-21
    Description: The folding and unfolding of a three-helix bundle protein were explored with molecular-dynamics simulations, cluster analysis, and weighted-histogram techniques. The folding-unfolding process occurs by means of a "folding funnel," in which a uniform and broad distribution of conformational states is accessible outside of the native manifold. This distribution narrows near a transition region and becomes compact within the native manifold. Key thermodynamic steps in folding include initial interactions around the amino-terminal helix-turn-helix motif, interactions between helices I and II, and, finally, the docking of helix III onto the helix I-II subdomain. A metastable minimum in the calculated free-energy surface is observed at approximately 1.5 times the native volume. Folding-unfolding thermodynamics are dominated by the opposing influences of protein-solvent energy, which favors unfolding, and the overall entropy, which favors folding by means of the hydrophobic effect.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boczko, E M -- Brooks, C L 3rd -- GM48807/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Jul 21;269(5222):393-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7618103" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Computer Graphics ; Helix-Loop-Helix Motifs ; Models, Molecular ; Molecular Sequence Data ; Peptide Fragments/*chemistry ; *Protein Folding ; *Protein Structure, Secondary ; Staphylococcal Protein A/*chemistry ; Thermodynamics
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    The crystal structure of urease from Klebsiella aerogenes (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-05-19
    Description: The crystal structure of urease from Klebsiella aerogenes has been determined at 2.2 A resolution and refined to an R factor of 18.2 percent. The enzyme contains four structural domains: three with novel folds playing structural roles, and an (alpha beta)8 barrel domain, which contains the bi-nickel center. The two active site nickels are 3.5 A apart. One nickel ion is coordinated by three ligands (with low occupancy of a fourth ligand) and the second is coordinated by five ligands. A carbamylated lysine provides an oxygen ligand to each nickel, explaining why carbon dioxide is required for the activation of urease apoenzyme. The structure is compatible with a catalytic mechanism whereby urea ligates Ni-1 to complete its tetrahedral coordination and a hydroxide ligand of Ni-2 attacks the carbonyl carbon. A surprisingly high structural similarity between the urease catalytic domain and that of the zinc-dependent adenosine deaminase reveals a remarkable example of active site divergence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jabri, E -- Carr, M B -- Hausinger, R P -- Karplus, P A -- 5T32-GM08384-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 May 19;268(5213):998-1004.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7754395" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Biopolymers ; Catalysis ; Crystallography, X-Ray ; Klebsiella pneumoniae/*enzymology ; Models, Molecular ; Mutagenesis, Site-Directed ; Nickel/analysis ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Urease/*chemistry/metabolism
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    Crystal structure of the beta chain of a T cell antigen receptor (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-03-31
    Description: The crystal structure of the extracellular portion of the beta chain of a murine T cell antigen receptor (TCR), determined at a resolution of 1.7 angstroms, shows structural homology to immunoglobulins. The structure of the first and second hypervariable loops suggested that, in general, they adopt more restricted sets of conformations in TCR beta chains than those found in immunoglobulins; the third hypervariable loop had certain structural characteristics in common with those of immunoglobulin heavy chain variable domains. The variable and constant domains were in close contact, presumably restricting the flexibility of the beta chain. This may facilitate signal transduction from the TCR to the associated CD3 molecules in the TCR-CD3 complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bentley, G A -- Boulot, G -- Karjalainen, K -- Mariuzza, R A -- New York, N.Y. -- Science. 1995 Mar 31;267(5206):1984-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Unite d'Immunologie Structurale (CNRS URA 359), Institut Pasteur, Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7701320" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Computer Graphics ; Crystallography, X-Ray ; Immunoglobulin Variable Region/chemistry ; Mice ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptor-CD3 Complex, Antigen, T-Cell/chemistry ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry ; Sequence Alignment ; Signal Transduction
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    Sulfite reductase structure at 1.6 A: evolution and catalysis for reduction of inorganic anions (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-10-06
    Description: Fundamental chemical transformations for biogeochemical cycling of sulfur and nitrogen are catalyzed by sulfite and nitrite reductases. The crystallographic structure of Escherichia coli sulfite reductase hemoprotein (SiRHP), which catalyzes the concerted six-electron reductions of sulfite to sulfide and nitrite to ammonia, was solved with multiwavelength anomalous diffraction (MAD) of the native siroheme and Fe4S4 cluster cofactors, multiple isomorphous replacement, and selenomethionine sequence markers. Twofold symmetry within the 64-kilodalton polypeptide generates a distinctive three-domain alpha/beta fold that controls cofactor assembly and reactivity. Homology regions conserved between the symmetry-related halves of SiRHP and among other sulfite and nitrite reductases revealed key residues for stability and function, and identified a sulfite or nitrite reductase repeat (SNiRR) common to a redox-enzyme superfamily. The saddle-shaped siroheme shares a cysteine thiolate ligand with the Fe4S4 cluster and ligates an unexpected phosphate anion. In the substrate complex, sulfite displaces phosphate and binds to siroheme iron through sulfur. An extensive hydrogen-bonding network of positive side chains, water molecules, and siroheme carboxylates activates S-O bonds for reductive cleavage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crane, B R -- Siegel, L M -- Getzoff, E D -- GM212226/GM/NIGMS NIH HHS/ -- GM37684/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Oct 6;270(5233):59-67.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7569952" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anions ; Binding Sites ; Catalysis ; Computer Graphics ; Crystallography, X-Ray ; Escherichia coli/*enzymology ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sulfite Reductase (NADPH) ; Sulfites/*metabolism
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  • 33
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    A nucleic acid triple helix formed by a peptide nucleic acid-DNA complex (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-15
    Description: The crystal structure of a nucleic acid triplex reveals a helix, designated P-form, that differs from previously reported nucleic acid structures. The triplex consists of one polypurine DNA strand complexed to a polypyrimidine hairpin peptide nucleic acid (PNA) and was successfully designed to promote Watson-Crick and Hoogsteen base pairing. The P-form helix is underwound, with a base tilt similar to B-form DNA. The bases are displaced from the helix axis even more than in A-form DNA. Hydrogen bonds between the DNA backbone and the Hoogsteen PNA backbone explain the observation that polypyrimidine PNA sequences form highly stable 2:1 PNA-DNA complexes. This structure expands the number of known stable helical forms that nucleic acids can adopt.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Betts, L -- Josey, J A -- Veal, J M -- Jordan, S R -- New York, N.Y. -- Science. 1995 Dec 15;270(5243):1838-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Glaxo Wellcome, Research Triangle Park, NC 27709, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8525381" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Crystallography, X-Ray ; DNA/*chemistry ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry ; Oligopeptides/*chemistry ; Protein Conformation
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    Trimeric G proteins: surprise witness tells a tale (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-11-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bourne, H R -- New York, N.Y. -- Science. 1995 Nov 10;270(5238):933-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology and Medicine, University of California, San Francisco 94143-0450, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7481796" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; GTP-Binding Proteins/*chemistry/metabolism ; Guanosine 5'-O-(3-Thiotriphosphate)/metabolism ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; Models, Molecular ; Polymers/chemistry ; Protein Conformation ; Protein Folding
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    Protein design: a hierarchic approach (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-11-10
    Description: The de novo design of peptides and proteins has recently emerged as an approach for investigating protein structure and function. Designed, helical peptides provide model systems for dissecting and quantifying the multiple interactions that stabilize secondary structure formation. De novo design is also useful for exploring the features that specify the stoichiometry and stability of alpha-helical coiled coils and for defining the requirements for folding into structures that resemble native, functional proteins. The design process often occurs in a series of discrete steps. Such steps reflect the hierarchy of forces required for stabilizing tertiary structures, beginning with hydrophobic forces and adding more specific interactions as required to achieve a unique, functional protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bryson, J W -- Betz, S F -- Lu, H S -- Suich, D J -- Zhou, H X -- O'Neil, K T -- DeGrado, W F -- New York, N.Y. -- Science. 1995 Nov 10;270(5238):935-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉DuPont Merck Pharmaceutical Company, Wilmington, DE 19880, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7481798" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; DNA-Binding Proteins/chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thermodynamics ; Zinc Fingers
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    A hot spot of binding energy in a hormone-receptor interface (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-01-20
    Description: The x-ray crystal structure of the complex between human growth hormone (hGH) and the extracellular domian of its first bound receptor (hGHbp) shows that about 30 side chains from each protein make contact. Individual replacement of contact residues in the hGHbp with alanine showed that a central hydrophobic region, dominated by two tryptophan residues, accounts for more than three-quarters of the binding free energy. This "functional epitope" is surrounded by less important contact residues that are generally hydrophilic and partially hydrated, so that the interface resembles a cross section through a globular protein. The functionally important residues on the hGHbp directly contact those on hGH. Thus, only a small and complementary set of contact residues maintains binding affinity, a property that may be general to protein-protein interfaces.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clackson, T -- Wells, J A -- New York, N.Y. -- Science. 1995 Jan 20;267(5196):383-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Protein Engineering, Genentech, South San Francisco, CA 94080.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7529940" target="_blank"〉PubMed〈/a〉
    Keywords: Carrier Proteins/chemistry/*metabolism ; Epitopes ; Growth Hormone/chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; Receptors, Somatotropin/chemistry/*metabolism ; Solubility ; Thermodynamics ; Water/chemistry
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  • 37
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    Solution structure of the activator contact domain of the RNA polymerase alpha subunit (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-12-01
    Description: The structure of the carboxyl-terminal domain of the Escherichia coli RNA polymerase alpha subunit (alpha CTD), which is regarded as the contact site for transcription activator proteins and for the promoter UP element, was determined by nuclear magnetic resonance spectroscopy. Its compact structure of four helices and two long arms enclosing its hydrophobic core shows a folding topology distinct from those of other DNA-binding proteins. The UP element binding site was found on the surface comprising helix 1, the amino-terminal end of helix 4, and the preceding loop. Mutation experiments indicated that the contact sites for transcription activator proteins are also on the same surface.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jeon, Y H -- Negishi, T -- Shirakawa, M -- Yamazaki, T -- Fujita, N -- Ishihama, A -- Kyogoku, Y -- New York, N.Y. -- Science. 1995 Dec 1;270(5241):1495-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Protein Research, Osaka University, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7491496" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; DNA/metabolism ; DNA-Directed RNA Polymerases/*chemistry/genetics/metabolism ; Escherichia coli/enzymology ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Promoter Regions, Genetic ; Protein Folding ; Protein Structure, Secondary ; Solutions ; Trans-Activators/metabolism
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  • 38
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    Structural basis for phosphotyrosine peptide recognition by protein tyrosine phosphatase 1B (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-06-23
    Description: The crystal structures of a cysteine-215--〉serine mutant of protein tyrosine phosphatase 1B complexed with high-affinity peptide substrates corresponding to an autophosphorylation site of the epidermal growth factor receptor were determined. Peptide binding to the protein phosphatase was accompanied by a conformational change of a surface loop that created a phosphotyrosine recognition pocket and induced a catalytically competent form of the enzyme. The phosphotyrosine side chain is buried within the period and anchors the peptide substrate to its binding site. Hydrogen bonds between peptide main-chain atoms and the protein contribute to binding affinity, and specific interactions of acidic residues of the peptide with basic residues on the surface of the enzyme confer sequence specificity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jia, Z -- Barford, D -- Flint, A J -- Tonks, N K -- CA53840/CA/NCI NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 1995 Jun 23;268(5218):1754-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biophysics, University of Oxford, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7540771" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Oligopeptides/chemistry/*metabolism ; Phosphotyrosine ; Protein Conformation ; Protein Structure, Secondary ; Protein Tyrosine Phosphatases/*chemistry/metabolism ; Receptor, Epidermal Growth Factor ; Tyrosine/*analogs & derivatives/metabolism
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  • 39
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    Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-01
    Description: The structure of the ternary complex consisting of yeast phenylalanyl-transfer RNA (Phe-tRNAPhe), Thermus aquaticus elongation factor Tu (EF-Tu), and the guanosine triphosphate (GTP) analog GDPNP was determined by x-ray crystallography at 2.7 angstrom resolution. The ternary complex participates in placing the amino acids in their correct order when messenger RNA is translated into a protein sequence on the ribosome. The EF-Tu-GDPNP component binds to one side of the acceptor helix of Phe-tRNAPhe involving all three domains of EF-Tu. Binding sites for the phenylalanylated CCA end and the phosphorylated 5' end are located at domain interfaces, whereas the T stem interacts with the surface of the beta-barrel domain 3. The binding involves many conserved residues in EF-Tu. The overall shape of the ternary complex is similar to that of the translocation factor, EF-G-GDP, and this suggests a novel mechanism involving "molecular mimicry" in the translational apparatus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nissen, P -- Kjeldgaard, M -- Thirup, S -- Polekhina, G -- Reshetnikova, L -- Clark, B F -- Nyborg, J -- New York, N.Y. -- Science. 1995 Dec 1;270(5241):1464-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biostructural Chemistry, Institute of Chemistry, Aarhus University, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7491491" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anticodon ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Guanosine Diphosphate/chemistry/metabolism ; Guanosine Triphosphate/*analogs & derivatives/chemistry/metabolism ; Histidine/metabolism ; Lysine/metabolism ; Models, Molecular ; Molecular Mimicry ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptide Elongation Factor G ; Peptide Elongation Factor Tu/*chemistry/metabolism ; Peptide Elongation Factors/chemistry/metabolism ; Peptide Initiation Factors/chemistry/metabolism ; Peptide Termination Factors/chemistry/metabolism ; Prokaryotic Initiation Factor-2 ; Protein Biosynthesis ; Protein Conformation ; Protein Structure, Secondary ; RNA, Transfer, Amino Acyl/*chemistry/metabolism ; Ribosomes/metabolism ; Thermus
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    Native Escherichia coli OmpF porin surfaces probed by atomic force microscopy (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-04-07
    Description: Topographs of two-dimensional porin OmpF crystals reconstituted in the presence of lipids were recorded in solution by atomic force microscopy (AFM) to a lateral resolution of 10 angstroms and a vertical resolution of 1 angstrom. Protein-protein interactions were demonstrated on the basis of the AFM results and earlier crystallographic findings. To assess protein-lipid interactions, the bilayer was modeled with kinked lipids by fitting the head groups to contours determined with AFM. Finally, two conformations of the extracellular porin surface were detected at forces of 0.1 nanonewton, demonstrating the potential of AFM to monitor conformational changes with high resolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schabert, F A -- Henn, C -- Engel, A -- New York, N.Y. -- Science. 1995 Apr 7;268(5207):92-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Maurice E. Muller Institute for Microscopic Structural Biology, Universitat Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7701347" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Escherichia coli/*chemistry ; Lipid Bilayers/chemistry ; Microscopy, Atomic Force ; Models, Molecular ; Molecular Conformation ; Porins/chemistry/*ultrastructure ; Protein Conformation
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  • 41
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    Crystal structure of a conserved protease that binds DNA: the bleomycin hydrolase, Gal6 (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-08-18
    Description: Bleomycin hydrolase is a cysteine protease that hydrolyzes the anticancer drug bleomycin. The homolog in yeast, Gal6, has recently been identified and found to bind DNA and to act as a repressor in the Gal4 regulatory system. The crystal structure of Gal6 at 2.2 A resolution reveals a hexameric structure with a prominent central channel. The papain-like active sites are situated within the central channel, in a manner resembling the organization of active sites in the proteasome. The Gal6 channel is lined with 60 lysine residues from the six subunits, suggesting a role in DNA binding. The carboxyl-terminal arm of Gal6 extends into the active site cleft and may serve a regulatory function. Rather than each residing in distinct, separable domains, the protease and DNA-binding activities appear structurally intertwined in the hexamer, implying a coupling of these two activities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joshua-Tor, L -- Xu, H E -- Johnston, S A -- Rees, D C -- GM40700/GM/NIGMS NIH HHS/ -- GM45162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Aug 18;269(5226):945-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Divison of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7638617" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Cysteine Endopeptidases/*chemistry/metabolism ; DNA/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 42
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    Structural basis for sugar translocation through maltoporin channels at 3.1 A resolution (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-01-27
    Description: Trimeric maltoporin (LamB protein) facilitates the diffusion of maltodextrins across the outer membrane of Gram-negative bacteria. The crystal structure of maltoporin from Escherichia coli, determined to a resolution of 3.1 angstroms, reveals an 18-stranded, antiparallel beta-barrel that forms the framework of the channel. Three inwardly folded loops contribute to a constriction about halfway through the channel. Six contingent aromatic residues line the channel and form a path from the vestibule to the periplasmic outlet. Soaking of a crystal with maltotriose revealed binding of the sugar to this hydrophobic track across the constriction, which suggests that maltose and linear oligosaccharides may be translocated across the membrane by guided diffusion along this path.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schirmer, T -- Keller, T A -- Wang, Y F -- Rosenbusch, J P -- New York, N.Y. -- Science. 1995 Jan 27;267(5197):512-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, University of Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7824948" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins ; Bacteriophage lambda/metabolism ; Binding Sites ; Carbohydrate Metabolism ; Cell Membrane/*chemistry/metabolism ; Computer Graphics ; Crystallography, X-Ray ; Escherichia coli/*chemistry/metabolism ; Hydrogen Bonding ; Maltose/*metabolism ; Models, Molecular ; Oligosaccharides/*metabolism ; Point Mutation ; Polysaccharides/metabolism ; Porins/*chemistry/genetics/metabolism ; Protein Folding ; Protein Structure, Secondary ; Receptors, Virus/*chemistry/genetics/metabolism
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  • 43
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    Crystal structure of the T4 regA translational regulator protein at 1.9 A resolution (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-05-26
    Description: The translational regulator protein regA is encoded by the T4 bacteriophage and binds to a region of messenger RNA (mRNA) that includes the initiator codon. RegA is unusual in that it represses the translation of about 35 early T4 mRNAs but does not affect nearly 200 other mRNAs. The crystal structure of regA was determined at 1.9 A resolution; the protein was shown to have an alpha-helical core and two regions with antiparallel beta sheets. One of these beta sheets has four antiparallel strands and has some sequence homology to RNP-1 and RNP-2, which are believed to be RNA-binding motifs and are found in a number of known RNA-binding proteins. Structurally guided mutants may help to uncover the basis for this variety of RNA interaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, C -- Chan, R -- Berger, I -- Lockshin, C -- Green, L -- Gold, L -- Rich, A -- New York, N.Y. -- Science. 1995 May 26;268(5214):1170-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7761833" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteriophage T4/*chemistry ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; RNA-Binding Proteins/*chemistry ; Structure-Activity Relationship ; Viral Proteins/*chemistry
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    Measurement of interhelical electrostatic interactions in the GCN4 leucine zipper (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-04-21
    Description: The dimerization specificity of the bZIP transcription factors resides in the leucine zipper region. It is commonly assumed that electrostatic interactions between oppositely charged amino acid residues on different helices of the leucine zipper contribute favorably to dimerization specificity. Crystal structures of the GCN4 leucine zipper contain interhelical salt bridges between Glu20 and Lys15' and between Glu22 and Lys27'. 13C-nuclear magnetic resonance measurements of the glutamic acid pKa values at physiological ionic strength indicate that the salt bridge involving Glu22 does not contribute to stability and that the salt bridge involving Glu20 is unfavorable, relative to the corresponding situation with a neutral (protonated) Glu residue. Moreover, the substitution of Glu20 by glutamine is stabilizing. Thus, salt bridges will not necessarily contribute favorably to bZIP dimerization specificity and may indeed be unfavorable, relative to alternative neutral-charge interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lumb, K J -- Kim, P S -- GM44162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Apr 21;268(5209):436-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7716550" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallization ; *DNA-Binding Proteins ; Fungal Proteins/*chemistry ; Glutamic Acid/chemistry ; Hydrogen-Ion Concentration ; *Leucine Zippers ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Osmolar Concentration ; Protein Conformation ; Protein Folding ; Protein Kinases/*chemistry ; Protein Structure, Secondary ; *Saccharomyces cerevisiae Proteins ; Trans-Activators/*chemistry
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  • 45
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    Crystal structure of DNA photolyase from Escherichia coli (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-06-30
    Description: Photolyase repairs ultraviolet (UV) damage to DNA by splitting the cyclobutane ring of the major UV photoproduct, the cis, syn-cyclobutane pyrimidine dimer (Pyr 〈〉 Pyr). The reaction is initiated by blue light and proceeds through long-range energy transfer, single electron transfer, and enzyme catalysis by a radical mechanism. The three-dimensional crystallographic structure of DNA photolyase from Escherichia coli is presented and the atomic model was refined to an R value of 0.172 at 2.3 A resolution. The polypeptide chain of 471 amino acids is folded into an amino-terminal alpha/beta domain resembling dinucleotide binding domains and a carboxyl-terminal helical domain; a loop of 72 residues connects the domains. The light-harvesting cofactor 5,10-methenyltetrahydrofolylpolyglutamate (MTHF) binds in a cleft between the two domains. Energy transfer from MTHF to the catalytic cofactor flavin adenine dinucleotide (FAD) occurs over a distance of 16.8 A. The FAD adopts a U-shaped conformation between two helix clusters in the center of the helical domain and is accessible through a hole in the surface of this domain. Dimensions and polarity of the hole match those of a Pyr 〈〉 Pyr dinucleotide, suggesting that the Pyr 〈〉 Pyr "flips out" of the helix to fit into this hole, and that electron transfer between the flavin and the Pyr 〈〉 Pyr occurs over van der Waals contact distance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, H W -- Kim, S T -- Sancar, A -- Deisenhofer, J -- GM31082/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Jun 30;268(5219):1866-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7604260" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Computer Graphics ; Crystallography, X-Ray ; DNA Damage ; DNA Repair ; DNA, Bacterial/metabolism ; Deoxyribodipyrimidine Photo-Lyase/*chemistry/metabolism ; Electron Transport ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Folic Acid/analogs & derivatives/metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyrimidine Dimers/metabolism
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  • 46
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    Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-05-12
    Description: Structural characterization of biomolecules in solution by nuclear magnetic resonance (NMR) spectroscopy is based primarily on the use of interproton distances derived from homonuclear cross-relaxation experiments. Information about short time-scale dynamics, on the other hand, is obtained from relaxation rates of heteronuclear spin pairs such as 15N-1H. By combining the two types of data and utilizing the dependence of heteronuclear NMR relaxation rates on anisotropic diffusional rotational tumbling, it is possible to obtain structural information about long-range motional correlations between protein domains. This approach was applied to characterize the relative orientations and mobilities of the first three zinc-finger domains of the Xenopus transcription factor TFIIIA in aqueous solution. The data indicate that the motions of the individual zinc-finger domains are highly correlated on time scales shorter than 10 nanoseconds and that the average conformation of the three-finger polypeptide is elongated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bruschweiler, R -- Liao, X -- Wright, P E -- GM 36643/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 May 12;268(5212):886-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratorium fur Physikalische Chemie, Eidgenossiche Technische Hochschule Zentrum, Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7754375" target="_blank"〉PubMed〈/a〉
    Keywords: Anisotropy ; DNA-Binding Proteins/*chemistry ; Magnetic Resonance Spectroscopy ; Mathematics ; Models, Molecular ; Protein Conformation ; Proteins/chemistry ; Solutions ; Transcription Factor TFIIIA ; Transcription Factors/*chemistry ; *Zinc Fingers
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  • 47
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    A left-handed parallel beta helix in the structure of UDP-N-acetylglucosamine acyltransferase (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-11-10
    Description: UDP-N-acetylglucosamine 3-O-acyltransferase (LpxA) catalyzes the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-N-acetylglucosamine. LpxA is the first enzyme in the lipid A biosynthetic pathway and is a target for the design of antibiotics. The x-ray crystal structure of LpxA has been determined to 2.6 angstrom resolution and reveals a domain motif composed of parallel beta strands, termed a left-handed parallel beta helix (L beta H). This unusual fold displays repeated violations of the protein folding constraint requiring right-handed crossover connections between strands of parallel beta sheets and may be present in other enzymes that share amino acid sequence homology to the repeated hexapeptide motif of LpxA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raetz, C R -- Roderick, S L -- AI38328/AI/NIAID NIH HHS/ -- GM51310/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Nov 10;270(5238):997-1000.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Duke University Medical Center, Durham, NC 22710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7481807" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/*chemistry ; Amino Acid Sequence ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; *Protein Structure, Secondary ; Sequence Alignment
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    Glycobiology: more functions for oligosaccharides (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-09-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dwek, R A -- New York, N.Y. -- Science. 1995 Sep 1;269(5228):1234-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Glycobiology Institute, University of Oxford, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7652569" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD2/*chemistry ; Glycoproteins/*chemistry ; Glycosylation ; Humans ; Models, Molecular ; Oligosaccharides/*chemistry ; *Protein Conformation ; Rats ; Ribonucleases/chemistry
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    Crystal structure and function of the isoniazid target of Mycobacterium tuberculosis (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-03-17
    Description: Resistance to isoniazid in Mycobacterium tuberculosis can be mediated by substitution of alanine for serine 94 in the InhA protein, the drug's primary target. InhA was shown to catalyze the beta-nicotinamide adenine dinucleotide (NADH)-specific reduction of 2-trans-enoyl-acyl carrier protein, an essential step in fatty acid elongation. Kinetic analyses suggested that isoniazid resistance is due to a decreased affinity of the mutant protein for NADH. The three-dimensional structures of wild-type and mutant InhA, refined to 2.2 and 2.7 angstroms, respectively, revealed that drug resistance is directly related to a perturbation in the hydrogen-bonding network that stabilizes NADH binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dessen, A -- Quemard, A -- Blanchard, J S -- Jacobs, W R Jr -- Sacchettini, J C -- AI30189/AI/NIAID NIH HHS/ -- AI33696/AI/NIAID NIH HHS/ -- AI36849/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1995 Mar 17;267(5204):1638-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7886450" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/drug effects/genetics/physiology ; Binding Sites ; Computer Graphics ; Crystallization ; Crystallography, X-Ray ; Drug Resistance, Microbial ; Hydrogen Bonding ; Isoniazid/*pharmacology ; Models, Molecular ; Mycobacterium tuberculosis/*chemistry/drug effects ; NAD/metabolism ; Oxidation-Reduction ; *Oxidoreductases ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary
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