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  • Models, Molecular  (59)
  • American Association for the Advancement of Science (AAAS)  (59)
  • Annual Reviews
  • 2005-2009
  • 1995-1999  (59)
  • 1990-1994
  • 1980-1984
  • 1945-1949
  • 1996  (59)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (59)
  • Annual Reviews
Years
  • 2005-2009
  • 1995-1999  (59)
  • 1990-1994
  • 1980-1984
  • 1945-1949
Year
  • 1
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    Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-12-13
    Description: The structure of the Staphylococcus aureus alpha-hemolysin pore has been determined to 1.9 A resolution. Contained within the mushroom-shaped homo-oligomeric heptamer is a solvent-filled channel, 100 A in length, that runs along the sevenfold axis and ranges from 14 A to 46 A in diameter. The lytic, transmembrane domain comprises the lower half of a 14-strand antiparallel beta barrel, to which each protomer contributes two beta strands, each 65 A long. The interior of the beta barrel is primarily hydrophilic, and the exterior has a hydrophobic belt 28 A wide. The structure proves the heptameric subunit stoichiometry of the alpha-hemolysin oligomer, shows that a glycine-rich and solvent-exposed region of a water-soluble protein can self-assemble to form a transmembrane pore of defined structure, and provides insight into the principles of membrane interaction and transport activity of beta barrel pore-forming toxins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, L -- Hobaugh, M R -- Shustak, C -- Cheley, S -- Bayley, H -- Gouaux, J E -- New York, N.Y. -- Science. 1996 Dec 13;274(5294):1859-66.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Chicago, 920 East 58 Street, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8943190" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Toxins/*chemistry/metabolism ; Cell Membrane/chemistry/metabolism ; Crystallography, X-Ray ; Hemolysin Proteins/*chemistry/metabolism ; Hydrogen Bonding ; Lipid Bilayers/*chemistry ; Membrane Potentials ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Staphylococcus aureus/*chemistry
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    Electronic ISSN: 1095-9203
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  • 2
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    Solution structure of a two-base DNA bulge complexed with an enediyne cleaving analog (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-06-28
    Description: Nucleic acid bulges have been implicated in a number of biological processes and are specific cleavage targets for the enediyne antitumor antibiotic neocarzinostatin chromophore in a base-catalyzed, radical-mediated reaction. The solution structure of the complex between an analog of the bulge-specific cleaving species and an oligodeoxynucleotide containing a two-base bulge was elucidated by nuclear magnetic resonance. An unusual binding mode involves major groove recognition by the drug carbohydrate unit and tight fitting of the wedge-shaped drug in the triangular prism pocket formed by the two looped-out bulge bases and the neighboring base pairs. The two drug rings mimic helical DNA bases, complementing the bent DNA structure. The putative abstracting drug radical is 2.2 +/- 0.1 angstroms from the pro-S H5' of the target bulge nucleotide. This structure clarifies the mechanism of bulge recognition and cleavage by a drug and provides insight into the design of bulge-specific nucleic acid binding molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stassinopoulos, A -- Ji, J -- Gao, X -- Goldberg, I H -- CA44257/CA/NCI NIH HHS/ -- GM53793/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jun 28;272(5270):1943-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658168" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; DNA/chemistry/*metabolism ; Enediynes ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/*metabolism ; Zinostatin/analogs & derivatives/chemistry/metabolism
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  • 3
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    Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-05-31
    Description: In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy. Both aptamers contain two asymmetrical internal loops that are not well ordered in the free RNA but that fold into a compact structure upon ligand binding. Those nucleotides common to both RNAs include a conserved cluster of purine residues, three of which form an uneven plane containing a G:G pair, and two other residues nearly perpendicular to that surface. Two of the three variant nucleotides are stacked on the cluster of purines and form a triple contact to the amino acid side chain, whereas the edge of the third variant nucleotide is capping the binding pocket.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Y -- Kochoyan, M -- Burgstaller, P -- Westhof, E -- Famulok, M -- New York, N.Y. -- Science. 1996 May 31;272(5266):1343-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre de Biochimie Structurale (CBS), Unite Mixte de Recherche, CNRS 9955, Montpellier, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8650546" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/chemistry/*metabolism ; Base Composition ; Base Sequence ; Citrulline/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Ligands ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Nucleic Acid Conformation ; RNA/*chemistry/genetics/*metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Crystal structure of a group I ribozyme domain: principles of RNA packing (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-09-20
    Description: Group I self-splicing introns catalyze their own excision from precursor RNAs by way of a two-step transesterification reaction. The catalytic core of these ribozymes is formed by two structural domains. The 2.8-angstrom crystal structure of one of these, the P4-P6 domain of the Tetrahymena thermophila intron, is described. In the 160-nucleotide domain, a sharp bend allows stacked helices of the conserved core to pack alongside helices of an adjacent region. Two specific long-range interactions clamp the two halves of the domain together: a two-Mg2+-coordinated adenosine-rich corkscrew plugs into the minor groove of a helix, and a GAAA hairpin loop binds to a conserved 11-nucleotide internal loop. Metal- and ribose-mediated backbone contacts further stabilize the close side-by-side helical packing. The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cate, J H -- Gooding, A R -- Podell, E -- Zhou, K -- Golden, B L -- Kundrot, C E -- Cech, T R -- Doudna, J A -- 5T32GM08283-07/GM/NIGMS NIH HHS/ -- GM22778-21/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Sep 20;273(5282):1678-85.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. doudna@csb.yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8781224" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/chemistry ; Animals ; Base Composition ; Base Sequence ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Hydrogen Bonding ; *Introns ; Magnesium/chemistry ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phosphates/chemistry ; Phylogeny ; RNA Splicing ; RNA, Catalytic/*chemistry/metabolism ; RNA, Protozoan/*chemistry/metabolism ; Ribose/chemistry ; Tetrahymena thermophila/genetics
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  • 5
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    Structure of the amino-terminal core domain of the HIV-1 capsid protein (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-07-12
    Description: The three-dimensional structure of the amino-terminal core domain (residues 1 through 151) of the human immunodeficiency virus-type 1 (HIV-1) capsid protein has been solved by multidimensional heteronuclear magnetic resonance spectroscopy. The structure is unlike those of previously characterized viral coat proteins and is composed of seven alpha helices, two beta hairpins, and an exposed partially ordered loop. The domain is shaped like an arrowhead, with the beta hairpins and loop exposed at the trailing edge and the carboxyl-terminal helix projecting from the tip. The proline residue Pro1 forms a salt bridge with a conserved, buried aspartate residue (Asp51), which suggests that the amino terminus of the protein rearranges upon proteolytic maturation. The binding site for cyclophilin A, a cellular rotamase that is packaged into the HIV-1 virion, is located on the exposed loop and encompasses the essential proline residue Pro90. In the free monomeric domain, Pro90 adopts kinetically trapped cis and trans conformations, raising the possibility that cyclophilin A catalyzes interconversion of the cis- and trans-Pro90 loop structures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gitti, R K -- Lee, B M -- Walker, J -- Summers, M F -- Yoo, S -- Sundquist, W I -- AI30917/AI/NIAID NIH HHS/ -- CA 42014/CA/NCI NIH HHS/ -- GM 42561/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 12;273(5272):231-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21228, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662505" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Isomerases/metabolism ; Amino Acid Sequence ; Aspartic Acid/chemistry ; Binding Sites ; Capsid/*chemistry/metabolism ; Carrier Proteins/metabolism ; HIV Core Protein p24/*chemistry/metabolism ; HIV-1/*chemistry ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Peptidylprolyl Isomerase ; Proline/chemistry ; Protein Conformation ; Protein Processing, Post-Translational ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Virion/chemistry
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  • 6
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    Catalytic role of 2'-hydroxyl groups within a group II intron active site (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-03-08
    Description: Domain 5 is an essential active-site component of group II intron ribozymes. The role of backbone substituents in D5 function was explored through synthesis of a series of derivatives containing deoxynucleotides at each position along the D5 strand. Kinetic screens revealed that eight 2'-hydroxyl groups were likely to be critical for activity of D5. Through two separate methods, including competitive inhibition and direct kinetic analysis, effects on binding and chemistry were distinguished. Depending on their function, important 2'-hydroxyl groups lie on opposite faces of the molecule, defining distinct loci for molecular recognition and catalysis by D5.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abramovitz, D L -- Friedman, R A -- Pyle, A M -- GM41371/GM/NIGMS NIH HHS/ -- GM50313/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Mar 8;271(5254):1410-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8596912" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Binding Sites ; Catalysis ; Exons ; Hydrogen Bonding ; Hydroxyl Radical/chemistry ; *Introns ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligoribonucleotides/chemistry/metabolism ; RNA/metabolism ; RNA, Catalytic/chemistry/*metabolism
    Print ISSN: 0036-8075
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  • 7
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    Structure of the FKBP12-rapamycin complex interacting with the binding domain of human FRAP (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-07-12
    Description: Rapamycin, a potent immunosuppressive agent, binds two proteins: the FK506-binding protein (FKBP12) and the FKBP-rapamycin-associated protein (FRAP). A crystal structure of the ternary complex of human FKBP12, rapamycin, and the FKBP12-rapamycin-binding (FRB) domain of human FRAP at a resolution of 2.7 angstroms revealed the two proteins bound together as a result of the ability of rapamycin to occupy two different hydrophobic binding pockets simultaneously. The structure shows extensive interactions between rapamycin and both proteins, but fewer interactions between the proteins. The structure of the FRB domain of FRAP clarifies both rapamycin-independent and -dependent effects observed for mutants of FRAP and its homologs in the family of proteins related to the ataxia-telangiectasia mutant gene product, and it illustrates how a small cell-permeable molecule can mediate protein dimerization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choi, J -- Chen, J -- Schreiber, S L -- Clardy, J -- CA59021/CA/NCI NIH HHS/ -- GM38625/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 12;273(5272):239-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Baker Laboratory, Cornell University, Ithaca, NY 14853-1301, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662507" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carrier Proteins/chemistry/genetics/*metabolism ; Crystallography, X-Ray ; DNA-Binding Proteins/chemistry/*metabolism ; Heat-Shock Proteins/chemistry/*metabolism ; Humans ; *Immunophilins ; Models, Molecular ; Mutation ; *Phosphotransferases (Alcohol Group Acceptor) ; Polyenes/*chemistry/*metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Sirolimus ; TOR Serine-Threonine Kinases ; Tacrolimus Binding Proteins
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  • 8
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    A mechanism of drug action revealed by structural studies of enoyl reductase (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-12-20
    Description: Enoyl reductase (ENR), an enzyme involved in fatty acid biosynthesis, is the target for antibacterial diazaborines and the front-line antituberculosis drug isoniazid. Analysis of the structures of complexes of Escherichia coli ENR with nicotinamide adenine dinucleotide and either thienodiazaborine or benzodiazaborine revealed the formation of a covalent bond between the 2' hydroxyl of the nicotinamide ribose and a boron atom in the drugs to generate a tight, noncovalently bound bisubstrate analog. This analysis has implications for the structure-based design of inhibitors of ENR, and similarities to other oxidoreductases suggest that mimicking this molecular linkage may have generic applications in other areas of medicinal chemistry.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baldock, C -- Rafferty, J B -- Sedelnikova, S E -- Baker, P J -- Stuitje, A R -- Slabas, A R -- Hawkes, T R -- Rice, D W -- New York, N.Y. -- Science. 1996 Dec 20;274(5295):2107-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK. D.Rice@sheffield.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8953047" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/*metabolism/pharmacology ; Binding Sites ; Boron Compounds/*metabolism/pharmacology ; Crystallography, X-Ray ; Drug Design ; Drug Resistance, Microbial ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH) ; Enzyme Inhibitors/*metabolism/pharmacology ; Escherichia coli/enzymology ; Escherichia coli Proteins ; Fatty Acid Synthase, Type II ; Fatty Acid Synthases/antagonists & inhibitors/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; NAD/*metabolism ; Oxidoreductases/antagonists & inhibitors/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary
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  • 9
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    Transcription factor IIA: a structure with multiple functions (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacobson, R H -- Tjian, R -- New York, N.Y. -- Science. 1996 May 10;272(5263):827-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, Berkeley 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8629011" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallography, X-Ray ; DNA/*chemistry/metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Humans ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; TATA Box ; TATA-Box Binding Protein ; Transcription Factor TFIIA ; Transcription Factor TFIID ; Transcription Factors/*chemistry/genetics/*metabolism ; *Transcription, Genetic
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  • 10
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    Another twist to MHC-peptide recognition (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-05-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, I A -- New York, N.Y. -- Science. 1996 May 17;272(5264):973-4.〈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/8638141" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigen Presentation ; Antigens/chemistry/*metabolism ; Antigens, Differentiation, B-Lymphocyte/chemistry/*metabolism ; HLA-DR1 Antigen/chemistry/metabolism ; Histocompatibility Antigens Class II/chemistry/immunology/*metabolism ; Humans ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Mice ; Models, Molecular ; Protein Conformation
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  • 11
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    Molecular orientation and two-component nature of the crystalline fraction of spider dragline silk (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-01-05
    Description: The molecular origin of the exceptional mechanical properties of spider silk is unclear. This paper presents solid-state 2H nuclear magnetic resonance data from unoriented, oriented, and supercontracted fibers, indicating that the crystalline fraction of dragline silk consists of two types of alanine-rich regions, one that is highly oriented and one that is poorly oriented and less densely packed. A new model for the molecular-level structure of individual silk molecules and their arrangement in the fibers is proposed. These data suggest that it will be necessary to control the secondary structure of individual polymer molecules in order to obtain optimum properties in bio-inspired polymers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simmons, A H -- Michal, C A -- Jelinski, L W -- New York, N.Y. -- Science. 1996 Jan 5;271(5245):84-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Advanced Technology in Biotechnology, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8539605" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/analysis ; Algorithms ; Amino Acid Sequence ; Animals ; Crystallization ; Crystallography, X-Ray ; *Fibroins ; Glycine/analysis ; *Insect Proteins ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Peptides/analysis ; Protein Conformation ; Protein Structure, Secondary ; Proteins/*chemistry ; Silk ; Spiders/*chemistry
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  • 12
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    Direct observation of protein solvation and discrete disorder with experimental crystallographic phases (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-01-05
    Description: A complete and accurate set of experimental crystallographic phases to a resolution of 1.8 angstroms was obtained for a 230-residue dimeric fragment of rat mannose-binding protein A with the use of multiwavelength anomalous dispersion (MAD) phasing. An accurate image of the crystal structure could thus be obtained without resort to phases calculated from a model. Partially reduced disulfide bonds, local disorder, and differences in the mobility of chemically equivalent molecules are apparent in the experimental electron density map. A solvation layer is visible that includes well-ordered sites of hydration around polar and charged protein atoms, as well as diffuse, partially disordered solvent shells around exposed hydrophobic groups. Because the experimental phases and the resulting electron density map are free from the influence of a model, they provide a stringent test of theoretical models of macromolecular solvation, motion, and conformational heterogeneity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burling, F T -- Weis, W I -- Flaherty, K M -- Brunger, A T -- GM50565/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jan 5;271(5245):72-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8539602" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carrier Proteins/*chemistry ; Chemistry, Physical ; Crystallization ; *Crystallography, X-Ray ; Hydrogen Bonding ; Mannose/*metabolism ; *Mannose-Binding Lectin ; Models, Molecular ; Molecular Sequence Data ; Physicochemical Phenomena ; *Protein Conformation ; Rats ; Solvents ; Water
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  • 13
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    Tricorn protease--the core of a modular proteolytic system (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-11-22
    Description: Large macromolecular assemblies have evolved as a means of compartmentalizing reactions in organisms lacking membrane-bounded compartments. A tricorn-shaped protease was isolated from the archaeon Thermoplasma and was shown to form a multisubunit proteolytic complex. The 120-kilodalton monomer assembled to form a hexameric toroid that could assemble further into a capsid structure. Tricorn protease appeared to act as the core of a proteolytic system; when it interacted with several smaller proteins, it displayed multicatalytic activities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tamura, T -- Tamura, N -- Cejka, Z -- Hegerl, R -- Lottspeich, F -- Baumeister, W -- New York, N.Y. -- Science. 1996 Nov 22;274(5291):1385-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institute for Biochemistry, D-82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8910281" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cloning, Molecular ; Cysteine Endopeptidases/metabolism ; Endopeptidases/*chemistry/genetics/isolation & purification/*metabolism ; Genes, Bacterial ; Microscopy, Electron ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Multienzyme Complexes/metabolism ; Peptides/metabolism ; Proteasome Endopeptidase Complex ; *Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Substrate Specificity ; Thermoplasma/*enzymology
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 14
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    Structure of the p53 tumor suppressor bound to the ankyrin and SH3 domains of 53BP2 (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-11-08
    Description: Mutations in the p53 tumor suppressor are among the most frequently observed genetic alterations in human cancer and map to the 200-amino acid core domain of the protein. The core domain contains the sequence-specific DNA binding activity and the in vitro 53BP2 protein binding activity of p53. The crystal structure of the p53 core domain bound to the 53BP2 protein, which contains an SH3 (Src homology 3) domain and four ankyrin repeats, revealed that (i) the SH3 domain binds the L3 loop of p53 in a manner distinct from that of previously characterized SH3-polyproline peptide complexes, and (ii) an ankyrin repeat, which forms an L-shaped structure consisting of a beta hairpin and two alpha helices, binds the L2 loop of p53. The structure of the complex shows that the 53BP2 binding site on the p53 core domain consists of evolutionarily conserved regions that are frequently mutated in cancer and that it overlaps the site of DNA binding. The six most frequently observed p53 mutations disrupt 53BP2 binding in vitro. The structure provides evidence that the 53BP2-p53 complex forms in vivo and may have a critical role in the p53 pathway of tumor suppression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gorina, S -- Pavletich, N P -- CA65698/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1996 Nov 8;274(5289):1001-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8875926" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Ankyrins/*chemistry ; Apoptosis Regulatory Proteins ; Binding Sites ; Carrier Proteins/*chemistry/metabolism ; Crystallography, X-Ray ; DNA/metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Neoplasms/genetics ; Protein Binding ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Tumor Suppressor Protein p53/*chemistry/genetics/metabolism ; *src Homology Domains
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 15
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    Iron metabolism in eukaryotes: Mars and Venus at it again (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-03-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaplan, J -- O'Halloran, T V -- R01 GM038784/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Mar 15;271(5255):1510-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, University of Utah School of Medicine, Salt Lake City, 84132, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8599104" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Biological Transport ; Carrier Proteins/genetics/*metabolism ; Ceruloplasmin/chemistry/*metabolism ; Copper/metabolism ; Ferric Compounds/metabolism ; Ferrous Compounds/metabolism ; Iron/*metabolism ; Membrane Transport Proteins/genetics/*metabolism ; Models, Molecular ; Oxidation-Reduction ; Oxidoreductases/*metabolism ; Protein Conformation ; Saccharomyces cerevisiae/genetics/*metabolism ; *Saccharomyces cerevisiae Proteins
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 16
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    The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-05-24
    Description: The crystal structure of bovine heart cytochrome c oxidase at 2.8 A resolution with an R value of 19.9 percent reveals 13 subunits, each different from the other, five phosphatidyl ethanolamines, three phosphatidyl glycerols and two cholates, two hemes A, and three copper, one magnesium, and one zinc. Of 3606 amino acid residues in the dimer, 3560 have been converged to a reasonable structure by refinement. A hydrogen-bonded system, including a propionate of a heme A (heme a), part of peptide backbone, and an imidazole ligand of CuA, could provide an electron transfer pathway between CuA and heme a. Two possible proton pathways for pumping, each spanning from the matrix to the cytosolic surfaces, were identified, including hydrogen bonds, internal cavities likely to contain water molecules, and structures that could form hydrogen bonds with small possible conformational change of amino acid side chains. Possible channels for chemical protons to produce H2O, for removing the produced water, and for O2, respectively, were identified.〈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. 1996 May 24;272(5265):1136-44.〈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/8638158" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cattle ; Cell Nucleus/genetics ; Copper/analysis ; Crystallography, X-Ray ; Electron Transport ; Electron Transport Complex IV/*chemistry/genetics/metabolism ; Heme/analogs & derivatives/analysis ; Hydrogen Bonding ; Iron/analysis ; Membrane Proteins/chemistry ; Mitochondria, Heart/genetics ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Myocardium/enzymology ; Nucleotides/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Phospholipids/analysis ; *Protein Conformation ; Protein Structure, Secondary ; Proton Pumps ; Water/metabolism
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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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    Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-09-13
    Description: The solution structure of a human immunodeficiency virus type-1 (HIV-1) Rev peptide bound to stem-loop IIB of the Rev response element (RRE) RNA was solved by nuclear magnetic resonance spectroscopy. The Rev peptide has an alpha-helical conformation and binds in the major groove of the RNA near a purine-rich internal loop. Several arginine side chains make base-specific contacts, and an asparagine residue contacts a G.A base pair. The phosphate backbone adjacent to a G.G base pair adopts an unusual structure that allows the peptide to access a widened major groove. The structure formed by the two purine-purine base pairs of the RRE creates a distinctive binding pocket that the peptide can use for specific recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Battiste, J L -- Mao, H -- Rao, N S -- Tan, R -- Muhandiram, D R -- Kay, L E -- Frankel, A D -- Williamson, J R -- GM-08344/GM/NIGMS NIH HHS/ -- GM-39589/GM/NIGMS NIH HHS/ -- GM-53320/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Sep 13;273(5281):1547-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8703216" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/chemistry ; Asparagine/chemistry ; Base Composition ; Base Sequence ; *DNA-Binding Proteins ; Fungal Proteins/chemistry ; Gene Products, rev/*chemistry/*metabolism ; *Genes, env ; HIV-1/*chemistry ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Protein Kinases/chemistry ; *Protein Structure, Secondary ; RNA, Viral/*chemistry/genetics/metabolism ; *Saccharomyces cerevisiae Proteins ; Threonine/chemistry ; rev Gene Products, Human Immunodeficiency Virus
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  • 18
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    Site-directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S5 (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-06-14
    Description: Cysteine residues were introduced into three different positions distributed on the surface of ribosomal protein S5, to serve as targets for derivatization with an Fe(II)-ethyl-enediaminetetraacetic acid linker. Hydroxyl radicals generated locally from the tethered Fe(II) in intermediate ribonucleoprotein particles or in 30S ribosomal subunits reconstituted from derivatized S5 caused cleavage of the RNA, resulting in characteristically different cleavage patterns for the three different tethering positions. These findings provide constraints for the three-dimensional folding of 16S ribosomal RNA (rRNA) and for the orientation of S5 in the 30S subunit, and they further suggest that antibiotic resistance and accuracy mutations in S5 may involve perturbation of 16S rRNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heilek, G M -- Noller, H F -- New York, N.Y. -- Science. 1996 Jun 14;272(5268):1659-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658142" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/pharmacology ; Cloning, Molecular ; Cysteine/chemistry ; Edetic Acid/analogs & derivatives ; Escherichia coli ; Ferrous Compounds/chemistry ; Hydroxyl Radical/*chemistry ; Models, Molecular ; Molecular Probes ; Mutagenesis, Site-Directed ; Nucleic Acid Conformation ; Organometallic Compounds ; Protein Conformation ; RNA, Ribosomal/*chemistry ; RNA, Ribosomal, 16S/chemistry/drug effects ; Ribosomal Proteins/*chemistry/genetics ; Spectinomycin/pharmacology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 19
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    Crystal structure of DMSO reductase: redox-linked changes in molybdopterin coordination (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-06-14
    Description: The molybdoenzyme dimethylsulfoxide (DMSO) reductase contributes to the release of dimethylsulfide, a compound that has been implicated in cloud nucleation and global climate regulation. The crystal structure of DMSO reductase from Rhodobacter sphaeroides reveals a monooxo molybdenum cofactor containing two molybdopterin guanine dinucleotides that asymmetrically coordinate the molybdenum through their dithiolene groups. One of the pterins exhibits different coordination modes to the molybdenum between the oxidized and reduced states, whereas the side chain oxygen of Ser147 coordinates the metal in both states. The change in pterin coordination between the Mo(VI) and Mo(IV) forms suggests a mechanism for substrate binding and reduction by this enzyme. Sequence comparisons of DMSO reductase with a family of bacterial oxotransferases containing molybdopterin guanine dinucleotide indicate a similar polypeptide fold and active site with two molybdopterins within this family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schindelin, H -- Kisker, C -- Hilton, J -- Rajagopalan, K V -- Rees, D C -- GM00091/GM/NIGMS NIH HHS/ -- GM50775/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jun 14;272(5268):1615-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division 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/8658134" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Coenzymes/*chemistry ; Crystallography, X-Ray ; *Iron-Sulfur Proteins ; Metalloproteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/*chemistry/metabolism ; Protein Conformation ; Pteridines/*chemistry ; Rhodobacter sphaeroides/*enzymology ; Sequence Homology, Amino Acid
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  • 20
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    Hats off to the tricorn protease (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-11-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schneider, C -- Hartl, F U -- New York, N.Y. -- Science. 1996 Nov 22;274(5291):1323-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. f-hartl@ski.mskcc.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8966603" target="_blank"〉PubMed〈/a〉
    Keywords: Cysteine Endopeptidases/chemistry/metabolism ; Endopeptidases/chemistry/*metabolism ; Models, Molecular ; Multienzyme Complexes/chemistry/metabolism ; Proteasome Endopeptidase Complex ; *Protein Conformation ; Thermoplasma/*enzymology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 21
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    Nanosecond crystallographic snapshots of protein structural changes (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-12-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eaton, W A -- Henry, E R -- Hofrichter, J -- New York, N.Y. -- Science. 1996 Dec 6;274(5293):1631-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA. eaton@helix.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8984630" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Monoxide/chemistry/metabolism ; Computer Simulation ; Crystallography, X-Ray/*methods ; Heme/chemistry ; Ligands ; Models, Molecular ; Myoglobin/*chemistry/metabolism ; Photolysis ; *Protein Conformation ; Time Factors
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 22
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    Bio-molecular dynamics comes of age (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-02-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berendsen, H J -- New York, N.Y. -- Science. 1996 Feb 16;271(5251):954-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysical Chemistry, University of Groningen, Netherlands. berendsen@chem.rug.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8584930" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry ; Biotin/*chemistry ; Chemistry, Physical ; Computer Graphics ; *Computer Simulation ; Hydrogen Bonding ; Microscopy, Atomic Force ; *Models, Chemical ; Models, Molecular ; Molecular Conformation ; Physicochemical Phenomena ; Protein Conformation ; Streptavidin ; Thermodynamics
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  • 23
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    Crystal structure of the lactose operon repressor and its complexes with DNA and inducer (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-03-01
    Description: The lac operon of Escherichia coli is the paradigm for gene regulation. Its key component is the lac repressor, a product of the lacI gene. The three-dimensional structures of the intact lac repressor, the lac repressor bound to the gratuitous inducer isopropyl-beta-D-1-thiogalactoside (IPTG) and the lac repressor complexed with a 21-base pair symmetric operator DNA have been determined. These three structures show the conformation of the molecule in both the induced and repressed states and provide a framework for understanding a wealth of biochemical and genetic information. The DNA sequence of the lac operon has three lac repressor recognition sites in a stretch of 500 base pairs. The crystallographic structure of the complex with DNA suggests that the tetrameric repressor functions synergistically with catabolite gene activator protein (CAP) and participates in the quaternary formation of repression loops in which one tetrameric repressor interacts simultaneously with two sites on the genomic DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewis, M -- Chang, G -- Horton, N C -- Kercher, M A -- Pace, H C -- Schumacher, M A -- Brennan, R G -- Lu, P -- 2-T32-GM082745/GM/NIGMS NIH HHS/ -- GM44617/GM/NIGMS NIH HHS/ -- P41-RR06017/RR/NCRR NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1996 Mar 1;271(5253):1247-54.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Johnson Research Foundation, University of Pennsylvania, Philadelphia 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8638105" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Bacterial Proteins/*chemistry/genetics/metabolism ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Cyclic AMP Receptor Protein/metabolism ; DNA, Bacterial/chemistry/*metabolism ; *Escherichia coli Proteins ; Hydrogen Bonding ; Isopropyl Thiogalactoside/*metabolism ; *Lac Operon ; Lac Repressors ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Operator Regions, Genetic ; Point Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Repressor Proteins/*chemistry/genetics/metabolism
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  • 24
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    The galvanization of biology: a growing appreciation for the roles of zinc (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-02-23
    Description: Zinc ions are key structural components of a large number of proteins. The binding of zinc stabilizes the folded conformations of domains so that they may facilitate interactions between the proteins and other macromolecules such as DNA. The modular nature of some of these zinc-containing proteins has allowed the rational design of site-specific DNA binding proteins. The ability of zinc to be bound specifically within a range of tetrahedral sites appears to be responsible for the evolution of the side range of zinc-stabilized structural domains now known to exist. The lack of redox activity for the zinc ion and its binding and exchange kinetics also may be important in the use of zinc for specific functional roles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berg, J M -- Shi, Y -- New York, N.Y. -- Science. 1996 Feb 23;271(5252):1081-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8599083" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; DNA/metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Engineering ; Transcription Factors/chemistry/*metabolism ; Zinc/chemistry/metabolism/*physiology ; Zinc Fingers/*physiology
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  • 25
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    Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-12-20
    Description: The crystal structure of an unmodified hammerhead RNA in the absence of divalent metal ions has been solved, and it was shown that this ribozyme can cleave itself in the crystal when divalent metal ions are added. This biologically active RNA fold is the same as that found previously for two modified hammerhead ribozymes. Addition of divalent cations at low pH makes it possible to capture the uncleaved RNA in metal-bound form. A conformational intermediate, having an additional Mg(II) bound to the cleavage-site phosphate, was captured by freeze-trapping the RNA at an active pH prior to cleavage. The most significant conformational changes were limited to the active site of the ribozyme, and the changed conformation requires only small additional movements to reach a proposed transition-state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, W G -- Murray, J B -- Arnold, J R -- Stoddard, B L -- Klug, A -- GM-49857/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Dec 20;274(5295):2065-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8953035" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Crystallization ; Crystallography, X-Ray ; Freezing ; Hydrogen-Ion Concentration ; Magnesium/metabolism ; Manganese/metabolism ; Models, Molecular ; *Nucleic Acid Conformation ; RNA, Catalytic/*chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 26
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    Structural basis of light harvesting by carotenoids: peridinin-chlorophyll-protein from Amphidinium carterae (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-06-21
    Description: Peridinin-chlorophyll-protein, a water-soluble light-harvesting complex that has a blue-green absorbing carotenoid as its main pigment, is present in most photosynthetic dinoflagellates. Its high-resolution (2.0 angstrom) x-ray structure reveals a noncrystallographic trimer in which each polypeptide contains an unusual jellyroll fold of the alpha-helical amino- and carboxyl-terminal domains. These domains constitute a scaffold with pseudo-twofold symmetry surrounding a hydrophobic cavity filled by two lipid, eight peridinin, and two chlorophyll a molecules. The structural basis for efficient excitonic energy transfer from peridinin to chlorophyll is found in the clustering of peridinins around the chlorophylls at van der Waals distances.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hofmann, E -- Wrench, P M -- Sharples, F P -- Hiller, R G -- Welte, W -- Diederichs, K -- New York, N.Y. -- Science. 1996 Jun 21;272(5269):1788-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Fakultat fur Biologie, Universitat Konstanz, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8650577" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carotenoids/*chemistry ; Chlorophyll/chemistry ; Crystallography, X-Ray ; Dinoflagellida/*chemistry/metabolism ; Energy Transfer ; Hydrogen Bonding ; Models, Molecular ; Molecular Conformation ; Photosynthesis ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protozoan Proteins/*chemistry
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    Organization of diphtheria toxin T domain in bilayers: a site-directed spin labeling study (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-08-09
    Description: The diphtheria toxin transmembrane (T) domain was spin-labeled at consecutive residues in a helical segment, TH9. After binding of the T domain to membranes at low pH, the nitroxide side chains generated by spin labeling were measured with respect to their frequency of collision with polar and nonpolar reagents. The data showed that the helical structure of TH9 in solution is conserved, with one face exposed to water and the other to the hydrophobic interior of the bilayer. Measurement of the depth of the nitroxide side chains from the membrane surfaces revealed an incremental change of about 5 angstroms per turn, which is consistent with a transmembrane orientation of an alpha helix. These results indicate that the helix forms the lining of a transmembrane water-filled channel.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oh, K J -- Zhan, H -- Cui, C -- Hideg, K -- Collier, R J -- Hubbell, W L -- AI-22021/AI/NIAID NIH HHS/ -- AI-22848/AI/NIAID NIH HHS/ -- EY-05216/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 1996 Aug 9;273(5276):810-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-7008, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8670424" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Diphtheria Toxin/*chemistry/genetics ; Edetic Acid/analogs & derivatives ; Electron Spin Resonance Spectroscopy ; Hydrogen-Ion Concentration ; *Lipid Bilayers ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nickel ; Oxygen ; Phospholipids ; *Protein Structure, Secondary ; *Protein Structure, Tertiary ; Spin Labels
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  • 28
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    A protein phosphorylation switch at the conserved allosteric site in GP (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-09-13
    Description: A phosphorylation-initiated mechanism of local protein refolding activates yeast glycogen phosphorylase (GP). Refolding of the phosphorylated amino-terminus was shown to create a hydrophobic cluster that wedges into the subunit interface of the enzyme to trigger activation. The phosphorylated threonine is buried in the allosteric site. The mechanism implicates glucose 6-phosphate, the allosteric inhibitor, in facilitating dephosphorylation by dislodging the buried covalent phosphate through binding competition. Thus, protein phosphorylation-dephosphorylation may also be controlled through regulation of the accessibility of the phosphorylation site to kinases and phosphatases. In mammalian glycogen phosphorylase, phosphorylation occurs at a distinct locus. The corresponding allosteric site binds a ligand activator, adenosine monophosphate, which triggers activation by a mechanism analogous to that of phosphorylation in the yeast enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, K -- Rath, V L -- Dai, S C -- Fletterick, R J -- Hwang, P K -- DK32822/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1996 Sep 13;273(5281):1539-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California at San Francisco, 513 Parnassus, San Francisco, CA 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8703213" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/metabolism ; Allosteric Site ; Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Enzyme Activation ; Enzyme Inhibitors/metabolism/pharmacology ; Glucose-6-Phosphate ; Glucosephosphates/metabolism/pharmacology ; Models, Molecular ; Molecular Sequence Data ; Phosphorylases/antagonists & inhibitors/*chemistry/*metabolism ; Phosphorylation ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Saccharomyces cerevisiae/enzymology
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    Close-up of a killer (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-10-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 1996 Oct 11;274(5285):176-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8927977" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cells, Cultured ; Crystallography, X-Ray ; Drosophila melanogaster ; H-2 Antigens/*chemistry/immunology/metabolism ; Killer Cells, Natural/immunology ; *Major Histocompatibility Complex ; Models, Molecular ; Peptides/immunology/metabolism ; Protein Conformation ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/immunology/metabolism ; Recombinant Proteins/chemistry ; T-Lymphocytes, Cytotoxic/*immunology
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  • 30
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    Structural analysis of substrate binding by the molecular chaperone DnaK (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-06-14
    Description: DnaK and other members of the 70-kilodalton heat-shock protein (hsp70) family promote protein folding, interaction, and translocation, both constitutively and in response to stress, by binding to unfolded polypeptide segments. These proteins have two functional units: a substrate-binding portion binds the polypeptide, and an adenosine triphosphatase portion facilitates substrate exchange. The crystal structure of a peptide complex with the substrate-binding unit of DnaK has now been determined at 2.0 angstroms resolution. The structure consists of a beta-sandwich subdomain followed by alpha-helical segments. The peptide is bound to DnaK in an extended conformation through a channel defined by loops from the beta sandwich. An alpha-helical domain stabilizes the complex, but does not contact the peptide directly. This domain is rotated in the molecules of a second crystal lattice, which suggests a model of conformation-dependent substrate binding that features a latch mechanism for maintaining long lifetime complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, X -- Zhao, X -- Burkholder, W F -- Gragerov, A -- Ogata, C M -- Gottesman, M E -- Hendrickson, W A -- GM 34102/GM/NIGMS NIH HHS/ -- GM 37219/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jun 14;272(5268):1606-14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658133" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chaperonins/chemistry/*metabolism ; Crystallography, X-Ray ; Escherichia coli ; *Escherichia coli Proteins ; HSP70 Heat-Shock Proteins/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Peptides/metabolism ; Protein Binding ; Protein Conformation ; Sequence Homology, Amino Acid
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    DNA: an extensible molecule (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-02-09
    Description: The force-displacement response of a single duplex DNA molecule was measured. The force saturates at a plateau around 70 piconewtons, which ends when the DNA has been stretched about 1.7 times its contour length. This behavior reveals a highly cooperative transition to a state here termed S-DNA. Addition of an intercalator suppresses this transition. Molecular modeling of the process also yields a force plateau and suggests a structure for the extended form. These results may shed light on biological processes involving DNA extension and open the route for mechanical studies on individual molecules in a previously unexplored range.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cluzel, P -- Lebrun, A -- Heller, C -- Lavery, R -- Viovy, J L -- Chatenay, D -- Caron, F -- New York, N.Y. -- Science. 1996 Feb 9;271(5250):792-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Curie URA Centre National de la Recherche Scientifique (CNRS), Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8628993" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; DNA/*chemistry ; Models, Molecular ; *Nucleic Acid Conformation ; Physicochemical Phenomena ; Software
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    Direct visualization of A-, P-, and E-site transfer RNAs in the Escherichia coli ribosome (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-02-16
    Description: Transfer RNA (tRNA) molecules play a crucial role in protein biosynthesis in all organisms. Their interactions with ribosomes mediate the translation of genetic messages into polypeptides. Three tRNAs bound to the Escherichia coli 70S ribosome were visualized directly with cryoelectron microscopy and three-dimensional reconstruction. The detailed arrangement of A- and P-site tRNAs inferred from this study allows localization of the sites for anticodon interaction and peptide bond formation on the ribosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Agrawal, R K -- Penczek, P -- Grassucci, R A -- Li, Y -- Leith, A -- Nierhaus, K H -- Frank, J -- 1R01 GM29169/GM/NIGMS NIH HHS/ -- P41 RR01219/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1996 Feb 16;271(5251):1000-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wadsworth Center, New York State Department of Health, Albany 12201-0509, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8584922" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon ; Binding Sites ; Codon ; Escherichia coli/*metabolism ; Image Processing, Computer-Assisted ; Microscopy, Electron ; Models, Molecular ; Nucleic Acid Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Transfer/*chemistry/metabolism ; RNA, Transfer, Amino Acyl/*chemistry/metabolism ; RNA, Transfer, Phe/*chemistry/metabolism ; Ribosomes/*metabolism
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  • 33
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    Design of a monomeric 23-residue polypeptide with defined tertiary structure (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-01-19
    Description: Small proteins or protein domains generally require disulfide bridges or metal sites for their stabilization. Here it is shown that the beta beta alpha architecture of zinc fingers can be reproduced in a 23-residue polypeptide in the absence of metal ions. The sequence was obtained through an iterative design process. A key feature of the final design is the incorporation of a type II' beta turn to aid in beta-hairpin formation. Nuclear magnetic resonance analysis reveals that the alpha helix and beta hairpin are held together by a defined hydrophobic core. The availability of this structural template has implications for the development of functional polypeptides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Struthers, M D -- Cheng, R P -- Imperiali, B -- New York, N.Y. -- Science. 1996 Jan 19;271(5247):342-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division 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/8553067" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Circular Dichroism ; DNA-Binding Proteins/chemistry ; *Genes, Synthetic ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Peptides/*chemistry ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Proteins/*chemistry ; Transcription Factors/chemistry ; Zinc Fingers
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  • 34
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    Crystal structure of the dual specificity protein phosphatase VHR (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-05-31
    Description: Dual specificity protein phosphatases (DSPs) regulate mitogenic signal transduction and control the cell cycle. Here, the crystal structure of a human DSP, vaccinia H1-related phosphatase (or VHR), was determined at 2.1 angstrom resolution. A shallow active site pocket in VHR allows for the hydrolysis of phosphorylated serine, threonine, or tyrosine protein residues, whereas the deeper active site of protein tyrosine phosphatases (PTPs) restricts substrate specificity to only phosphotyrosine. Positively charged crevices near the active site may explain the enzyme's preference for substrates with two phosphorylated residues. The VHR structure defines a conserved structural scaffold for both DSPs and PTPs. A "recognition region," connecting helix alpha1 to strand beta1, may determine differences in substrate specificity between VHR, the PTPs, and other DSPs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yuvaniyama, J -- Denu, J M -- Dixon, J E -- Saper, M A -- AI 34095/AI/NIAID NIH HHS/ -- DK18024/DK/NIDDK NIH HHS/ -- DK18849/DK/NIDDK NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1996 May 31;272(5266):1328-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Research Division and Department of Biological Chemistry, University of Michigan, Ann Arbor 48109-1055, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8650541" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Dual Specificity Phosphatase 3 ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Phosphorylation ; Phosphoserine/metabolism ; Phosphothreonine/metabolism ; Phosphotyrosine/metabolism ; *Protein Conformation ; Protein Folding ; *Protein Structure, Secondary ; Protein Tyrosine Phosphatases/*chemistry/metabolism ; Sequence Alignment ; Substrate Specificity ; Water/metabolism ; Yersinia/enzymology
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  • 35
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    An asymmetric model for the nucleosome: a binding site for linker histones inside the DNA gyres (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-10-25
    Description: Histone-DNA contacts within a nucleosome influence the function of trans-acting factors and the molecular machines required to activate the transcription process. The internal architecture of a positioned nucleosome has now been probed with the use of photoactivatable cross-linking reagents to determine the placement of histones along the DNA molecule. A model for the nucleosome is proposed in which the winged-helix domain of the linker histone is asymmetrically located inside the gyres of DNA that also wrap around the core histones. This domain extends the path of the protein superhelix to one side of the core particle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pruss, D -- Bartholomew, B -- Persinger, J -- Hayes, J -- Arents, G -- Moudrianakis, E N -- Wolffe, A P -- New York, N.Y. -- Science. 1996 Oct 25;274(5287):614-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2710, USA. awlme@helix.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8849453" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Cross-Linking Reagents ; DNA/*chemistry/metabolism ; Histones/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleosomes/*chemistry ; Protein Conformation ; Protein Structure, Secondary ; RNA, Ribosomal/genetics ; Recombinant Proteins/chemistry ; Xenopus
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  • 36
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    Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-10-18
    Description: The Escherichia coli DNA binding protein RuvA acts in concert with the helicase RuvB to drive branch migration of Holliday intermediates during recombination and DNA repair. The atomic structure of RuvA was determined at a resolution of 1.9 angstroms. Four monomers of RuvA are related by fourfold symmetry in a manner reminiscent of a four-petaled flower. The four DNA duplex arms of a Holliday junction can be modeled in a square planar configuration and docked into grooves on the concave surface of the protein around a central pin that may facilitate strand separation during the migration reaction. The model presented reveals how a RuvAB-junction complex may also accommodate the resolvase RuvC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rafferty, J B -- Sedelnikova, S E -- Hargreaves, D -- Artymiuk, P J -- Baker, P J -- Sharples, G J -- Mahdi, A A -- Lloyd, R G -- Rice, D W -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 1996 Oct 18;274(5286):415-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK. d.rice@sheffield.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8832889" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Base Composition ; Crystallography, X-Ray ; DNA Helicases/metabolism ; DNA, Bacterial/chemistry/*metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Endodeoxyribonucleases/metabolism ; Escherichia coli ; *Escherichia coli Proteins ; Hydrogen Bonding ; Models, Molecular ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Recombination, Genetic
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    Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-11-08
    Description: The MDM2 oncoprotein is a cellular inhibitor of the p53 tumor suppressor in that it can bind the transactivation domain of p53 and downregulate its ability to activate transcription. In certain cancers, MDM2 amplification is a common event and contributes to the inactivation of p53. The crystal structure of the 109-residue amino-terminal domain of MDM2 bound to a 15-residue transactivation domain peptide of p53 revealed that MDM2 has a deep hydrophobic cleft on which the p53 peptide binds as an amphipathic alpha helix. The interface relies on the steric complementarity between the MDM2 cleft and the hydrophobic face of the p53 alpha helix and, in particular, on a triad of p53 amino acids-Phe19, Trp23, and Leu26-which insert deep into the MDM2 cleft. These same p53 residues are also involved in transactivation, supporting the hypothesis that MDM2 inactivates p53 by concealing its transactivation domain. The structure also suggests that the amphipathic alpha helix may be a common structural motif in the binding of a diverse family of transactivation factors to the TATA-binding protein-associated factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kussie, P H -- Gorina, S -- Marechal, V -- Elenbaas, B -- Moreau, J -- Levine, A J -- Pavletich, N P -- CA65698/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1996 Nov 8;274(5289):948-53.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. nikola@xray2.mskcc.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8875929" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; *Nuclear Proteins ; Protein Binding ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proto-Oncogene Proteins/*chemistry/metabolism ; Proto-Oncogene Proteins c-mdm2 ; Transcription Factors/chemistry/metabolism ; *Transcriptional Activation ; Tumor Suppressor Protein p53/*chemistry/metabolism
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  • 38
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    Parallel and antiparallel (G.GC)2 triple helix fragments in a crystal structure (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-09-20
    Description: Nucleic acid triplexes are formed by sequence-specific interactions between single-stranded polynucleotides and the double helix. These triplexes are implicated in genetic recombination in vivo and have application to areas that include genome analysis and antigene therapy. Despite the importance of the triple helix, only limited high-resolution structural information is available. The x-ray crystal structure of the oligonucleotide d(GGCCAATTGG) is described; it was designed to contain the d(G middle dotGC)2 fragment and thus provide the basic repeat unit of a DNA triple helix. Parameters derived from this crystal structure have made it possible to construct models of both parallel and antiparallel triple helices.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vlieghe, D -- Van Meervelt, L -- Dautant, A -- Gallois, B -- Precigoux, G -- Kennard, O -- New York, N.Y. -- Science. 1996 Sep 20;273(5282):1702-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Heverlee, Belgium. Structurale, EP CNRS, Universite de Bordeaux.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8781231" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Crystallography, X-Ray ; DNA/*chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/*chemistry
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  • 39
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    Flexing muscle with just one amino acid (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-01-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 1996 Jan 5;271(5245):31.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8539593" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Calcium/*metabolism ; Glutamic Acid/*physiology ; Humans ; Magnetic Resonance Spectroscopy ; Models, Molecular ; *Muscle Contraction ; Muscle, Skeletal/chemistry ; Mutation ; Myocardium/chemistry ; *Protein Conformation ; Protein Structure, Secondary ; Troponin/*chemistry/genetics/metabolism ; Troponin C
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    Bipartite Ca2+-binding motif in C2 domains of synaptotagmin and protein kinase C (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-07-12
    Description: C2 domains are found in many proteins involved in membrane traffic or signal transduction. Although C2 domains are thought to bind calcium ions, the structural basis for calcium binding is unclear. Analysis of calcium binding to C2 domains of synaptotagmin I and protein kinase C-beta by nuclear magnetic resonance spectroscopy revealed a bipartite calcium-binding motif that involves the coordination of two calcium ions by five aspartate residues located on two separate loops. Sequence comparisons indicated that this may be a widely used calcium-binding motif, designated here as the C2 motif.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shao, X -- Davletov, B A -- Sutton, R B -- Sudhof, T C -- Rizo, J -- R01-MH52804-01/MH/NIMH NIH HHS/ -- R29 NS33731-01A1/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 12;273(5272):248-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75235, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662510" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid/chemistry ; Base Sequence ; Calcium/*metabolism ; *Calcium-Binding Proteins ; Crystallography, X-Ray ; Hydrogen-Ion Concentration ; Magnetic Resonance Spectroscopy ; Membrane Glycoproteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Nerve Tissue Proteins/*chemistry/*metabolism ; Phospholipids/metabolism ; Protein Conformation ; Protein Folding ; Protein Kinase C/chemistry/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Synaptotagmin I ; Synaptotagmins ; Temperature
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    The crystal structure of a five-stranded coiled coil in COMP: a prototype ion channel? (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-11-01
    Description: Oligomerization by the formation of alpha-helical bundles is common in many proteins. The crystal structure of a parallel pentameric coiled coil, constituting the oligomerization domain in the cartilage oligomeric matrix protein (COMP), was determined at 2.05 angstroms resolution. The same structure probably occurs in two other extracellular matrix proteins, thrombospondins 3 and 4. Complementary hydrophobic interactions and conserved disulfide bridges between the alpha helices result in a thermostable structure with unusual properties. The long hydrophobic axial pore is filled with water molecules but can also accommodate small apolar groups. An "ion trap" is formed inside the pore by a ring of conserved glutamines, which binds chloride and probably other monatomic anions. The oligomerization domain of COMP has marked similarities with proposed models of the pentameric transmembrane ion channels in phospholamban and the acetylcholine receptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Malashkevich, V N -- Kammerer, R A -- Efimov, V P -- Schulthess, T -- Engel, J -- New York, N.Y. -- Science. 1996 Nov 1;274(5288):761-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8864111" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cartilage Oligomeric Matrix Protein ; Chloride Channels/chemistry ; Chlorides/chemistry ; Crystallography, X-Ray ; Disulfides/chemistry ; Extracellular Matrix Proteins/*chemistry ; Glutamine/chemistry ; Glycoproteins/*chemistry ; Humans ; Hydrogen Bonding ; Ion Channels/*chemistry ; Matrilin Proteins ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; *Protein Structure, Secondary ; Sequence Alignment
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    Bioinformatics. Working the Web with a virtual lab and some Java (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-08-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fischman, J -- New York, N.Y. -- Science. 1996 Aug 2;273(5275):591-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8701313" target="_blank"〉PubMed〈/a〉
    Keywords: *Amino Acid Sequence ; *Base Sequence ; *Computer Communication Networks ; DNA/*genetics ; *Information Systems ; Models, Molecular ; *Programming Languages ; Protein Conformation ; Proteins/chemistry
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    Linker histones, DNA's protein custodians, gain new respect (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-10-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 1996 Oct 25;274(5287):503-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8928004" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; Gene Expression Regulation ; Histones/chemistry/*metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Nucleosomes/*chemistry/genetics ; Tetrahymena thermophila/genetics ; Xenopus
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    Tumor-killer made; how does it work? (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-12-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 1996 Dec 20;274(5295):2009.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8984658" target="_blank"〉PubMed〈/a〉
    Keywords: *Alkanes ; Antineoplastic Agents/*chemical synthesis/chemistry/metabolism/*pharmacology ; *Carbamates ; Computer Simulation ; *Epothilones ; Epoxy Compounds/*chemical synthesis/chemistry/metabolism/*pharmacology ; Lactones/chemical synthesis/chemistry/pharmacology ; Microtubules/drug effects/metabolism ; Models, Molecular ; Molecular Conformation ; Paclitaxel/chemistry/pharmacology ; Pyrones ; Thiazoles/*chemical synthesis/chemistry/metabolism/*pharmacology ; Tumor Cells, Cultured
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  • 45
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    Crystal structure of the Aequorea victoria green fluorescent protein (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-09-06
    Description: The green fluorescent protein (GFP) from the Pacific Northwest jellyfish Aequorea victoria has generated intense interest as a marker for gene expression and localization of gene products. The chromophore, resulting from the spontaneous cyclization and oxidation of the sequence -Ser65 (or Thr65)-Tyr66-Gly67-, requires the native protein fold for both formation and fluorescence emission. The structure of Thr65 GFP has been determined at 1.9 angstrom resolution. The protein fold consists of an 11-stranded beta barrel with a coaxial helix, with the chromophore forming from the central helix. Directed mutagenesis of one residue adjacent to the chromophore, Thr203, to Tyr or His results in significantly red-shifted excitation and emission maxima.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ormo, M -- Cubitt, A B -- Kallio, K -- Gross, L A -- Tsien, R Y -- Remington, S J -- New York, N.Y. -- Science. 1996 Sep 6;273(5280):1392-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Department of Physics, University of Oregon, Eugene, OR 97403-1226, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8703075" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Green Fluorescent Proteins ; Hydrogen Bonding ; Luminescent Proteins/*chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Spectrometry, Fluorescence
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    Functional mimicry of a protein hormone by a peptide agonist: the EPO receptor complex at 2.8 A (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-07-26
    Description: The functional mimicry of a protein by an unrelated small molecule has been a formidable challenge. Now, however, the biological activity of a 166-residue hematopoietic growth hormone, erythropoietin (EPO), with its class 1 cytokine receptor has been mimicked by a 20-residue cyclic peptide unrelated in sequence to the natural ligand. The crystal structure at 2.8 A resolution of a complex of this agonist peptide with the extracellular domain of EPO receptor reveals that a peptide dimer induces an almost perfect twofold dimerization of the receptor. The dimer assembly differs from that of the human growth hormone (hGH) receptor complex and suggests that more than one mode of dimerization may be able to induce signal transduction and cell proliferation. The EPO receptor binding site, defined by peptide interaction, corresponds to the smaller functional epitope identified for hGH receptor. Similarly, the EPO mimetic peptide ligand can be considered as a minimal hormone, and suggests the design of nonpeptidic small molecule mimetics for EPO and other cytokines may indeed be achievable.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Livnah, O -- Stura, E A -- Johnson, D L -- Middleton, S A -- Mulcahy, L S -- Wrighton, N C -- Dower, W J -- Jolliffe, L K -- Wilson, I A -- GM-49497/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 26;273(5274):464-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10666 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662530" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Drug Design ; Erythropoietin/*chemistry/*metabolism ; Growth Hormone/chemistry/metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; *Molecular Mimicry ; Molecular Sequence Data ; Peptides, Cyclic/*chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Erythropoietin/*agonists/chemistry/metabolism ; Receptors, Somatotropin/chemistry/metabolism
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    Intercalation, DNA kinking, and the control of transcription (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-02-09
    Description: Biological processes involved in the control and regulation of transcription are dependent on protein-induced distortions in DNA structure that enhance the recruitment of proteins to their specific DNA targets. This function is often accomplished by accessory factors that bind sequence specifically and locally bend or kink the DNA. The recent determination of the three-dimensional structures of several protein-DNA complexes, involving proteins that perform such architectural tasks, brings to light a common theme of side chain intercalation as a mechanism capable of driving the deformation of the DNA helix. The protein scaffolds orienting the intercalating side chain (or side chains) are structurally diverse, presently comprising four distinct topologies that can accomplish the same task. The intercalating side chain (or side chains), however, is exclusively hydrophobic. Intercalation can either kink or bend the DNA, unstacking one or more adjacent base pairs and locally unwinding the DNA over as much as a full turn of helix. Despite these distortions, the return to B-DNA helical parameters generally occurs within the adjacent half-turns of DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Werner, M H -- Gronenborn, A M -- Clore, G M -- New York, N.Y. -- Science. 1996 Feb 9;271(5250):778-84.〈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 20892-0520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8628992" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; DNA/*chemistry/metabolism ; DNA Helicases/chemistry/metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Hydrogen Bonding ; Intercalating Agents/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Transcription Factors/chemistry/*metabolism ; *Transcription, Genetic
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    Heparin structure and interactions with basic fibroblast growth factor (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-02-23
    Description: Crystal structures of heparin-derived tetra- and hexasaccharides complexed with basic fibroblast growth factor (bFGF) were determined at resolutions of 1.9 and 2.2 angstroms, respectively. The heparin structure may be approximated as a helical polymer with a disaccharide rotation of 174 degrees and a translation of 8.6 angstroms along the helix axis. Both molecules bound similarly to a region of the bFGF surface containing residues asparagine-28, arginine-121, lysine-126, and glutamine-135, the hexasaccharide also interacted with an additional binding site formed by lysine-27, asparagine-102, and lysine-136. No significant conformational change in bFGF occurred upon heparin oligosaccharide binding, which suggests that heparin primarily serves to juxtapose components of the FGF signal transduction pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Faham, S -- Hileman, R E -- Fromm, J R -- Linhardt, R J -- Rees, D C -- GM38060/GM/NIGMS NIH HHS/ -- GM45162/GM/NIGMS NIH HHS/ -- T32 GM08346/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Feb 23;271(5252):1116-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8599088" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbohydrate Conformation ; Carbohydrate Sequence ; Crystallization ; Crystallography, X-Ray ; Fibroblast Growth Factor 2/*metabolism ; Heparin/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Oligosaccharides/chemistry/metabolism ; Protein Conformation
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    An alphabeta T cell receptor structure at 2.5 A and its orientation in the TCR-MHC complex (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-10-11
    Description: The central event in the cellular immune response to invading microorganisms is the specific recognition of foreign peptides bound to major histocompatibility complex (MHC) molecules by the alphabeta T cell receptor (TCR). The x-ray structure of the complete extracellular fragment of a glycosylated alphabeta TCR was determined at 2.5 angstroms, and its orientation bound to a class I MHC-peptide (pMHC) complex was elucidated from crystals of the TCR-pMHC complex. The TCR resembles an antibody in the variable Valpha and Vbeta domains but deviates in the constant Calpha domain and in the interdomain pairing of Calpha with Cbeta. Four of seven possible asparagine-linked glycosylation sites have ordered carbohydrate moieties, one of which lies in the Calpha-Cbeta interface. The TCR combining site is relatively flat except for a deep hydrophobic cavity between the hypervariable CDR3s (complementarity-determining regions) of the alpha and beta chains. The 2C TCR covers the class I MHC H-2Kb binding groove so that the Valpha CDRs 1 and 2 are positioned over the amino-terminal region of the bound dEV8 peptide, the Vbeta chain CDRs 1 and 2 are over the carboxyl-terminal region of the peptide, and the Valpha and Vbeta CDR3s straddle the peptide between the helices around the central position of the peptide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia, K C -- Degano, M -- Stanfield, R L -- Brunmark, A -- Jackson, M R -- Peterson, P A -- Teyton, L -- Wilson, I A -- R01 CA58896/CA/NCI NIH HHS/ -- T32-A107244/PHS HHS/ -- New York, N.Y. -- Science. 1996 Oct 11;274(5285):209-19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute of Chemical Biology, Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8824178" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carbohydrate Sequence ; Cells, Cultured ; Crystallization ; Crystallography, X-Ray ; Drosophila melanogaster ; Glycosylation ; H-2 Antigens/*chemistry/immunology/metabolism ; Hydrogen Bonding ; Major Histocompatibility Complex ; Mice ; Models, Molecular ; Molecular Sequence Data ; Peptides/*chemistry/immunology/metabolism ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/immunology/metabolism ; Recombinant Proteins ; T-Lymphocytes, Cytotoxic/*immunology
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    RNA tertiary structure mediation by adenosine platforms (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-09-20
    Description: The crystal structure of a group I intron domain reveals an unexpected motif that mediates both intra- and intermolecular interactions. At three separate locations in the 160-nucleotide domain, adjacent adenosines in the sequence lie side-by-side and form a pseudo-base pair within a helix. This adenosine platform opens the minor groove for base stacking or base pairing with nucleotides from a noncontiguous RNA strand. The platform motif has a distinctive chemical modification signature that may enable its detection in other structured RNAs. The ability of this motif to facilitate higher order folding provides one explanation for the abundance of adenosine residues in internal loops of many RNAs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cate, J H -- Gooding, A R -- Podell, E -- Zhou, K -- Golden, B L -- Szewczak, A A -- Kundrot, C E -- Cech, T R -- Doudna, J A -- 5T32GM08283-07/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Sep 20;273(5282):1696-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8781229" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/*chemistry ; Animals ; Base Composition ; Hydrogen Bonding ; *Introns ; Models, Molecular ; *Nucleic Acid Conformation ; RNA, Catalytic/*chemistry ; RNA, Protozoan/*chemistry ; Tetrahymena thermophila/genetics
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    Computational molecular biology. Software matchmakers help make sense of sequences (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-08-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Taubes, G -- New York, N.Y. -- Science. 1996 Aug 2;273(5275):588-90.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8701312" target="_blank"〉PubMed〈/a〉
    Keywords: *Algorithms ; *Amino Acid Sequence ; Base Sequence ; Computer Communication Networks ; *Databases, Factual ; Evolution, Molecular ; Markov Chains ; Models, Molecular ; Molecular Sequence Data ; Neural Networks (Computer) ; *Protein Conformation ; Sequence Alignment
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  • 52
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    Crystal structure of the yeast TFIIA/TBP/DNA complex (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-05-10
    Description: The crystal structure of the yeast TFIIA/TBP/TATA promoter complex was solved to 3 angstrom resolution by double-edge multiple wavelength anomalous diffraction from two different species of anomalous scattering elements in the same crystal. The large and small subunits of TFIIA associate intimately to form both domains of a two-domain folding pattern. TFIIA binds as a heterodimer to the side of the TBP/TATA complex opposite to the side that binds TFIIB and does not alter the TBP/DNA interaction. The six-stranded beta-sandwich domain interacts with the amino-terminal end of TBP through a stereospecific parallel beta-strand interface and with the backbone of the TATA box and the 5'-flanking B-DNA segment. The four-helix-bundle domain projects away from the TBP/TATA complex, thereby presenting a substantial surface for further protein-protein interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Geiger, J H -- Hahn, S -- Lee, S -- Sigler, P B -- New York, N.Y. -- Science. 1996 May 10;272(5263):830-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8629014" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Crystallography, X-Ray ; DNA, Fungal/*chemistry/metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Nucleic Acid Conformation ; Promoter Regions, Genetic ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Saccharomyces cerevisiae/chemistry/genetics/metabolism ; TATA Box ; TATA-Box Binding Protein ; Transcription Factor TFIIA ; Transcription Factor TFIIB ; Transcription Factors/*chemistry/metabolism ; Transcription, Genetic
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    Which came first, protein sequence or structure? (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-08-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Karkar, M -- New York, N.Y. -- Science. 1996 Aug 2;273(5275):610.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8701315" target="_blank"〉PubMed〈/a〉
    Keywords: *Amino Acid Sequence ; Models, Molecular ; Mutation ; *Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry/genetics ; Thermodynamics
    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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  • 54
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    Structure of gene-tag protein solved (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-09-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gura, T -- New York, N.Y. -- Science. 1996 Sep 6;273(5280):1336.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8801627" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Green Fluorescent Proteins ; Luminescent Proteins/*chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; *Protein Conformation
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 55
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    Discovering high-affinity ligands for proteins: SAR by NMR (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-11-29
    Description: A nuclear magnetic resonance (NMR)-based method is described in which small organic molecules that bind to proximal subsites of a protein are identified, optimized, and linked together to produce high-affinity ligands. The approach is called "SAR by NMR" because structure-activity relationships (SAR) are obtained from NMR. With this technique, compounds with nanomolar affinities for the FK506 binding protein were rapidly discovered by tethering two ligands with micromolar affinities. The method reduces the amount of chemical synthesis and time required for the discovery of high-affinity ligands and appears particularly useful in target-directed drug research.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shuker, S B -- Hajduk, P J -- Meadows, R P -- Fesik, S W -- New York, N.Y. -- Science. 1996 Nov 29;274(5292):1531-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, IL 60064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8929414" target="_blank"〉PubMed〈/a〉
    Keywords: Anilides/metabolism ; Binding Sites ; Carrier Proteins/*metabolism ; DNA-Binding Proteins/*metabolism ; Heat-Shock Proteins/*metabolism ; *Ligands ; *Magnetic Resonance Spectroscopy ; Models, Molecular ; Proteins/*metabolism ; Structure-Activity Relationship ; Tacrolimus/*metabolism ; Tacrolimus Binding Proteins
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 56
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    Structure of the heat shock protein chaperonin-10 of Mycobacterium leprae (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-01-12
    Description: Members of the chaperonin-10 (cpn10) protein family, also called heat shock protein 10 and in Escherichia coli GroES, play an important role in ensuring the proper folding of many proteins. The crystal structure of the Mycobacterium leprae cpn10 (Ml-cpn10) oligomer has been elucidated at a resolution of 3.5 angstroms. The architecture of the Ml-cpn10 heptamer resembles a dome with an oculus in its roof. The inner surface of the dome is hydrophilic and highly charged. A flexible region, known to interact with cpn60, extends from the lower rim of the dome. With the structure of a cpn10 heptamer now revealed and the structure of the E. coli GroEL previously known, models of cpn10:cpn60 and GroEL:GroES complexes are proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mande, S C -- Mehra, V -- Bloom, B R -- Hol, W G -- AI07118/AI/NIAID NIH HHS/ -- AI23545/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1996 Jan 12;271(5246):203-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Structure, University of Washington, Seattle 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8539620" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chaperonin 10/*chemistry/metabolism ; Chaperonin 60/chemistry/metabolism ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Mycobacterium leprae/*chemistry ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Sequence Alignment
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 57
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    Mapping the protein universe (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-08-02
    Description: The comparison of the three-dimensional shapes of protein molecules poses a complex algorithmic problem. Its solution provides biologists with computational tools to organize the rapidly growing set of thousands of known protein shapes, to identify new types of protein architecture, and to discover unexpected evolutionary relations, reaching back billions of years, between protein molecules. Protein shape comparison also improves tools for identifying gene functions in genome databases by defining the essential sequence-structure features of a protein family. Finally, an exhaustive all-on-all shape comparison provides a map of physical attractor regions in the abstract shape space of proteins, with implications for the processes of protein folding and evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holm, L -- Sander, C -- New York, N.Y. -- Science. 1996 Aug 2;273(5275):595-603.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton Hall, Cambridge CB10 1SD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662544" target="_blank"〉PubMed〈/a〉
    Keywords: *Algorithms ; Amino Acid Sequence ; Computer Communication Networks ; *Databases, Factual ; *Evolution, Molecular ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry ; Sequence Alignment
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 58
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    Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-11-22
    Description: Aminoglycoside antibiotics that bind to 30S ribosomal A-site RNA cause misreading of the genetic code and inhibit translocation. The aminoglycoside antibiotic paromomycin binds specifically to an RNA oligonucleotide that contains the 30S subunit A site, and the solution structure of the RNA-paromomycin complex was determined by nuclear magnetic resonance spectroscopy. The antibiotic binds in the major groove of the model A-site RNA within a pocket created by an A-A base pair and a single bulged adenine. Specific interactions occur between aminoglycoside chemical groups important for antibiotic activity and conserved nucleotides in the RNA. The structure explains binding of diverse aminoglycosides to the ribosome, their specific activity against prokaryotic organisms, and various resistance mechanisms, and provides insight into ribosome function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fourmy, D -- Recht, M I -- Blanchard, S C -- Puglisi, J D -- GM51266-01A1/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Nov 22;274(5291):1367-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8910275" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/chemistry/*metabolism/pharmacology ; Base Composition ; Binding Sites ; Escherichia coli/drug effects/*genetics ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Methylation ; Models, Molecular ; *Nucleic Acid Conformation ; Oligoribonucleotides/chemistry/metabolism ; Paromomycin/chemistry/*metabolism/pharmacology ; RNA, Bacterial/*chemistry/metabolism ; RNA, Ribosomal, 16S/*chemistry/metabolism ; Ribosomes/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 59
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    Structures of an MHC class II molecule with covalently bound single peptides (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-05-17
    Description: The high-resolution x-ray crystal structures of the murine major histocompatibility complex (MHC) class II molecule, I-E(k), occupied by either of two antigenic peptides were determined. They reveal the structural basis for the I-E(k) peptide binding motif and suggest general principles for additional alleles. A buried cluster of acidic amino acids in the binding groove predicted to be conserved among all murine I-E and human DR MHC class II molecules suggests how pH may influence MHC binding or exchange of peptides. These structures also complement mutational studies on the importance of individual peptide residues to T cell receptor recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fremont, D H -- Hendrickson, W A -- Marrack, P -- Kappler, J -- New York, N.Y. -- Science. 1996 May 17;272(5264):1001-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8638119" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/chemistry ; Animals ; Antigen Presentation ; Antigens/*chemistry/immunology/metabolism ; Crystallography, X-Ray ; HLA-DR Antigens/chemistry/immunology/metabolism ; HSP70 Heat-Shock Proteins/chemistry ; Hemoglobins/chemistry ; Histocompatibility Antigens Class II/*chemistry/immunology/metabolism ; Humans ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Mice ; Models, Molecular ; Molecular Sequence Data ; Peptide Fragments/*chemistry/immunology/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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