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  • Articles  (138)
  • Protein Conformation  (138)
  • 1990-1994  (138)
  • 1985-1989
  • 1950-1954
  • 1945-1949
  • 1994  (36)
  • 1992  (48)
  • 1991  (54)
  • Computer Science  (138)
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  • Articles  (138)
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  • 1990-1994  (138)
  • 1985-1989
  • 1950-1954
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  • 1
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    Structure of an electron transfer complex: methylamine dehydrogenase, amicyanin, and cytochrome c551i (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-04-01
    Description: The crystal structure of a ternary protein complex has been determined at 2.4 angstrom resolution. The complex is composed of three electron transfer proteins from Paracoccus denitrificans, the quinoprotein methylamine dehydrogenase, the blue copper protein amicyanin, and the cytochrome c551i. The central region of the c551i is folded similarly to several small bacterial c-type cytochromes; there is a 45-residue extension at the amino terminus and a 25-residue extension at the carboxyl terminus. The methylamine dehydrogenase-amicyanin interface is largely hydrophobic, whereas the amicyanin-cytochrome interface is more polar, with several charged groups present on each surface. Analysis of the simplest electron transfer pathways between the redox partners points out the importance of other factors such as energetics in determining the electron transfer rates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, L -- Durley, R C -- Mathews, F S -- Davidson, V L -- GM41574/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Apr 1;264(5155):86-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8140419" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Computer Graphics ; Cytochrome c Group/*chemistry/metabolism ; Electron Transport ; Hydrogen Bonding ; *Indolequinones ; Models, Molecular ; Oxidation-Reduction ; Oxidoreductases Acting on CH-NH Group Donors/*chemistry/metabolism ; Paracoccus denitrificans/*chemistry/enzymology ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Quinones/chemistry/metabolism ; Software ; Tryptophan/analogs & derivatives/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-10-21
    Description: The structure of the heterodimeric flavocytochrome c sulfide dehydrogenase from Chromatium vinosum was determined at a resolution of 2.53 angstroms. It contains a glutathione reductase-like flavin-binding subunit and a diheme cytochrome subunit. The diheme cytochrome folds as two domains, each resembling mitochondrial cytochrome c, and has an unusual interpropionic acid linkage joining the two heme groups in the interior of the subunit. The active site of the flavoprotein subunit contains a catalytically important disulfide bridge located above the pyrimidine portion of the flavin ring. A tryptophan, threonine, or tyrosine side chain may provide a partial conduit for electron transfer to one of the heme groups located 10 angstroms from the flavin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Z W -- Koh, M -- Van Driessche, G -- Van Beeumen, J J -- Bartsch, R G -- Meyer, T E -- Cusanovich, M A -- Mathews, F S -- GM-20530/GM/NIGMS NIH HHS/ -- GM-21277/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Oct 21;266(5184):430-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939681" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chromatium/*enzymology ; Computer Graphics ; Crystallography, X-Ray ; Cytochrome c Group/*chemistry ; Electron Transport ; Flavin-Adenine Dinucleotide/metabolism ; Hydrogen Bonding ; Models, Molecular ; Oxidoreductases/*chemistry ; Protein Conformation ; Protein Structure, Secondary
    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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  • 3
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    Structure of the RGD protein decorsin: conserved motif and distinct function in leech proteins that affect blood clotting (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-06-24
    Description: The structure of the leech protein decorsin, a potent 39-residue antagonist of glycoprotein IIb-IIIa and inhibitor of platelet aggregation, was determined by nuclear magnetic resonance. In contrast to other disintegrins, the Arg-Gly-Asp (RGD)-containing region of decorsin is well defined. The three-dimensional structure of decorsin is similar to that of hirudin, an anticoagulant leech protein that potently inhibits thrombin. Amino acid sequence comparisons suggest that ornatin, another glycoprotein IIb-IIIa antagonist, and antistasin, a potent Factor Xa inhibitor and anticoagulant found in leeches, share the same structural motif. Although decorsin, hirudin, and antistasin all affect the blood clotting process and appear similar in structure, their mechanisms of action and epitopes important for binding to their respective targets are distinct.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krezel, A M -- Wagner, G -- Seymour-Ulmer, J -- Lazarus, R A -- New York, N.Y. -- Science. 1994 Jun 24;264(5167):1944-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8009227" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Hirudins/chemistry ; Invertebrate Hormones/chemistry ; *Leeches ; Magnetic Resonance Spectroscopy ; Molecular Sequence Data ; Oligopeptides/chemistry ; Platelet Membrane Glycoproteins/*antagonists & inhibitors ; Protein Conformation ; Protein Structure, Secondary ; Proteins/*chemistry
    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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    Structural clues to prion replication (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-04-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, F E -- Pan, K M -- Huang, Z -- Baldwin, M -- Fletterick, R J -- Prusiner, S B -- New York, N.Y. -- Science. 1994 Apr 22;264(5158):530-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, University of California, San Francisco 94143-0518.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7909169" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Mice ; Mice, Transgenic ; Models, Biological ; Mutation ; PrPSc Proteins ; Prion Diseases/*metabolism/transmission ; Prions/*biosynthesis/chemistry/genetics/metabolism ; Protein Conformation ; Protein Structure, Secondary
    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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  • 5
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    The prion connection: now in yeast? (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-04-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weissmann, C -- New York, N.Y. -- Science. 1994 Apr 22;264(5158):528-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Molecularbiologie I, Universitat Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7909168" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid/analogs & derivatives/metabolism ; Fungal Proteins/chemistry/*genetics ; Genes, Fungal ; Glutathione Peroxidase ; Mutation ; PrPSc Proteins ; Prions/chemistry/genetics ; Protein Conformation ; Saccharomyces cerevisiae/*genetics/metabolism ; *Saccharomyces cerevisiae Proteins
    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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  • 6
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    Crystal structure of human protein tyrosine phosphatase 1B (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-11
    Description: Protein tyrosine phosphatases (PTPs) constitute a family of receptor-like and cytoplasmic signal transducing enzymes that catalyze the dephosphorylation of phosphotyrosine residues and are characterized by homologous catalytic domains. The crystal structure of a representative member of this family, the 37-kilodalton form (residues 1 to 321) of PTP1B, has been determined at 2.8 A resolution. The enzyme consists of a single domain with the catalytic site located at the base of a shallow cleft. The phosphate recognition site is created from a loop that is located at the amino-terminus of an alpha helix. This site is formed from an 11-residue sequence motif that is diagnostic of PTPs and the dual specificity phosphatases, and that contains the catalytically essential cysteine and arginine residues. The position of the invariant cysteine residue within the phosphate binding site is consistent with its role as a nucleophile in the catalytic reaction. The structure of PTP1B should serve as a model for other members of the PTP family and as a framework for understanding the mechanism of tyrosine dephosphorylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barford, D -- Flint, A J -- Tonks, N K -- CA53840/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1994 Mar 11;263(5152):1397-404.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, NY 11724.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8128219" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Molecular Sequence Data ; Phosphates/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Tyrosine Phosphatases/*chemistry/isolation & purification/metabolism ; Substrate Specificity ; Tungsten Compounds/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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  • 7
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    Insertion of a coiled-coil peptide from influenza virus hemagglutinin into membranes (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-10-14
    Description: The trimeric protein hemagglutinin (HA) of the influenza viral envelope is essential for cell entry. To investigate the interaction of HA with membranes, two 40-residue, cysteine-substituted peptides comprising the loop region and the first part of the coiled-coil stem were synthesized and modified with a nitroxide spin label. Electron paramagnetic resonance analysis revealed that the peptide inserts reversibly into phospholipid vesicles under endosomal pH conditions. This result suggests that some or all of the long coiled-coil trimer of HA may insert into membranes, which could bring the viral and cell membranes closer together and facilitate fusion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Y G -- King, D S -- Shin, Y K -- New York, N.Y. -- Science. 1994 Oct 14;266(5183):274-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939662" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Electron Spin Resonance Spectroscopy ; Endocytosis ; Hemagglutinin Glycoproteins, Influenza Virus ; Hemagglutinins, Viral/chemistry/*metabolism ; Hydrogen-Ion Concentration ; Lipid Bilayers/*metabolism ; *Membrane Fusion ; Molecular Sequence Data ; Orthomyxoviridae/physiology ; Protein Conformation ; Protein Structure, Secondary ; Temperature ; Viral Envelope Proteins/chemistry/*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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  • 8
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    The structural basis of sequence-independent peptide binding by OppA protein (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-06-10
    Description: Specific protein-ligand interactions are critical for cellular function, and most proteins select their partners with sharp discrimination. However, the oligopeptide-binding protein of Salmonella typhimurium (OppA) binds peptides of two to five amino acid residues without regard to sequence. The crystal structure of OppA reveals a three-domain organization, unlike other periplasmic binding proteins. In OppA-peptide complexes, the ligands are completely enclosed in the protein interior, a mode of binding that normally imposes tight specificity. The protein fulfills the hydrogen bonding and electrostatic potential of the ligand main chain and accommodates the peptide side chains in voluminous hydrated cavities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tame, J R -- Murshudov, G N -- Dodson, E J -- Neil, T K -- Dodson, G G -- Higgins, C F -- Wilkinson, A J -- New York, N.Y. -- Science. 1994 Jun 10;264(5165):1578-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of York, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8202710" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/*metabolism ; Binding Sites ; Carrier Proteins/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Ligands ; Lipoproteins/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Oligopeptides/chemistry/*metabolism ; Protein Conformation ; Protein Structure, Secondary
    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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  • 9
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    Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-11-04
    Description: The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A resolution by x-ray crystallography. The bipartite structure of PurR consists of an amino-terminal DNA-binding domain and a larger carboxyl-terminal corepressor binding and dimerization domain that is similar to that of the bacterial periplasmic binding proteins. The DNA-binding domain contains a helix-turn-helix motif that makes base-specific contacts in the major groove of the DNA. Base contacts are also made by residues of symmetry-related alpha helices, the "hinge" helices, which bind deeply in the minor groove. Critical to hinge helix-minor groove binding is the intercalation of the side chains of Leu54 and its symmetry-related mate, Leu54', into the central CpG-base pair step. These residues thereby act as "leucine levers" to pry open the minor groove and kink the purF operator by 45 degrees.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schumacher, M A -- Choi, K Y -- Zalkin, H -- Brennan, R G -- GM 24658/GM/NIGMS NIH HHS/ -- GM 49244/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Nov 4;266(5186):763-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Oregon Health Sciences University, Portland 97201-3098.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7973627" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/metabolism ; Base Sequence ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA-Binding Proteins/*chemistry/genetics/metabolism ; *Escherichia coli Proteins ; Hydrogen Bonding ; Hypoxanthine ; Hypoxanthines/metabolism ; Lac Repressors ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Operator Regions, Genetic ; Protein Conformation ; Protein Structure, Secondary ; Repressor Proteins/*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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  • 10
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    Flu virus invasion: halfway there (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-10-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carr, C M -- Kim, P S -- New York, N.Y. -- Science. 1994 Oct 14;266(5183):234-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Cambridge, MA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939658" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/metabolism/virology ; Endocytosis ; Endosomes/virology ; Hemagglutinin Glycoproteins, Influenza Virus ; Hemagglutinins, Viral/chemistry/*physiology ; Hydrogen-Ion Concentration ; *Membrane Fusion ; Models, Biological ; Models, Molecular ; Orthomyxoviridae/immunology/*physiology ; Protein Conformation ; Viral Envelope Proteins/chemistry/*physiology
    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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  • 11
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    Protein-DNA recognition: new perspectives and underlying themes (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-02-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Hippel, P H -- GM-15792/GM/NIGMS NIH HHS/ -- GM-29158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Feb 11;263(5148):769-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, University of Oregon, Eugene 97403.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8303292" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Thermodynamics
    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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  • 12
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    Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-04-15
    Description: The most frequently occurring resistance of Gram-negative bacteria against tetracyclines is triggered by drug recognition of the Tet repressor. This causes dissociation of the repressor-operator DNA complex and enables expression of the resistance protein TetA, which is responsible for active efflux of tetracycline. The 2.5 angstrom resolution crystal structure of the homodimeric Tet repressor complexed with tetracycline-magnesium reveals detailed drug recognition. The orientation of the operator-binding helix-turn-helix motifs of the repressor is inverted in comparison with other DNA binding proteins. The repressor-drug complex is unable to interact with DNA because the separation of the DNA binding motifs is 5 angstroms wider than usually observed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hinrichs, W -- Kisker, C -- Duvel, M -- Muller, A -- Tovar, K -- Hillen, W -- Saenger, W -- New York, N.Y. -- Science. 1994 Apr 15;264(5157):418-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Kristallographie, Freie Universitat Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8153629" target="_blank"〉PubMed〈/a〉
    Keywords: Antiporters/*chemistry/genetics/metabolism ; Bacterial Proteins/*chemistry/genetics/metabolism ; Crystallography, X-Ray ; DNA, Bacterial/metabolism ; Helix-Loop-Helix Motifs ; Hydrogen Bonding ; Magnesium/chemistry ; Models, Molecular ; Mutation ; Operator Regions, Genetic ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Repressor Proteins/*chemistry/genetics/metabolism ; Tetracycline/*chemistry/metabolism ; *Tetracycline Resistance/genetics
    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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  • 13
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    Molecule makers learn the rules of a crooked game (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Flam, F -- New York, N.Y. -- Science. 1994 Mar 18;263(5153):1563-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8128241" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Models, Molecular ; Protein Conformation ; *Protein Engineering ; *Protein Folding ; Protein Structure, Secondary
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  • 14
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    Coupling of local folding to site-specific binding of proteins to DNA (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-02-11
    Description: Thermodynamic studies have demonstrated the central importance of a large negative heat capacity change (delta C degree assoc) in site-specific protein-DNA recognition. Dissection of the large negative delta C degree assoc and the entropy change of protein-ligand and protein-DNA complexation provide a thermodynamic signature identifying processes in which local folding is coupled to binding. Estimates of the number of residues that fold on binding obtained from this analysis agree with structural data. Structural comparisons indicate that these local folding transitions create key parts of the protein-DNA interface. The energetic implications of this "induced fit" model for DNA site recognition are considered.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spolar, R S -- Record, M T Jr -- GM23467/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Feb 11;263(5148):777-84.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Wisconsin-Madison 53706.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8303294" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; *Protein Folding ; Thermodynamics
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  • 15
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    Neutrophil activation by monomeric interleukin-8 (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-04-01
    Description: Interleukin-8 (IL-8), a pro-inflammatory protein, has been shown by nuclear magnetic resonance (NMR) and x-ray techniques to exist as a homodimer. An IL-8 analog was chemically synthesized, with the amide nitrogen of leucine-25 methylated to selectivity block formation of hydrogen bonds between monomers and thereby prevent dimerization. This analog was shown to be a monomer, as assessed by analytical ultracentrifugation and NMR. Nevertheless, it was equivalent to IL-8 in assays of neutrophil activation, which indicates that the monomer is a functional form of IL-8.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rajarathnam, K -- Sykes, B D -- Kay, C M -- Dewald, B -- Geiser, T -- Baggiolini, M -- Clark-Lewis, I -- New York, N.Y. -- Science. 1994 Apr 1;264(5155):90-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Protein Engineering Network of Centres of Excellence (PENCE), University of Alberta, Edmonton, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8140420" target="_blank"〉PubMed〈/a〉
    Keywords: Calcium/metabolism ; Chemotaxis, Leukocyte ; Humans ; Hydrogen Bonding ; Interleukin-8/analogs & derivatives/chemistry/metabolism/*pharmacology ; Leukocyte Elastase ; Models, Chemical ; Neutrophils/drug effects/*physiology ; Pancreatic Elastase/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Interleukin/chemistry/metabolism ; Receptors, Interleukin-8A
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  • 16
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    Crystal structure of P22 tailspike protein: interdigitated subunits in a thermostable trimer (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-07-15
    Description: The tailspike protein (TSP) of Salmonella typhimurium phage P22 is a part of the apparatus by which the phage attaches to the bacterial host and hydrolyzes the O antigen. It has served as a model system for genetic and biochemical analysis of protein folding. The x-ray structure of a shortened TSP (residues 109 to 666) was determined to a 2.0 angstrom resolution. Each subunit of the homotrimer contains a large parallel beta helix. The interdigitation of the polypeptide chains at the carboxyl termini is important to protrimer formation in the folding pathway and to thermostability of the mature protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Steinbacher, S -- Seckler, R -- Miller, S -- Steipe, B -- Huber, R -- Reinemer, P -- New York, N.Y. -- Science. 1994 Jul 15;265(5170):383-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Biochemie, Abteilung Strukturforschung, Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8023158" target="_blank"〉PubMed〈/a〉
    Keywords: *Bacteriophage P22 ; Computer Graphics ; Crystallization ; Crystallography, X-Ray ; Glycoside Hydrolases/*chemistry/genetics ; Models, Molecular ; Point Mutation ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Viral Proteins/*chemistry/genetics ; *Viral Tail Proteins
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  • 17
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    Structure of the equine infectious anemia virus Tat protein (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-06-10
    Description: Trans-activator (Tat) proteins regulate the transcription of lentiviral DNA in the host cell genome. These RNA binding proteins participate in the life cycle of all known lentiviruses, such as the human immunodeficiency viruses (HIV) or the equine infectious anemia virus (EIAV). The consensus RNA binding motifs [the trans-activation responsive element (TAR)] of HIV-1 as well as EIAV Tat proteins are well characterized. The structure of the 75-amino acid EIAV Tat protein in solution was determined by two- and three-dimensional nuclear magnetic resonance methods and molecular dynamics calculations. The protein structure exhibits a well-defined hydrophobic core of 15 amino acids that serves as a scaffold for two flexible domains corresponding to the NH2- and COOH-terminal regions. The core region is a strictly conserved sequence region among the known Tat proteins. The structural data can be used to explain several of the observed features of Tat proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Willbold, D -- Rosin-Arbesfeld, R -- Sticht, H -- Frank, R -- Rosch, P -- New York, N.Y. -- Science. 1994 Jun 10;264(5165):1584-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lehrstuhl fur Biopolymere, Universitat Bayreuth, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7515512" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Gene Products, tat/*chemistry/metabolism ; Infectious Anemia Virus, Equine/*chemistry ; Magnetic Resonance Spectroscopy ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; RNA/metabolism ; Sequence Alignment
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  • 18
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    Design of a G.C-specific DNA minor groove-binding peptide (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-10-28
    Description: A four-ring tripeptide containing alternating imidazole and pyrrole carboxamides specifically binds six-base pair 5'-(A,T)GCGC(A,T)-3' sites in the minor groove of DNA. The designed peptide has a specificity completely reversed from that of the tripyrrole distamycin, which binds A,T sequences. Structural studies with nuclear magnetic resonance revealed that two peptides bound side-by-side and in an antiparallel orientation in the minor groove. Each of the four imidazoles in the 2:1 ligand-DNA complex recognized a specific guanine amino group in the GCGC core through a hydrogen bond. Targeting a designated four-base pair G.C tract by this synthetic ligand supports the generality of the 2:1 peptide-DNA motif for sequence-specific minor groove recognition of DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Geierstanger, B H -- Mrksich, M -- Dervan, P B -- Wemmer, D E -- GM-27681/GM/NIGMS NIH HHS/ -- GM-43129/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Oct 28;266(5185):646-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Group in Biophysics, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939719" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Computer Graphics ; DNA/chemistry/*metabolism ; Drug Design ; Hydrogen Bonding ; Imidazoles/chemical synthesis/*chemistry/metabolism ; Ligands ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; Oligopeptides/chemical synthesis/*chemistry/metabolism ; Protein Conformation ; Pyrroles/chemical synthesis/*chemistry/metabolism
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  • 19
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    Crystal structure of the principal neutralization site of HIV-1 (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-04-01
    Description: The crystal structure of a complex between a 24-amino acid peptide from the third variable (V3) loop of human immunodeficiency virus-type 1 (HIV-1) gp 120 and the Fab fragment of a broadly neutralizing antibody (59.1) was determined to 3 angstrom resolution. The tip of the V3 loop containing the Gly-Pro-Gly-Arg-Ala-Phe sequence adopts a double-turn conformation, which may be the basis of its conservation in many HIV-1 isolates. A complete map of the HIV-1 principal neutralizing determinant was constructed by stitching together structures of V3 loop peptides bound to 59.1 and to an isolate-specific (MN) neutralizing antibody (50.1). Structural conservation of the overlapping epitopes suggests that this biologically relevant conformation could be of use in the design of synthetic vaccines and drugs to inhibit HIV-1 entry and virus-related cellular fusion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ghiara, J B -- Stura, E A -- Stanfield, R L -- Profy, A T -- Wilson, I A -- GM-46192/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Apr 1;264(5155):82-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7511253" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/immunology ; Antigen-Antibody Complex/*chemistry/immunology ; Antigen-Antibody Reactions ; Computer Graphics ; Crystallography, X-Ray ; Epitopes/chemistry/immunology ; HIV Antibodies/*chemistry/immunology ; HIV Envelope Protein gp120/*chemistry/immunology ; HIV-1/*chemistry/immunology ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/*chemistry/immunology ; Models, Molecular ; Molecular Sequence Data ; Neutralization Tests ; Peptide Fragments/*chemistry/immunology ; Protein Conformation ; Protein Structure, Secondary
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  • 20
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    Crystal structure of a catalytic antibody with a serine protease active site (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-08-19
    Description: The three-dimensional structure of an unusually active hydrolytic antibody with a phosphonate transition state analog (hapten) bound to the active site has been solved to 2.5 A resolution. The antibody (17E8) catalyzes the hydrolysis of norleucine and methionine phenyl esters and is selective for amino acid esters that have the natural alpha-carbon L configuration. A plot of the pH-dependence of the antibody-catalyzed reaction is bell-shaped with an activity maximum at pH 9.5; experiments on mechanism lend support to the formation of a covalent acyl-antibody intermediate. The structural and kinetic data are complementary and support a hydrolytic mechanism for the antibody that is remarkably similar to that of the serine proteases. The antibody active site contains a Ser-His dyad structure proximal to the phosphorous atom of the bound hapten that resembles two of the three components of the Ser-His-Asp catalytic triad of serine proteases. The antibody active site also contains a Lys residue to stabilize oxyanion formation, and a hydrophobic binding pocket for specific substrate recognition of norleucine and methionine side chains. The structure identifies active site residues that mediate catalysis and suggests specific mutations that may improve the catalytic efficiency of the antibody. This high resolution structure of a catalytic antibody-hapten complex shows that antibodies can converge on active site structures that have arisen through natural enzyme evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, G W -- Guo, J -- Huang, W -- Fletterick, R J -- Scanlan, T S -- DK39304/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1994 Aug 19;265(5175):1059-64.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8066444" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Catalytic/*chemistry/immunology/metabolism ; Binding Sites ; Computer Graphics ; Crystallization ; Crystallography, X-Ray ; Haptens/metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrolysis ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Serine Endopeptidases/*chemistry/metabolism
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  • 21
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    An all D-amino acid opioid peptide with central analgesic activity from a combinatorial library (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-12-23
    Description: A synthetic combinatorial library containing 52,128,400 D-amino acid hexapeptides was used to identify a ligand for the mu opioid receptor. The peptide, Ac-rfwink-NH2, bears no resemblance to any known opioid peptide. Simulations using molecular dynamics, however, showed that three amino acid moieties have the same spatial orientation as the corresponding pharmacophoric groups of the opioid peptide PLO17. Ac-rfwink-NH2 was shown to be a potent agonist at the mu receptor and induced long-lasting analgesia in mice. Analgesia produced by intraperitoneally administered Ac-rfwink-NH2 was blocked by intracerebroventricular administration of naloxone, demonstrating that this peptide may cross the blood-brain barrier.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dooley, C T -- Chung, N N -- Wilkes, B C -- Schiller, P W -- Bidlack, J M -- Pasternak, G W -- Houghten, R A -- DA-000138/DA/NIDA NIH HHS/ -- DA-02615/DA/NIDA NIH HHS/ -- DA-03742/DA/NIDA NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1994 Dec 23;266(5193):2019-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Torrey Pines Institute for Molecular Studies, San Diego, CA 92121.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7801131" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Analgesics/chemistry/metabolism/*pharmacology ; Animals ; Brain/metabolism ; Dose-Response Relationship, Drug ; Endorphins/pharmacology ; Enkephalin, Ala(2)-MePhe(4)-Gly(5)- ; Enkephalin, D-Penicillamine (2,5)- ; Enkephalins/metabolism ; Guinea Pigs ; Injections, Intraventricular ; Male ; Mice ; Models, Molecular ; Molecular Sequence Data ; Naloxone/administration & dosage/pharmacology ; Opioid Peptides/chemistry/metabolism/*pharmacology ; Pain Measurement ; Protein Conformation ; Rats ; Receptors, Opioid, mu/agonists/metabolism ; Stereoisomerism
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  • 22
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    How a protein binds B12: A 3.0 A X-ray structure of B12-binding domains of methionine synthase (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-12-09
    Description: The crystal structure of a 27-kilodalton methylcobalamin-containing fragment of methionine synthase from Escherichia coli was determined at 3.0 A resolution. This structure depicts cobalamin-protein interactions and reveals that the corrin macrocycle lies between a helical amino-terminal domain and an alpha/beta carboxyl-terminal domain that is a variant of the Rossmann fold. Methylcobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in the adenosylcobalamin-dependent enzymes methylmalonyl-coenzyme A mutase and glutamate mutase, suggesting that displacement of the dimethylbenzimidazole will be a feature common to many cobalamin-binding proteins. Thus the cobalt ligand, His759, and the neighboring residues Asp757 and Ser810, may form a catalytic quartet, Co-His-Asp-Ser, that modulates the reactivity of the B12 prosthetic group in methionine synthase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Drennan, C L -- Huang, S -- Drummond, J T -- Matthews, R G -- Lidwig, M L -- GM08570/GM/NIGMS NIH HHS/ -- GM16429/GM/NIGMS NIH HHS/ -- GM24908/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1994 Dec 9;266(5191):1669-74.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Research Division, University of Michigan, Ann Arbor 48109-1055.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7992050" target="_blank"〉PubMed〈/a〉
    Keywords: 5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase/*chemistry/metabolism ; Amino Acid Isomerases/chemistry ; Amino Acid Sequence ; Benzimidazoles ; Catalysis ; Computer Graphics ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Escherichia coli/*enzymology ; Histidine/metabolism ; *Intramolecular Transferases ; Ligands ; Methylation ; Methylmalonyl-CoA Mutase/chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Vitamin B 12/*analogs & derivatives/chemistry/metabolism
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  • 23
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    Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-01-21
    Description: The structure of the 52-amino acid DNA-binding domain of the prokaryotic Hin recombinase, complexed with a DNA recombination half-site, has been solved by x-ray crystallography at 2.3 angstrom resolution. The Hin domain consists of a three-alpha-helix bundle, with the carboxyl-terminal helix inserted into the major groove of DNA, and two flanking extended polypeptide chains that contact bases in the minor groove. The overall structure displays features resembling both a prototypical bacterial helix-turn-helix and the eukaryotic homeodomain, and in many respects is an intermediate between these two DNA-binding motifs. In addition, a new structural motif is seen: the six-amino acid carboxyl-terminal peptide of the Hin domain runs along the minor groove at the edge of the recombination site, with the peptide backbone facing the floor of the groove and side chains extending away toward the exterior. The x-ray structure provides an almost complete explanation for DNA mutant binding studies in the Hin system and for DNA specificity observed in the Hin-related family of DNA invertases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feng, J A -- Johnson, R C -- Dickerson, R E -- GM-31299/GM/NIGMS NIH HHS/ -- GM-38509/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Jan 21;263(5145):348-55.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology Institute, University of California, Los Angeles 90024.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8278807" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Composition ; Base Sequence ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA Nucleotidyltransferases/chemistry/*metabolism ; Helix-Loop-Helix Motifs ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; *Recombination, Genetic
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  • 24
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    Toxic shock syndrome toxin-1 complexed with a class II major histocompatibility molecule HLA-DR1 (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-12-16
    Description: The three-dimensional structure of a Staphylococcus aureus superantigen, toxic shock syndrome toxin-1 (TSST-1), complexed with a human class II major histocompatibility molecule (DR1), was determined by x-ray crystallography. The TSST-1 binding site on DR1 overlaps that of the superantigen S. aureus enterotoxin B (SEB), but the two binding modes differ. Whereas SEB binds primarily off one edge of the peptide binding site of DR1, TSST-1 extends over almost one-half of the binding site and contacts both the flanking alpha helices of the histocompatibility antigen and the bound peptide. This difference suggests that the T cell receptor (TCR) would bind to TSST-1:DR1 very differently than to DR1:peptide or SEB:DR1. It also suggests that TSST-1 binding may be dependent on the peptide, though less so than TCR binding, providing a possible explanation for the inability of TSST-1 to competitively block SEB binding to all DR1 molecules on cells (even though the binding sites of TSST-1 and SEB on DR1 overlap almost completely) and suggesting the possibility that T cell activation by superantigen could be directed by peptide antigen.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, J -- Urban, R G -- Strominger, J L -- Wiley, D C -- New York, N.Y. -- Science. 1994 Dec 16;266(5192):1870-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Children's Hospital, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7997880" target="_blank"〉PubMed〈/a〉
    Keywords: *Bacterial Toxins ; Binding Sites ; Crystallography, X-Ray ; Enterotoxins/*chemistry/metabolism ; HLA-DR1 Antigen/*chemistry/metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell/metabolism ; *Staphylococcus aureus ; Superantigens/*chemistry/metabolism
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  • 25
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    A unified polymerase mechanism for nonhomologous DNA and RNA polymerases (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-12-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Steitz, T A -- Smerdon, S J -- Jager, J -- Joyce, C M -- GM28550/GM/NIGMS NIH HHS/ -- GM39546/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Dec 23;266(5193):2022-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7528445" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA Polymerase I/*chemistry/metabolism ; DNA-Directed RNA Polymerases/*chemistry/metabolism ; HIV Reverse Transcriptase ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; RNA-Directed DNA Polymerase/*chemistry/metabolism ; Viral Proteins
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  • 26
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    The mobile flavin of 4-OH benzoate hydroxylase (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-10-07
    Description: Para-hydroxybenzoate hydroxylase inserts oxygen into substrates by means of the labile intermediate, flavin C(4a)-hydroperoxide. This reaction requires transient isolation of the flavin and substrate from the bulk solvent. Previous crystal structures have revealed the position of the substrate para-hydroxybenzoate during oxygenation but not how it enters the active site. In this study, enzyme structures with the flavin ring displaced relative to the protein were determined, and it was established that these or similar flavin conformations also occur in solution. Movement of the flavin appears to be essential for the translocation of substrates and products into the solvent-shielded active site during catalysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gatti, D L -- Palfey, B A -- Lah, M S -- Entsch, B -- Massey, V -- Ballou, D P -- Ludwig, M L -- GM 11106/GM/NIGMS NIH HHS/ -- GM 16429/GM/NIGMS NIH HHS/ -- GM 20877/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1994 Oct 7;266(5182):110-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, University of Michigan, Ann Arbor 48109.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939628" target="_blank"〉PubMed〈/a〉
    Keywords: Benzoate 4-Monooxygenase ; Binding Sites ; Catalysis ; Computer Graphics ; Flavin-Adenine Dinucleotide/chemistry/metabolism ; Flavins/*chemistry/metabolism ; Hydrogen Bonding ; Mixed Function Oxygenases/*chemistry/metabolism ; Models, Molecular ; Molecular Conformation ; Oxidation-Reduction ; Parabens/metabolism ; Protein Conformation
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  • 27
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    Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-11
    Description: Crystal structures of seryl-tRNA synthetase from Thermus thermophilus complexed with two different analogs of seryl adenylate have been determined at 2.5 A resolution. The first complex is between the enzyme and seryl-hydroxamate-AMP (adenosine monophosphate), produced enzymatically in the crystal from adenosine triphosphate (ATP) and serine hydroxamate, and the second is with a synthetic analog of seryl adenylate (5'-O-[N-(L-seryl)-sulfamoyl]adenosine), which is a strong inhibitor of the enzyme. Both molecules are bound in a similar fashion by a network of hydrogen bond interactions in a deep hydrophilic cleft formed by the antiparallel beta sheet and surrounding loops of the synthetase catalytic domain. Four regions in the primary sequence are involved in the interactions, including the motif 2 and 3 regions of class 2 synthetases. Apart from the specific recognition of the serine side chain, the interactions are likely to be similar in all class 2 synthetases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Belrhali, H -- Yaremchuk, A -- Tukalo, M -- Larsen, K -- Berthet-Colominas, C -- Leberman, R -- Beijer, B -- Sproat, B -- Als-Nielsen, J -- Grubel, G -- New York, N.Y. -- Science. 1994 Mar 11;263(5152):1432-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉EMBL Grenoble Outstation, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8128224" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/*analogs & derivatives/chemical synthesis/metabolism ; Adenosine Monophosphate/*analogs & derivatives/chemical synthesis/metabolism ; Amino Acid Sequence ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Sequence Alignment ; Serine/*analogs & derivatives/chemical synthesis/metabolism ; Serine-tRNA Ligase/*chemistry/metabolism ; Thermus thermophilus/*enzymology
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    Nanosecond dynamics of the R--〉T transition in hemoglobin: ultraviolet Raman studies (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-09-16
    Description: Pulse-probe transient Raman spectroscopy, with probe excitation at 230 nanometers, reveals changes in signals arising from tyrosine and tryptophan residues of the hemoglobin molecule as it moves from the relaxed (R) to the tense (T) state after photodeligation. Signals associated with intersubunit contacts in the T state develop in about 10 microseconds but are preceded by quite different signals, which reach maximum amplitude in about 50 nanoseconds. These signals involve the interior tryptophan residues that bridge the A and E helices by means of H bonds between the indole rings and serine or threonine side chains. Alterations of the H bond strengths, as a result of interhelix motions, can account for the signals. A model is proposed here in which loss of the ligand from the heme binding pocket is concerted with inward motion of the adjacent E helix; this motion, along with a complementary motion of the proximal F helix, transmits the energy associated with heme deligation to the subunit interfaces, leading to the T state rearrangement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rodgers, K R -- Spiro, T G -- GM 25158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Sep 16;265(5179):1697-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, North Dakota State University, Fargo 58105.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8085153" target="_blank"〉PubMed〈/a〉
    Keywords: Carboxyhemoglobin/chemistry ; Heme/chemistry ; Hemoglobins/*chemistry ; Hydrogen Bonding ; Protein Conformation ; Protein Structure, Secondary ; Spectrum Analysis, Raman
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    The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser) (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-11
    Description: The crystal structure of Thermus thermophilus seryl-transfer RNA synthetase, a class 2 aminoacyl-tRNA synthetase, complexed with a single tRNA(Ser) molecule was solved at 2.9 A resolution. The structure revealed how insertion of conserved base G20b from the D loop into the core of the tRNA determines the orientation of the long variable arm, which is a characteristic feature of most serine specific tRNAs. On tRNA binding, the antiparallel coiled-coil domain of one subunit of the synthetase makes contacts with the variable arm and T psi C loop of the tRNA and directs the acceptor stem of the tRNA into the active site of the other subunit. Specificity depends principally on recognition of the shape of tRNA(Ser) through backbone contacts and secondarily on sequence specific interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Biou, V -- Yaremchuk, A -- Tukalo, M -- Cusack, S -- New York, N.Y. -- Science. 1994 Mar 11;263(5152):1404-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Grenoble Outstation, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8128220" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Base Composition ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; RNA, Transfer, Amino Acyl/*chemistry/metabolism ; Serine-tRNA Ligase/*chemistry/metabolism ; Substrate Specificity ; Thermus thermophilus/*enzymology
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    High-resolution solution structure of the beta chemokine hMIP-1 beta by multidimensional NMR (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-25
    Description: The three-dimensional structure of a member of the beta subfamily of chemokines, human macrophage inflammatory protein-1 beta (hMIP-1 beta), has been determined with the use of solution multidimensional heteronuclear magnetic resonance spectroscopy. Human MIP-1 beta is a symmetric homodimer with a relative molecular mass of approximately 16 kilodaltons. The structure of the hMIP-1 beta monomer is similar to that of the related alpha chemokine interleukin-8 (IL-8). However, the quaternary structures of the two proteins are entirely distinct, and the dimer interface is formed by a completely different set of residues. Whereas the IL-8 dimer is globular, the hMIP-1 beta dimer is elongated and cylindrical. This provides a rational explanation for the absence of cross-binding and reactivity between the alpha and beta chemokine subfamilies. Calculation of the solvation free energies of dimerization suggests that the formation and stabilization of the two different types of dimers arise from the burial of hydrophobic residues.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lodi, P J -- Garrett, D S -- Kuszewski, J -- Tsang, M L -- Weatherbee, J A -- Leonard, W J -- Gronenborn, A M -- Clore, G M -- New York, N.Y. -- Science. 1994 Mar 25;263(5154):1762-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8134838" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chemokine CCL4 ; Computer Graphics ; Cytokines/*chemistry ; Humans ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Interleukin-8/chemistry ; Macrophage Inflammatory Proteins ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Monokines/*chemistry ; Protein Conformation ; Protein Structure, Secondary ; Sequence Alignment
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    Synthesis of proteins by native chemical ligation (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-11-04
    Description: A simple technique has been devised that allows the direct synthesis of native backbone proteins of moderate size. Chemoselective reaction of two unprotected peptide segments gives an initial thioester-linked species. Spontaneous rearrangement of this transient intermediate yields a full-length product with a native peptide bond at the ligation site. The utility of native chemical ligation was demonstrated by the one-step preparation of a cytokine containing multiple disulfides. The polypeptide ligation product was folded and oxidized to form the native disulfide-containing protein molecule. Native chemical ligation is an important step toward the general application of chemistry to proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dawson, P E -- Muir, T W -- Clark-Lewis, I -- Kent, S B -- GM 50969-01/GM/NIGMS NIH HHS/ -- GM48870-03/GM/NIGMS NIH HHS/ -- GM48897-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Nov 4;266(5186):776-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7973629" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Humans ; Interleukin-8/*chemical synthesis/chemistry ; Molecular Sequence Data ; Oxidation-Reduction ; Protein Conformation ; *Protein Folding ; Proteins/*chemical synthesis/chemistry
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    Discontinuous mechanism of transcription elongation (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-08-05
    Description: During transcription elongation, three flexibly connected parts of RNA polymerase of Escherichia coli advance along the template so that the front-end domain is followed by the catalytic site which in turn is followed by the RNA product binding site. The advancing enzyme was found to maintain the same conformation throughout extended segments of the transcribed region. However, when the polymerase traveled across certain DNA sites that seemed to briefly anchor the front-end domain, cyclic shifting of the three parts, accompanied by buildup and relief of internal strain, was observed. Thus, elongation proceeded in alternating laps of monotonous and inchworm-like movement with the flexible RNA polymerase configuration being subject to direct sequence control.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nudler, E -- Goldfarb, A -- Kashlev, M -- GM49242/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Aug 5;265(5173):793-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Public Health Research Institute, New York, NY 10016.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8047884" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; DNA-Directed RNA Polymerases/*metabolism ; *Escherichia coli Proteins ; *Models, Genetic ; Molecular Sequence Data ; Movement ; Peptide Elongation Factors/metabolism ; Protein Conformation ; RNA, Messenger/metabolism ; RNA-Binding Proteins/metabolism ; Templates, Genetic ; Transcription Factors/metabolism ; Transcription, Genetic/*physiology ; Transcriptional Elongation Factors
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    New enzyme structure reveals cell's rotary engine (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-08-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Brien, C -- New York, N.Y. -- Science. 1994 Aug 26;265(5176):1176-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8066459" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/biosynthesis ; Crystallization ; Crystallography, X-Ray ; Intracellular Membranes/enzymology ; Mitochondria/enzymology ; Models, Molecular ; Protein Conformation ; Proton-Translocating ATPases/*chemistry/metabolism ; Protons
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    Parallel computing in biomedical research (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-08-12
    Description: Scalable parallel computer architectures provide the computational performance needed for advanced biomedical computing problems. The National Institutes of Health have developed a number of parallel algorithms and techniques useful in determining biological structure and function. These applications include processing electron micrographs to determine the three-dimensional structure of viruses, calculating the solvent-accessible surface area of proteins to help predict the three-dimensional conformation of these molecules from their primary structures, and searching for homologous DNA or amino acid sequences in large biological databases. Timing results demonstrate substantial performance improvements with parallel implementations compared with conventional sequential systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martino, R L -- Johnson, C A -- Suh, E B -- Trus, B L -- Yap, T K -- New York, N.Y. -- Science. 1994 Aug 12;265(5174):902-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computational Bioscience and Engineering Laboratory, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8052847" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Capsid/ultrastructure ; *Computer Simulation ; *Computers ; Databases, Factual ; Image Processing, Computer-Assisted ; National Institutes of Health (U.S.) ; Protein Conformation ; Protein Folding ; *Research ; Sequence Homology, Nucleic Acid ; Simplexvirus/ultrastructure ; Tomography, Emission-Computed ; United States
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    Taking a first look at a tyrosine phosphatase (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-03-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J -- New York, N.Y. -- Science. 1994 Mar 11;263(5152):1373.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8128216" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Phosphates/metabolism ; Protein Conformation ; Protein Folding ; Protein Tyrosine Phosphatases/*chemistry/metabolism ; Tungsten Compounds/metabolism
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    Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-11-18
    Description: Solution structures of two Src homology 3 (SH3) domain-ligand complexes have been determined by nuclear magnetic resonance. Each complex consists of the SH3 domain and a nine-residue proline-rich peptide selected from a large library of ligands prepared by combinatorial synthesis. The bound ligands adopt a left-handed polyproline type II (PPII) helix, although the amino to carboxyl directionalities of their helices are opposite. The peptide orientation is determined by a salt bridge formed by the terminal arginine residues of the ligands and the conserved aspartate-99 of the SH3 domain. Residues at positions 3, 4, 6, and 7 of both peptides also intercalate into the ligand-binding site; however, the respective proline and nonproline residues show exchanged binding positions in the two complexes. These structural results led to a model for the interactions of SH3 domains with proline-rich peptides that can be used to predict critical residues in complexes of unknown structure. The model was used to identify correctly both the binding orientation and the contact and noncontact residues of a peptide derived from the nucleotide exchange factor Sos in association with the amino-terminal SH3 domain of the adaptor protein Grb2.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feng, S -- Chen, J K -- Yu, H -- Simon, J A -- Schreiber, S L -- GM44993/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Nov 18;266(5188):1241-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7526465" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptor Proteins, Signal Transducing ; Alanine/chemistry ; Amino Acid Sequence ; Arginine/chemistry ; Binding Sites ; GRB2 Adaptor Protein ; Glycine/chemistry ; Guanine Nucleotide Exchange Factors ; Ligands ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Oligopeptides/chemistry/*metabolism ; Peptides/chemistry/metabolism ; Proline/chemistry ; Proline-Rich Protein Domains ; Protein Conformation ; Protein Structure, Secondary ; Protein-Tyrosine Kinases/chemistry/*metabolism ; Proteins/chemistry/metabolism ; Proto-Oncogene Proteins pp60(c-src)/chemistry/*metabolism ; src-Family Kinases
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    Three-dimensional structure of dimeric human recombinant macrophage colony-stimulating factor (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-11-20
    Description: Macrophage colony-stimulating factor (M-CSF) triggers the development of cells of the monocyte-macrophage lineage and has a variety of stimulatory effects on mature cells of this class. The biologically active form of M-CSF is a disulfide-linked dimer that activates an intrinsic tyrosine kinase activity on the M-CSF receptor by inducing dimerization of the receptor molecules. The structure of a recombinant human M-CSF dimer, determined at 2.5 angstroms by x-ray crystallography, contains two bundles of four alpha helices laid end-to-end, with an interchain disulfide bond. Individual monomers of M-CSF show a close structural similarity to the cytokines granulocyte-macrophage colony-stimulating factor and human growth hormone. Both of these cytokines are monomeric in their active form, and their specific receptors lack intrinsic tyrosine kinase activity. The similarity of these structures suggests that the receptor binding determinants for all three cytokines may be similar.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pandit, J -- Bohm, A -- Jancarik, J -- Halenbeck, R -- Koths, K -- Kim, S H -- New York, N.Y. -- Science. 1992 Nov 20;258(5086):1358-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1455231" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography ; Disulfides ; Granulocyte-Macrophage Colony-Stimulating Factor/ultrastructure ; Growth Hormone/chemistry ; Macrophage Colony-Stimulating Factor/*ultrastructure ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/ultrastructure ; Sequence Homology, Amino Acid ; X-Ray Diffraction
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    Nucleotide-iron-sulfur cluster signal transduction in the nitrogenase iron-protein: the role of Asp125 (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-11-06
    Description: Electron transfer in nitrogenase involves a gating process initiated by MgATP (magnesium adenosine triphosphate) binding to Fe-protein. The redox site, an 4Fe:4S cluster, is structurally separated from the MgATP binding site. For MgATP hydrolysis to be coupled to electron transfer, a signal transduction mechanism is proposed that is similar to that in guanosine triphosphatase proteins. Based on the three-dimensional structure of Fe-protein, Asp125 is likely to be part of a putative transduction path. Altered Fe-protein with Glu replacing Asp has been prepared and retains the ability for the initial nucleotide-dependent conformational change. However, either MgADP or MgATP can induce the shift and Mg binding to the nucleotide is no longer essential.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wolle, D -- Dean, D R -- Howard, J B -- New York, N.Y. -- Science. 1992 Nov 6;258(5084):992-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Minnesota, Minneapolis 55455.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1359643" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/*metabolism ; Aspartic Acid/*metabolism ; Azotobacter vinelandii/enzymology ; Binding Sites ; Crystallization ; Electron Transport ; Glutamates ; Glutamic Acid ; Iron-Sulfur Proteins/*metabolism ; Molecular Structure ; Mutagenesis, Site-Directed ; Nitrogenase/chemistry/genetics/*metabolism ; Protein Conformation ; Signal Transduction/*physiology
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    Predicted structural similarities of the DNA binding domains of c-Myc and endonuclease Eco RI (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-24
    Description: The c-Myc oncoprotein belongs to a family of proteins whose DNA binding domains contain a basic region-helix-loop-helix (bHLH) motif. Systematic mutagenesis of c-Myc revealed that dimerized bHLH motifs formed a parallel four-helix bundle with the amino termini of helices 1 and 2 directed toward the inner and outer nucleotides of the DNA binding site, respectively. Both the basic region and the carboxyl-terminal end of the loop contributed to DNA binding specificity. The DNA binding domain of c-Myc may therefore be structurally similar to that of restriction endonuclease Eco RI.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Halazonetis, T D -- Kandil, A N -- New York, N.Y. -- Science. 1992 Jan 24;255(5043):464-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cancer Research, Merck Sharp and Dohme Research Laboratories, West Point, PA 19486.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1734524" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; DNA-Binding Proteins/*chemistry ; Deoxyribonuclease EcoRI/*chemistry ; Humans ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Proto-Oncogene Proteins c-myc/*chemistry ; Sequence Alignment ; Transcription Factors/chemistry
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    Converting trypsin to chymotrypsin: the role of surface loops (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-03-06
    Description: Trypsin (Tr) and chymotrypsin (Ch) have similar tertiary structures, yet Tr cleaves peptides at arginine and lysine residues and Ch prefers large hydrophobic residues. Although replacement of the S1 binding site of Tr with the analogous residues of Ch is sufficient to transfer Ch specificity for ester hydrolysis, specificity for amide hydrolysis is not transferred. Trypsin is converted to a Ch-like protease when the binding pocket alterations are further modified by exchange of the Ch surface loops 185 through 188 and 221 through 225 for the analogous Tr loops. These loops are not structural components of either the S1 binding site or the extended substrate binding sites. This mutant enzyme is equivalent to Ch in its catalytic rate, but its substrate binding is impaired. Like Ch, this mutant utilizes extended substrate binding to accelerate catalysis, and substrate discrimination occurs during the acylation step rather than in substrate binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hedstrom, L -- Szilagyi, L -- Rutter, W J -- DK21344/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 Mar 6;255(5049):1249-53.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hormone Research Institute, University of California, San Francisco 94143-0534.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1546324" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Chymotrypsin/*chemistry/metabolism ; Hydrolysis ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Mutagenesis, Site-Directed ; Protein Conformation ; Substrate Specificity ; Trypsin/*chemistry/genetics/metabolism
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    Interaction cloning: identification of a helix-loop-helix zipper protein that interacts with c-Fos (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-05-15
    Description: A facile method for isolating genes that encode interacting proteins has been developed with a polypeptide probe that contains an amino-terminal extension with recognition sites for a monoclonal antibody, a specific endopeptidase, and a site-specific protein kinase. This probe, containing the basic region-leucine zipper dimerization motif of c-Fos, was used to screen a complementary DNA library. A complementary DNA that encoded a member of the basic-helix-loop-helix-zipper (bHLH-Zip) family of proteins was isolated. The complementary DNA-encoded polypeptide FIP (Fos interacting protein) bound to oligonucleotide probes that contained DNA binding motifs for other HLH proteins. When cotransfected with c-Fos, FIP stimulated transcription of an AP-1-responsive promoter.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blanar, M A -- Rutter, W J -- DK-21344/DK/NIDDK NIH HHS/ -- DK-41822/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 May 15;256(5059):1014-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hormone Research Institute, University of California, San Francisco 94143.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1589769" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; *Cloning, Molecular ; DNA/isolation & purification ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; *Genes, fos/genetics ; HeLa Cells ; Humans ; Leucine Zippers/*genetics ; Macromolecular Substances ; Molecular Sequence Data ; Oligonucleotide Probes/chemistry/metabolism ; Protein Conformation ; Proto-Oncogene Proteins c-fos/chemistry/metabolism ; Proto-Oncogene Proteins c-jun/chemistry/metabolism ; Sequence Homology, Nucleic Acid ; Transfection
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    Electron-tunneling pathways in proteins (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-12-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beratan, D N -- Onuchic, J N -- Winkler, J R -- Gray, H B -- New York, N.Y. -- Science. 1992 Dec 11;258(5089):1740-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Pittsburgh, PA 15260.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1334572" target="_blank"〉PubMed〈/a〉
    Keywords: Cytochrome c Group/*chemistry/metabolism ; Cytochrome-c Peroxidase/*chemistry/metabolism ; *Electron Transport ; Models, Molecular ; Photosynthesis ; Protein Conformation ; Proteins/*chemistry ; Saccharomyces cerevisiae/metabolism ; X-Ray Diffraction
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    On the other hand (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-06-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Petsko, G A -- New York, N.Y. -- Science. 1992 Jun 5;256(5062):1403-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1604313" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/chemistry ; Enzymes/*chemistry/metabolism ; *Functional Laterality ; HIV Protease/chemical synthesis/*chemistry ; Humans ; *Isomerism ; Protein Conformation
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  • 44
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    Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-10
    Description: Six "cavity-creating" mutants, Leu46----Ala (L46A), L99A, L118A, L121A, L133A, and Phe153----Ala (F153A), were constructed within the hydrophobic core of phage T4 lysozyme. The substitutions decreased the stability of the protein at pH 3.0 by different amounts, ranging from 2.7 kilocalories per mole (kcal mol-1) for L46A and L121A to 5.0 kcal mol-1 for L99A. The double mutant L99A/F153A was also constructed and decreased in stability by 8.3 kcal mol-1. The x-ray structures of all of the variants were determined at high resolution. In every case, removal of the wild-type side chain allowed some of the surrounding atoms to move toward the vacated space but a cavity always remained, which ranged in volume from 24 cubic angstroms (A3) for L46A to 150 A3 for L99A. No solvent molecules were observed in any of these cavities. The destabilization of the mutant Leu----Ala proteins relative to wild type can be approximated by a constant term (approximately 2.0 kcal mol-1) plus a term that increases in proportion to the size of the cavity. The constant term is approximately equal to the transfer free energy of leucine relative to alanine as determined from partitioning between aqueous and organic solvents. The energy term that increases with the size of the cavity can be expressed either in terms of the cavity volume (24 to 33 cal mol-1 A-3) or in terms of the cavity surface area (20 cal mol-1 A-2). The results suggest how to reconcile a number of conflicting reports concerning the strength of the hydrophobic effect in proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eriksson, A E -- Baase, W A -- Zhang, X J -- Heinz, D W -- Blaber, M -- Baldwin, E P -- Matthews, B W -- GM12989/GM/NIGMS NIH HHS/ -- GM13709/GM/NIGMS NIH HHS/ -- GM21967/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Jan 10;255(5041):178-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, Howard Hughes Medical Institute, Eugene, OR.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1553543" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Calorimetry ; Models, Molecular ; Molecular Sequence Data ; Muramidase/*chemistry/*genetics ; Mutagenesis, Site-Directed ; Protein Conformation ; Structure-Activity Relationship ; T-Phages/enzymology/genetics ; Thermodynamics ; X-Ray Diffraction
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  • 45
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    An unlikely sugar substrate site in the 1.65 A structure of the human aldose reductase holoenzyme implicated in diabetic complications (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-07-03
    Description: Aldose reductase, which catalyzes the reduced form of nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of a wide variety of aromatic and aliphatic carbonyl compounds, is implicated in the development of diabetic and galactosemic complications involving the lens, retina, nerves, and kidney. A 1.65 angstrom refined structure of a recombinant human placenta aldose reductase reveals that the enzyme contains a parallel beta 8/alpha 8-barrel motif and establishes a new motif for NADP-binding oxidoreductases. The substrate-binding site is located in a large, deep elliptical pocket at the COOH-terminal end of the beta barrel with a bound NADPH in an extended conformation. The highly hydrophobic nature of the active site pocket greatly favors aromatic and apolar substrates over highly polar monosaccharides. The structure should allow for the rational design of specific inhibitors that might provide molecular understanding of the catalytic mechanism, as well as possible therapeutic agents.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, D K -- Bohren, K M -- Gabbay, K H -- Quiocho, F A -- DK-39,044/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 Jul 3;257(5066):81-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1621098" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Reductase/*chemistry/metabolism ; Amino Acid Sequence ; Binding Sites ; *Diabetes Complications ; Diabetes Mellitus/*enzymology ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; X-Ray Diffraction/methods
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  • 46
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    Site-specific incorporation of novel backbone structures into proteins (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-10
    Description: A number of unnatural amino acids and amino acid analogs with modified backbone structures were substituted for alanine-82 in T4 lysozyme. Replacements included alpha,alpha-disubstituted amino acids, N-alkyl amino acids, and lactic acid, an isoelectronic analog of alanine. The effects of these electronic and structural perturbations on the stability of T4 lysozyme were determined. The relatively broad substrate specificity of the Escherichia coli protein biosynthetic machinery suggests that a wide range of backbone and side-chain substitutions can be introduced, allowing a more precise definition of the factors affecting protein stability.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ellman, J A -- Mendel, D -- Schultz, P G -- New York, N.Y. -- Science. 1992 Jan 10;255(5041):197-200.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1553546" target="_blank"〉PubMed〈/a〉
    Keywords: *Alanine ; Amino Acid Sequence ; *Amino Acids ; Circular Dichroism ; Codon ; Enzyme Stability ; Escherichia coli/enzymology/genetics ; Muramidase/*biosynthesis/*chemistry/genetics ; *Mutagenesis, Site-Directed ; Protein Conformation ; Structure-Activity Relationship ; Substrate Specificity ; T-Phages/enzymology
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  • 47
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    Interaction of p107 with cyclin A independent of complex formation with viral oncoproteins (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-03
    Description: The p107 protein and the retinoblastoma protein (RB) both bind specifically to two viral oncoproteins, the SV40 T antigen (T) and adenoviral protein E1A (E1A). Like RB, p107 contains a segment (the pocket) that, alone, can bind specifically to T, E1A, and multiple cellular proteins. Cyclin A bound to the p107 pocket, but not the RB pocket. Although both pockets contain two, related collinear subsegments (A and B), the unique sequence in the p107 pocket that occupies the space between A and B is required for the interaction with cyclin A.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ewen, M E -- Faha, B -- Harlow, E -- Livingston, D M -- New York, N.Y. -- Science. 1992 Jan 3;255(5040):85-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dana-Farber Cancer Institute, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1532457" target="_blank"〉PubMed〈/a〉
    Keywords: Adenovirus Early Proteins ; Amino Acid Sequence ; Antigens, Polyomavirus Transforming/*metabolism ; Base Sequence ; Binding Sites ; Cell Line ; Cloning, Molecular ; Cyclins/*metabolism ; Escherichia coli/genetics ; Eye Neoplasms ; Glutathione Transferase/genetics/metabolism ; Humans ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; *Nuclear Proteins ; Oligodeoxyribonucleotides ; Oncogene Proteins, Viral/genetics/*metabolism ; Protein Conformation ; Proteins/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Retinoblastoma ; Retinoblastoma Protein/genetics/*metabolism ; Retinoblastoma-Like Protein p107 ; Structure-Activity Relationship
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    Vacuolar chitinases of tobacco: a new class of hydroxyproline-containing proteins (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-08-10
    Description: The fungicidal type I chitinases contribute to the defense response of plants against pathogens. Two tobacco chitinases represent a different class of hydroxyproline-containing proteins. Hydroxyproline-rich proteins are predominantly extracellular, structural glycoproteins proteins that lack enzymatic activity and contain many hydroxyproline residues. In contrast, type I chitinases are vacuolar enzymes. They are not glycosylated and contain a small number of hydroxyproline residues restricted to a single, short peptide sequence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sticher, L -- Hofsteenge, J -- Milani, A -- Neuhaus, J M -- Meins, F Jr -- New York, N.Y. -- Science. 1992 Jul 31;257(5070):655-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Friedrich Miescher-Institut, Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1496378" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chitinase/*chemistry/metabolism ; Glycosylation ; Hydroxylation ; Hydroxyproline/*analysis ; Molecular Sequence Data ; Molecular Weight ; *Plants, Toxic ; Protein Conformation ; Tobacco/*enzymology/ultrastructure ; Vacuoles/*enzymology
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    Emerging principles for the recognition of peptide antigens by MHC class I molecules (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-08-14
    Description: Class I major histocompatibility complex (MHC) molecules interact with self and foreign peptides of diverse amino acid sequences yet exhibit distinct allele-specific selectivity for peptide binding. The structures of the peptide-binding specificity pockets (subsites) in the groove of murine H-2Kb as well as human histocompatibility antigen class I molecules have been analyzed. Deep but highly conserved pockets at each end of the groove bind the amino and carboxyl termini of peptide through extensive hydrogen bonding and, hence, dictate the orientation of peptide binding. A deep polymorphic pocket in the middle of the groove provides the chemical and structural complementarity for one of the peptide's anchor residues, thereby playing a major role in allele-specific peptide binding. Although one or two shallow pockets in the groove may also interact with specific peptide side chains, their role in the selection of peptide is minor. Thus, usage of a limited number of both deep and shallow pockets in multiple combinations appears to allow the binding of a broad range of peptides. This binding occurs with high affinity, primarily because of extensive interactions with the peptide backbone and the conserved hydrogen bonding network at both termini of the peptide. Interactions between the anchor residue (or residues) and the corresponding allele-specific pocket provide sufficient extra binding affinity not only to enhance specificity but also to endure the presentation of the peptide at the cell surface for recognition by T cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matsumura, M -- Fremont, D H -- Peterson, P A -- Wilson, I A -- CA-09523/CA/NCI NIH HHS/ -- CA-97489/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):927-34.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1323878" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antigens/chemistry/*metabolism ; Binding Sites ; H-2 Antigens/chemistry/*metabolism ; HLA-A2 Antigen/chemistry ; Histocompatibility Antigens Class I/chemistry/*metabolism ; Hydrogen Bonding ; Mice ; Models, Molecular ; Molecular Sequence Data ; Ovalbumin/chemistry/metabolism ; Peptide Fragments/chemistry/metabolism ; Peptides/chemistry/*metabolism ; Protein Conformation ; Solvents ; Vesicular stomatitis Indiana virus/metabolism ; Viral Proteins/chemistry/*metabolism
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    A conformation of cyclosporin A in aqueous environment revealed by the X-ray structure of a cyclosporin-Fab complex (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-03
    Description: The conformation of the immunosuppressive drug cyclosporin A (CsA) in a complex with a Fab molecule has been established by crystallographic analysis to 2.65 angstrom resolution. This conformation of CsA is similar to that recently observed in the complex with the rotamase cyclophilin, its binding protein in vivo, and totally different from its conformation in an isolated form as determined from x-ray and nuclear magnetic resonance analysis. Because the surfaces of CsA interacting with cyclophilin or with the Fab are not identical, these results suggest that the conformation of CsA observed in the bound form preexists in aqueous solution and is not produced by interaction with the proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Altschuh, D -- Vix, O -- Rees, B -- Thierry, J C -- New York, N.Y. -- Science. 1992 Apr 3;256(5053):92-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1566062" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Isomerases/chemistry/metabolism ; Amino Acid Sequence ; Carrier Proteins/chemistry/metabolism ; Cyclosporine/*chemistry/immunology/metabolism ; Immunoglobulin Fab Fragments/*chemistry/metabolism ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Peptidylprolyl Isomerase ; Protein Binding ; Protein Conformation ; Solutions ; X-Ray Diffraction/methods
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    Solution structure of the SH3 domain of Src and identification of its ligand-binding site (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-12-04
    Description: The Src homology 3 (SH3) region is a protein domain of 55 to 75 amino acids found in many cytoplasmic proteins, including those that participate in signal transduction pathways. The solution structure of the SH3 domain of the tyrosine kinase Src was determined by multidimensional nuclear magnetic resonance methods. The molecule is composed of two short three-stranded anti-parallel beta sheets packed together at approximately right angles. Studies of the SH3 domain bound to proline-rich peptide ligands revealed a hydrophobic binding site on the surface of the protein that is lined with the side chains of conserved aromatic amino acids.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, H -- Rosen, M K -- Shin, T B -- Seidel-Dugan, C -- Brugge, J S -- Schreiber, S L -- 1-S10-RR04870/RR/NCRR NIH HHS/ -- CA27951/CA/NCI NIH HHS/ -- GM44993/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Dec 4;258(5088):1665-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1280858" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Cloning, Molecular ; Escherichia coli/genetics ; Glutathione Transferase/chemistry/genetics/isolation & purification ; Ligands ; Magnetic Resonance Spectroscopy ; Molecular Sequence Data ; Neurons/physiology ; Protein Conformation ; *Protein Structure, Secondary ; Protein-Tyrosine Kinases/*genetics ; Proto-Oncogene Proteins pp60(c-src)/*chemistry ; Recombinant Fusion Proteins/chemistry/isolation & purification ; Solutions ; X-Ray Diffraction
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    A site on rod G protein alpha subunit that mediates effector activation (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-05-15
    Description: The heterotrimeric guanine nucleotide binding proteins (G proteins) are activated by sensory or hormone receptors. In turn, the G proteins activate effector proteins such as adenylyl cyclase, cyclic guanosine 3',5'-monophosphate phosphodiesterase (cGMP PDE), phospholipase C, and potassium and calcium ion channels by mechanisms that are poorly understood. A site on the alpha subunit of the G protein transducin (alpha t) has been identified that interacts with and activates cGMP phosphodiesterase, the effector enzyme in rod photoreceptors. A 22-amino acid peptide, corresponding to residues 293 to 314 from the COOH-terminal region of alpha t, fully mimicked alpha t and potently activated PDE. This region is adjacent to the receptor activation domain; thus, the alpha subunit of this G protein has a site for interaction with both its effector and receptor that maps near the COOH-terminus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rarick, H M -- Artemyev, N O -- Hamm, H E -- EY 06062/EY/NEI NIH HHS/ -- T32 HL 07692-02/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1992 May 15;256(5059):1031-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology and Biophysics, University of Illinois College of Medicine, Chicago 60680.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1317058" target="_blank"〉PubMed〈/a〉
    Keywords: 3',5'-Cyclic-GMP Phosphodiesterases/*metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Cattle ; Chromatography, High Pressure Liquid ; Enzyme Activation/drug effects ; GTP-Binding Proteins/*chemistry/*physiology ; Guanosine 5'-O-(3-Thiotriphosphate)/metabolism ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; Macromolecular Substances ; Molecular Sequence Data ; Peptide Fragments/chemistry/*pharmacology ; Protein Conformation
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  • 53
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    Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-06-26
    Description: A 3.5 angstrom resolution electron density map of the HIV-1 reverse transcriptase heterodimer complexed with nevirapine, a drug with potential for treatment of AIDS, reveals an asymmetric dimer. The polymerase (pol) domain of the 66-kilodalton subunit has a large cleft analogous to that of the Klenow fragment of Escherichia coli DNA polymerase I. However, the 51-kilodalton subunit of identical sequence has no such cleft because the four subdomains of the pol domain occupy completely different relative positions. Two of the four pol subdomains appear to be structurally related to subdomains of the Klenow fragment, including one containing the catalytic site. The subdomain that appears likely to bind the template strand at the pol active site has a different structure in the two polymerases. Duplex A-form RNA-DNA hybrid can be model-built into the cleft that runs between the ribonuclease H and pol active sites. Nevirapine is almost completely buried in a pocket near but not overlapping with the pol active site. Residues whose mutation results in drug resistance have been approximately located.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kohlstaedt, L A -- Wang, J -- Friedman, J M -- Rice, P A -- Steitz, T A -- GM 39546/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Jun 26;256(5065):1783-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1377403" target="_blank"〉PubMed〈/a〉
    Keywords: Azepines/pharmacology ; Binding Sites ; Crystallography ; DNA Polymerase I/chemistry ; Escherichia coli/genetics ; HIV-1/*enzymology ; Models, Molecular ; Molecular Structure ; Nevirapine ; Protein Conformation ; Pyridines/pharmacology ; RNA-Directed DNA Polymerase/*chemistry
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  • 54
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    Primary structure and functional expression of the beta 1 subunit of the rat brain sodium channel (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-05-08
    Description: Voltage-sensitive sodium channels are responsible for the initiation and propagation of the action potential and therefore are important for neuronal excitability. Complementary DNA clones encoding the beta 1 subunit of the rat brain sodium channel were isolated by a combination of polymerase chain reaction and library screening techniques. The deduced primary structure indicates that the beta 1 subunit is a 22,851-dalton protein that contains a single putative transmembrane domain and four potential extracellular N-linked glycosylation sites, consistent with biochemical data. Northern blot analysis reveals a 1,400-nucleotide messenger RNA in rat brain, heart, skeletal muscle, and spinal cord. Coexpression of beta 1 subunits with alpha subunits increases the size of the peak sodium current, accelerates its inactivation, and shifts the voltage dependence of inactivation to more negative membrane potentials. These results indicate that the beta 1 subunit is crucial in the assembly, expression, and functional modulation of the heterotrimeric complex of the rat brain sodium channel.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Isom, L L -- De Jongh, K S -- Patton, D E -- Reber, B F -- Offord, J -- Charbonneau, H -- Walsh, K -- Goldin, A L -- Catterall, W A -- NS15751/NS/NINDS NIH HHS/ -- NS25704/NS/NINDS NIH HHS/ -- NS26729/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1992 May 8;256(5058):839-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Washington, Seattle 98195.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1375395" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Blotting, Northern ; Brain/*physiology ; Cloning, Molecular ; DNA/genetics/isolation & purification ; Female ; Kinetics ; Macromolecular Substances ; Membrane Potentials ; Molecular Sequence Data ; Oocytes/physiology ; Polymerase Chain Reaction/methods ; Protein Conformation ; RNA/genetics/isolation & purification ; RNA, Messenger/genetics ; Rats ; Sodium Channels/*genetics/*physiology ; Voltage-Gated Sodium Channel beta-1 Subunit ; Xenopus
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    Constructing proteins by dovetailing unprotected synthetic peptides: backbone-engineered HIV protease (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-10
    Description: Backbone-engineered HIV-1 protease was prepared by a total chemical synthesis approach that combines the act of joining two peptides with the generation of an analog structure. Unprotected synthetic peptide segments corresponding to the two halves of the HIV-1 protease monomer polypeptide chain were joined cleanly and in high yield through unique mutually reactive functional groups, one on each segment. Ligation was performed in 6 molar guanidine hydrochloride, thus circumventing limited solubility of protected peptide segments, the principal problem of the classical approach to the chemical synthesis of proteins. The resulting fully active HIV-1 protease analog contained a thioester replacement for the natural peptide bond between Gly51-Gly52 in each of the two active site flaps, a region known to be highly sensitive to mutational changes of amino acid side chains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schnolzer, M -- Kent, S B -- New York, N.Y. -- Science. 1992 Apr 10;256(5054):221-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1566069" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Guanidine ; Guanidines ; HIV Protease/*chemical synthesis/metabolism ; HIV-1/*enzymology ; Indicators and Reagents ; Mass Spectrometry ; Models, Molecular ; Molecular Sequence Data ; Peptides/*chemical synthesis ; Protein Conformation
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  • 56
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    Small-angle synchrotron x-ray scattering reveals distinct shape changes of the myosin head during hydrolysis of ATP (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-10-16
    Description: In the energy transduction of muscle contraction, it is important to know the nature and extent of conformational changes of the head portion of the myosin molecules. In the presence of magnesium adenosine triphosphate (MgATP), fairly large conformational changes of the myosin head [subfragment-1 (S1)] in solution were observed by small-angle x-ray scattering with the use of synchrotron radiation as an intense and stable x-ray source. The presence of MgATP reduced the radius of gyration of the molecule by about 3 angstrom units and the maximum chord length by about 10 angstroms, showing that the shape of S1 becomes more compact or round during hydrolysis of MgATP. Comparison with various nucleotide-bound S1 complexes that correspond to the known intermediate states during ATP hydrolysis indicates that the shape of S1 in a key intermediate state, S1-bound adenosine diphosphate (ADP) and phosphate [S1**.ADP.P(i)], differs significantly from the shape in the other intermediate states of the S1 adenosine triphosphatase cycle as well as that of nucleotide-free S1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wakabayashi, K -- Tokunaga, M -- Kohno, I -- Sugimoto, Y -- Hamanaka, T -- Takezawa, Y -- Wakabayashi, T -- Amemiya, Y -- New York, N.Y. -- Science. 1992 Oct 16;258(5081):443-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysical Engineering, Faculty of Engineering Science, Osaka University, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1411537" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Chickens ; Ligands ; Motion ; *Muscle Contraction ; Myosin Subfragments/*ultrastructure ; Myosins/*chemistry/ultrastructure ; Protein Conformation ; Scattering, Radiation ; X-Rays
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  • 57
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    Molecular code for cooperativity in hemoglobin (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-03
    Description: Although tetrameric hemoglobin has been studied extensively as a prototype for understanding mechanisms of allosteric regulation, the functional and structural properties of its eight intermediate ligation forms have remained elusive. Recent experiments on the energetics of cooperativity of these intermediates, along with assignments of their quaternary structures, have revealed that the allosteric mechanism is controlled by a previously unrecognized symmetry feature: quaternary switching from form T to form R occurs whenever heme-site binding creates a tetramer with at least one ligated subunit on each dimeric half-molecule. This "symmetry rule" translates the configurational isomers of heme-site ligation into six observed switchpoints of quaternary transition. Cooperativity arises from both "concerted" quaternary switching and "sequential" modulation of binding within each quaternary form, T and R. Binding affinity is regulated through a hierarchical code of tertiary-quaternary coupling that includes the classical allosteric models as limiting cases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ackers, G K -- Doyle, M L -- Myers, D -- Daugherty, M A -- P01-HL40453/HL/NHLBI NIH HHS/ -- R37-GM24486/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Jan 3;255(5040):54-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1553532" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Calorimetry ; Circular Dichroism ; Hemoglobins/*chemistry/genetics/metabolism ; Kinetics ; Ligands ; Macromolecular Substances ; Models, Molecular ; Mutation ; Oxyhemoglobins/chemistry/metabolism ; Protein Conformation ; Thermodynamics
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    Total chemical synthesis of a D-enzyme: the enantiomers of HIV-1 protease show reciprocal chiral substrate specificity [corrected] (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-06-05
    Description: The D and L forms of the enzyme HIV-1 protease have been prepared by total chemical synthesis. The two proteins had identical covalent structures. However, the folded protein-enzyme enantiomers showed reciprocal chiral specificity on peptide substrates. That is, each enzyme enantiomer cut only the corresponding substrate enantiomer. Reciprocal chiral specificity was also evident in the effect of enantiomeric inhibitors. These data imply that the folded forms of the chemically synthesized D- and L-enzyme molecules are mirror images of one another in all elements of the three-dimensional structure. Enantiomeric proteins are expected to display reciprocal chiral specificity in all aspects of their biochemical interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Milton, R C -- Milton, S C -- Kent, S B -- New York, N.Y. -- Science. 1992 Jun 5;256(5062):1445-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1604320" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Amino Acids ; HIV Protease/chemical synthesis/*chemistry/*metabolism ; Kinetics ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Oligopeptides/pharmacology ; Protein Conformation ; Stereoisomerism ; Substrate Specificity ; X-Ray Diffraction
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    Lambda Int protein bridges between higher order complexes at two distant chromosomal loci attL and attR (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-10
    Description: The excisive recombination reaction of bacteriophage lambda involves a specific and efficient juxtaposition of two distant higher order protein-DNA complexes on the chromosome of Escherichia coli. These complexes, which mediate synapsis and strand exchange, consist of two DNA sequences, attL and attR, the bivalent DNA binding protein Int, and the sequence-specific DNA bending proteins, IHF, Xis, and Fis. The protein-protein and protein-DNA interactions within, and between, these complexes were studied by various biochemical techniques and the patterns of synergism among pairs of mutants with marginally impaired recombination function were analyzed. The DNA bending proteins facilitated long-range tethering of high- and low-affinity DNA sites by the bivalent Int protein, and a specific map is proposed for the resulting Int bridges. These structural motifs provide a basis for postulating the mechanism of site-specific recombination and may also be relevant to other pathways in which two distant chromosomal sites become associated.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904348/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904348/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, S -- Landy, A -- AI 13544/AI/NIAID NIH HHS/ -- GM 33928/GM/NIGMS NIH HHS/ -- R01 GM033928/GM/NIGMS NIH HHS/ -- R01 GM062723/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Apr 10;256(5054):198-203.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology and Medicine, Brown University, Providence, RI 02912.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1533056" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/*enzymology ; Base Sequence ; Chromosome Mapping ; *Chromosomes, Bacterial ; Crosses, Genetic ; DNA Nucleotidyltransferases/*metabolism ; DNA, Bacterial/genetics ; DNA-Binding Proteins/*metabolism ; Escherichia coli/*genetics/metabolism ; Genes, Bacterial ; Genetic Linkage ; Integrases ; Models, Structural ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Nucleic Acid Conformation ; Plasmids ; Protein Conformation ; Recombination, Genetic
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    Evidence that eukaryotes and eocyte prokaryotes are immediate relatives (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-07-03
    Description: The phylogenetic origin of eukaryotes has been unclear because eukaryotic nuclear genes have diverged substantially from prokaryotic ones. The genes coding for elongation factor EF-1 alpha were compared among various organisms. The EF-1 alpha sequences of eukaryotes contained an 11-amino acid segment that was also found in eocytes (extremely thermophilic, sulfur-metabolizing bacteria) but that was absent in all other bacteria. The related (paralogous) genes encoding elongation factor EF-2 and initiation factor IF-2 also lacked the 11-amino acid insert. These data imply that the eocytes are the closest surviving relatives (sister taxon) of the eukaryotes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rivera, M C -- Lake, J A -- New York, N.Y. -- Science. 1992 Jul 3;257(5066):74-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology Institute, University of California, Los Angeles 90024.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1621096" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteria/*genetics ; Base Sequence ; *Biological Evolution ; DNA, Bacterial/genetics ; Humans ; Models, Molecular ; Molecular Sequence Data ; Peptide Elongation Factor 1 ; Peptide Elongation Factor G ; Peptide Elongation Factor Tu/chemistry/*genetics ; Peptide Elongation Factors/*genetics ; Peptide Initiation Factors/*genetics ; Phylogeny ; Plants/genetics ; Prokaryotic Initiation Factor-2 ; Protein Conformation ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Nucleic Acid
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    The role of solvent viscosity in the dynamics of protein conformational changes (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-06-26
    Description: Nanosecond lasers were used to measure the rate of conformational changes in myoglobin after ligand dissociation at ambient temperatures. At low solvent viscosities the rate is independent of viscosity, but at high viscosities it depends on approximately the inverse first power of the viscosity. Kramers theory for unimolecular rate processes can be used to explain this result if the friction term is modified to include protein as well as solvent friction. The theory and experiment suggest that the dominant factor in markedly reducing the rate of conformational changes in myoglobin at low temperatures (less than 200 K) is the very high viscosity (greater than 10(7) centipoise) of the glycerol-water solvent. That is, at low temperatures conformational substates may not be "frozen" so much as "stuck."〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ansari, A -- Jones, C M -- Henry, E R -- Hofrichter, J -- Eaton, W A -- New York, N.Y. -- Science. 1992 Jun 26;256(5065):1796-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1615323" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Monoxide ; Hot Temperature ; Lasers ; Myoglobin/*chemistry ; Protein Conformation ; Solvents/*adverse effects ; Spectrophotometry, Atomic ; Viscosity
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    Acquisition of myogenic specificity by replacement of three amino acid residues from MyoD into E12 (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-05-15
    Description: The basic helix-loop-helix (bHLH) protein MyoD is a transcription factor that is important for the induction of the myogenic phenotype. The DNA binding basic region (13 amino acids) is necessary for recognition of the consensus MyoD binding site, for transcriptional activation, and for conversion of fibroblasts to muscle. In contrast, the non-tissue-specific bHLH protein E12 can bind to the MyoD binding site but does not induce myogenesis. Here, it is shown that only two amino acids in the MyoD basic region and a single amino acid from the junction, which separates the basic region and helix 1, are sufficient for myogenic specificity when substituted into the corresponding region of E12. These findings suggest that the recognition of particular determinants in the basic region is required for conversion of fibroblasts to muscle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davis, R L -- Weintraub, H -- New York, N.Y. -- Science. 1992 May 15;256(5059):1027-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute Laboratory, Fred Hutchinson Cancer Research Center, Seattle, WA 98104.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1317057" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Cell Differentiation ; Cell Line ; DNA/metabolism ; DNA Probes ; DNA-Binding Proteins/chemistry/metabolism/pharmacology ; Fibroblasts/cytology ; Fluorescent Antibody Technique ; Molecular Sequence Data ; Muscle Proteins/chemistry/genetics/*physiology ; Muscles/*cytology ; MyoD Protein ; Protein Conformation ; Structure-Activity Relationship ; Transcription Factors/chemistry/metabolism/pharmacology ; Transfection
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    Peptide binding by chaperone SecB: implications for recognition of nonnative structure (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-07-10
    Description: The molecular basis for recognition of nonnative proteins by the molecular chaperone SecB was investigated with an in vitro assay based on the protection of SecB from proteolysis when a ligand is bound. The SecB tetramer has multiple binding sites for positively charged peptides. When the peptide binding sites are occupied, the complex undergoes a conformational change to expose hydrophobic sites that bind the fluorescent probe 1-anilinonaphthalene-8-sulfonate. A model is proposed for interaction of nonnative polypeptides with both hydrophilic and hydrophobic sites on SecB.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Randall, L L -- GM29798/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Jul 10;257(5067):241-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, Washington State University, Pullman 99164-4660.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1631545" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*metabolism ; Binding Sites/physiology ; Electrophoresis, Polyacrylamide Gel ; In Vitro Techniques ; Models, Chemical ; Molecular Sequence Data ; Osmolar Concentration ; Peptides/*metabolism ; Protein Conformation
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    Molecular characterization of helix-loop-helix peptides (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-02-21
    Description: A class of regulators of eukaryotic gene expression contains a conserved amino acid sequence responsible for protein oligomerization and binding to DNA. This structure consists of an arginine- and lysine-rich basic region followed by a helix-loop-helix motif, which together mediate specific binding to DNA. Peptides were prepared that span this motif in the MyoD protein; in solution, they formed alpha-helical dimers and tetramers. They bound to DNA as dimers and their alpha-helical content increased on binding. Parallel and antiparallel four-helix models of the DNA-bound dimer were constructed. Peptides containing disulfide bonds were engineered to test the correctness of the two models. A disulfide that is compatible with the parallel model promotes specific interaction with DNA, whereas a disulfide compatible with the antiparallel model abolishes specific binding. Electron paramagnetic resonance (EPR) measurements of nitroxide-labeled peptides provided intersubunit distance measurements that also supported the parallel model.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anthony-Cahill, S J -- Benfield, P A -- Fairman, R -- Wasserman, Z R -- Brenner, S L -- Stafford, W F 3rd -- Altenbach, C -- Hubbell, W L -- DeGrado, W F -- GM13731/GM/NIGMS NIH HHS/ -- GM14321/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Feb 21;255(5047):979-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biotechnology Department, DuPont Merck Pharmaceutical Co., Wilmington, DE 19880-0328.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1312255" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Circular Dichroism ; DNA-Binding Proteins/*chemistry ; Disulfides ; Electron Spin Resonance Spectroscopy ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Regulatory Sequences, Nucleic Acid ; Sequence Alignment ; Transcription Factors/*chemistry
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    Structural evidence for induced fit as a mechanism for antibody-antigen recognition (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-02-21
    Description: The three-dimensional structure of a specific antibody (Fab 17/9) to a peptide immunogen from influenza virus hemagglutinin [HA1(75-110)] and two independent crystal complexes of this antibody with bound peptide (TyrP100-LeuP108) have been determined by x-ray crystallographic techniques at 2.0 A, 2.9 A, and 3.1 A resolution, respectively. The nonapeptide antigen assumes a type I beta turn in the antibody combining site and interacts primarily with the Fab hypervariable loops L3, H2, and H3. Comparison of the bound and unbound Fab structures shows that a major rearrangement in the H3 loop accompanies antigen binding. This conformational change results in the creation of a binding pocket for the beta turn of the peptide, allowing TyrP105 to be accommodated. The conformation of the peptide bound to the antibody shows similarity to its cognate sequence in the HA1, suggesting a possible mechanism for the cross-reactivity of this Fab with monomeric hemagglutinin. The structures of the free and antigen bound antibodies demonstrate the flexibility of the antibody combining site and provide an example of induced fit as a mechanism for antibody-antigen recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rini, J M -- Schulze-Gahmen, U -- Wilson, I A -- AI-23498/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1992 Feb 21;255(5047):959-65.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1546293" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Monoclonal/ultrastructure ; *Antigen-Antibody Reactions ; Hemagglutinins, Viral/*immunology ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/*ultrastructure ; Immunoglobulin G/ultrastructure ; In Vitro Techniques ; Influenza A virus/immunology ; Mice ; Models, Molecular ; Molecular Sequence Data ; Motion ; Peptides/chemistry/immunology ; Protein Binding ; Protein Conformation ; X-Ray Diffraction
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    Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-28
    Description: The crystal structure of calcium-bound calmodulin (Ca(2+)-CaM) bound to a peptide analog of the CaM-binding region of chicken smooth muscle myosin light chain kinase has been determined and refined to a resolution of 2.4 angstroms (A). The structure is compact and has the shape of an ellipsoid (axial ratio approximately 2:1). The bound CaM forms a tunnel diagonal to its long axis that engulfs the helical peptide, with the hydrophobic regions of CaM melded into a single area that closely covers the hydrophobic side of the peptide. There is a remarkably high pseudo-twofold symmetry between the closely associated domains. The central helix of the native CaM is unwound and expanded into a bend between residues 73 and 77. About 185 contacts (less than 4 A) are formed between CaM and the peptide, with van der Waals contacts comprising approximately 80% of this total.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meador, W E -- Means, A R -- Quiocho, F A -- New York, N.Y. -- Science. 1992 Aug 28;257(5074):1251-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1519061" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Calmodulin/*chemistry ; Crystallography ; Models, Molecular ; Molecular Sequence Data ; Myosin-Light-Chain Kinase/*metabolism ; Protein Conformation
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    Magnetoferritin: in vitro synthesis of a novel magnetic protein (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-07-24
    Description: The iron storage protein ferritin consists of a spherical polypeptide shell (apoferritin) surrounding a 6-nanometer inorganic core of the hydrated iron oxide ferrihydrite (5Fe2O3.9H2O). Previous studies have shown that the in vitro reconstitution of apoferritin yields mineral cores essentially identical to those of the native proteins. A magnetic mineral was synthesized within the nanodimensional cavity of horse spleen ferritin by the use of controlled reconstitution conditions. Transmission electron microscopy and electron diffraction analysis indicate that the entrapped mineral particles are discrete 6-nanometer spherical single crystals of the ferrimagnetic iron oxide magnetite (Fe3O4). The resulting magnetic protein, "magnetoferritin," could have uses in biomedical imaging, cell labeling, and separation procedures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meldrum, F C -- Heywood, B R -- Mann, S -- New York, N.Y. -- Science. 1992 Jul 24;257(5069):522-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemistry, University of Bath, United Kingdom.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1636086" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ferric Compounds ; Ferritins/*chemistry/ultrastructure ; Horses ; *Magnetics ; Microscopy, Electron ; Protein Conformation ; Spleen/metabolism
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    Ordered self-assembly of polypeptide fragments to form nativelike dimeric trp repressor (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-31
    Description: Subdomain-size proteolytic fragments of Escherichia coli trp repressor have been produced that assemble in defined order to regenerate fully native dimers. By characterization of the secondary and tertiary structures of isolated and recombined fragments, the structure of assembly intermediates can be correlated with the kinetic folding pathway of the intact repressor deduced from spectroscopic measurement of folding rates. The nativelike structure of these intermediates provides further evidence that protein folding pathways reflect the stabilities of secondary structural units and assemblies found in the native state. The proteolytic method should be generally useful in adding structural detail to spectroscopically determined folding mechanisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tasayco, M L -- Carey, J -- GM43558/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Jan 31;255(5044):594-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chemistry Department, Princeton University, NJ 08544.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1736361" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry ; Circular Dichroism ; Escherichia coli/metabolism ; Kinetics ; Macromolecular Substances ; Magnetic Resonance Spectroscopy/methods ; Models, Structural ; Molecular Sequence Data ; Peptide Fragments/chemistry ; Protein Conformation ; Repressor Proteins/*chemistry/metabolism
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    Three-dimensional structure of an angiotensin II-Fab complex at 3 A: hormone recognition by an anti-idiotypic antibody (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-07-24
    Description: The elucidation of bioactive conformations of small peptide hormones remains an elusive goal to structural chemists because of the inherent flexibility of these molecules. Angiotensin II (AII), the major effector of the renin-angiotensin system, is an octapeptide hormone for which no clear structural models exist. Peptide hormones such as AII share the property that they bind to their receptors with high affinities, in spite of the fact that they must overcome an extremely large conformational entropy barrier to bind in one conformation. A "surrogate system" that consists of a high-affinity monoclonal antibody (MAb) and AII has been used to study a bound conformation of AII. The crystallographic structure of the complex reveals a structure of AII that is compatible with predicted bioactive conformations of AII derived from structure-activity studies and theoretical calculations. In the complex, the deeply bound hormone is folded into a compact structure in which two turns bring the amino and carboxyl termini close together. The antibody of this complex (MAb 131) has the unusual property that it was not generated against AII, but rather against an anti-idiotypic antibody reactive with a MAb to AII, which renders this antibody an anti-anti-idiotypic antibody. The high affinity for AII of the original MAb to AII was passed on to MAb 131 through a structural determinant on the anti-idiotypic antibody. Strikingly, the conformation of AII in this complex is highly similar to complementarity determining region loops of antibodies, possibly indicating that a true molecular mimic of bound AII was present on the anti-idiotypic antibody against which MAb 131 was elicited.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia, K C -- Ronco, P M -- Verroust, P J -- Brunger, A T -- Amzel, L M -- GM44692/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Jul 24;257(5069):502-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1636085" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Angiotensin II/*chemistry/immunology/metabolism ; Animals ; Antibodies, Anti-Idiotypic/*chemistry/metabolism ; Antibodies, Monoclonal/*chemistry/metabolism ; Antigen-Antibody Complex ; Humans ; Immunoglobulin Fab Fragments/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; X-Ray Diffraction
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    Mutations in the rod domains of keratins 1 and 10 in epidermolytic hyperkeratosis (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-08-21
    Description: Epidermolytic hyperkeratosis is a hereditary skin disorder characterized by blistering and a marked thickening of the stratum corneum. In one family, affected individuals exhibited a mutation in the highly conserved carboxyl terminal of the rod domain of keratin 1. In two other families, affected individuals had mutations in the highly conserved amino terminal of the rod domain of keratin 10. Structural analysis of these mutations predicts that heterodimer formation would be unaffected, although filament assembly and elongation would be severely compromised. These data imply that an intact keratin intermediate filament network is required for the maintenance of both cellular and tissue integrity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rothnagel, J A -- Dominey, A M -- Dempsey, L D -- Longley, M A -- Greenhalgh, D A -- Gagne, T A -- Huber, M -- Frenk, E -- Hohl, D -- Roop, D R -- HD25479/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 1992 Aug 21;257(5073):1128-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Baylor College of Medicine, Houston, TX 77030.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1380725" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; DNA/chemistry ; Humans ; Ichthyosiform Erythroderma, Congenital/*genetics ; Keratins/chemistry/*genetics ; Macromolecular Substances ; Molecular Sequence Data ; *Mutation ; Pedigree ; Polymerase Chain Reaction ; Protein Conformation
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    Crystal structures of two viral peptides in complex with murine MHC class I H-2Kb (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-08-14
    Description: The x-ray structures of a murine MHC class I molecule (H-2Kb) were determined in complex with two different viral peptides, derived from the vesicular stomatitis virus nucleoprotein (52-59), VSV-8, and the Sendai virus nucleoprotein (324-332), SEV-9. The H-2Kb complexes were refined at 2.3 A for VSV-8 and 2.5 A for SEV-9. The structure of H-2Kb exhibits a high degree of similarity with human HLA class I, although the individual domains can have slightly altered dispositions. Both peptides bind in extended conformations with most of their surfaces buried in the H-2Kb binding groove. The nonamer peptide maintains the same amino- and carboxyl-terminal interactions as the octamer primarily by the insertion of a bulge in the center of an otherwise beta conformation. Most of the specific interactions are between side-chain atoms of H-2Kb and main-chain atoms of peptide. This binding scheme accounts in large part for the enormous diversity of peptide sequences that bind with high affinity to class I molecules. Small but significant conformational changes in H-2Kb are associated with peptide binding, and these synergistic movements may be an integral part of the T cell receptor recognition process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fremont, D H -- Matsumura, M -- Stura, E A -- Peterson, P A -- Wilson, I A -- CA-09523/CA/NCI NIH HHS/ -- CA-97489/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):919-27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1323877" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; H-2 Antigens/*chemistry/metabolism ; Mice ; Models, Molecular ; Molecular Sequence Data ; Parainfluenza Virus 1, Human/metabolism ; Protein Binding ; Protein Conformation ; Solvents ; Vesicular stomatitis Indiana virus/metabolism ; Viral Proteins/*chemistry/metabolism ; X-Ray Diffraction
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    Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-10-16
    Description: The crystal structure of the DNA repair enzyme endonuclease III, which recognizes and cleaves DNA at damaged bases, has been solved to 2.0 angstrom resolution with an R factor of 0.185. This iron-sulfur [4Fe-4S] enzyme is elongated and bilobal with a deep cleft separating two similarly sized domains: a novel, sequence-continuous, six-helix domain (residues 22 to 132) and a Greek-key, four-helix domain formed by the amino-terminal and three carboxyl-terminal helices (residues 1 to 21 and 133 to 211) together with the [4Fe-4S] cluster. The cluster is bound entirely within the carboxyl-terminal loop with a ligation pattern (Cys-X6-Cys-X2-Cys-X5-Cys) distinct from all other known [4Fe-4S] proteins. Sequence conservation and the positive electrostatic potential of conserved regions identify a surface suitable for binding duplex B-DNA across the long axis of the enzyme, matching a 46 angstrom length of protected DNA. The primary role of the [4Fe-4S] cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone. The crystallographically identified inhibitor binding region, which recognizes the damaged base thymine glycol, is a seven-residue beta-hairpin (residues 113 to 119). Location and side chain orientation at the base of the inhibitor binding site implicate Glu112 in the N-glycosylase mechanism and Lys120 in the beta-elimination mechanism. Overall, the structure reveals an unusual fold and a new biological function for [4Fe-4S] clusters and provides a structural basis for studying recognition of damaged DNA and the N-glycosylase and apurinic/apyrimidinic-lyase mechanisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuo, C F -- McRee, D E -- Fisher, C L -- O'Handley, S F -- Cunningham, R P -- Tainer, J A -- GM 46312/GM/NIGMS NIH HHS/ -- HL07695/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1992 Oct 16;258(5081):434-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1411536" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/ultrastructure ; Base Sequence ; Crystallography ; Cysteine/chemistry ; *DNA Repair ; DNA-Binding Proteins/*ultrastructure ; Deoxyribonuclease (Pyrimidine Dimer) ; Endodeoxyribonucleases/*ultrastructure ; Iron-Sulfur Proteins/*ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Oligodeoxyribonucleotides/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; X-Ray Diffraction
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    A critical role for conserved residues in the cleft of HLA-A2 in presentation of a nonapeptide to T cells (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-14
    Description: The peptide binding cleft of the class I human histocompatibility antigen, HLA-A2, contains conserved amino acid residues clustered in the two ends of the cleft in pockets A and F as well as polymorphic residues. The function of two conserved tyrosines in the A pocket was investigated by mutating them to phenylalanines and of a conserved tyrosine and threonine in the F pocket by mutating them to phenylalanine and valine, respectively. Presentation of influenza virus peptides and of intact virus to cytolytic T lymphocytes (CTLs) was then examined. The magnitude of the reduction seen by the mutation of the two tyrosines in the A pocket suggests that hydrogen bonds involving them have a critical function in the binding of the NH2-terminal NH3+ of the peptide nonamer and possibly of all bound peptide nonamers. In contrast, the mutations in the F pocket had no effect on CTL recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Latron, F -- Pazmany, L -- Morrison, J -- Moots, R -- Saper, M A -- McMichael, A -- Strominger, J L -- AI 20182/AI/NIAID NIH HHS/ -- CA 47554/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):964-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1380181" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; B-Lymphocytes/immunology ; Binding Sites ; Cell Line ; Cloning, Molecular ; Epitopes/immunology/metabolism ; HLA-A2 Antigen/chemistry/genetics/*metabolism ; Influenza A virus ; Kinetics ; Models, Molecular ; Mutagenesis, Site-Directed ; Oligopeptides/immunology/*metabolism ; Protein Conformation ; Recombinant Proteins/chemistry/metabolism ; T-Lymphocytes, Cytotoxic/*immunology ; Transfection ; Viral Proteins/metabolism
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    X-ray structure of T4 endonuclease V: an excision repair enzyme specific for a pyrimidine dimer (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-24
    Description: The x-ray structure of T4 endonuclease V, an enzyme responsible for the first step of a pyrimidine-dimer-specific excision-repair pathway, was determined at a 1.6-angstrom resolution. The enzyme consists of a single compact domain classified into an all-alpha structure. This single domain has two distinct catalytic activities; it functions as a pyrimidine dimer glycosylase and as an apurinic-apyrimidinic endonuclease. The amino-terminal segment penetrates between two major helices and prevents their direct contact. The refined structure suggests the residues involved in the substrate binding and the catalysis of the glycosylation reaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morikawa, K -- Matsumoto, O -- Tsujimoto, M -- Katayanagi, K -- Ariyoshi, M -- Doi, T -- Ikehara, M -- Inaoka, T -- Ohtsuka, E -- New York, N.Y. -- Science. 1992 Apr 24;256(5056):523-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Protein Engineering Research Institute, Osaka, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1575827" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *DNA Repair ; Deoxyribonuclease (Pyrimidine Dimer) ; Electrochemistry ; Endodeoxyribonucleases/*chemistry/metabolism ; Glycosylation ; Hydrogen Bonding ; Molecular Sequence Data ; Molecular Structure ; Mutagenesis, Site-Directed ; Protein Conformation ; Pyrimidine Dimers/*metabolism ; Structure-Activity Relationship ; Substrate Specificity ; T-Phages/enzymology ; *Viral Proteins ; X-Ray Diffraction
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    Recognition of angiotensin II: antibodies at different levels of an idiotypic network are superimposable (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-07-24
    Description: Genetic and sequence information are reported for an angiotensin II-reactive antibody (Ab1, MAb 110) and an anti--anti-idiotypic antibody (Ab3, MAb 131) that have identical antigen binding properties and that are related by an anti-idiotypic antibody (Ab2-beta) that satisfies accepted biochemical criteria for an internal image-bearing antibody. The sequences of the variable regions of the Ab3 and of the Ab1 are nearly identical, even though the Ab1 is an antibody to a peptide and the Ab3 is an antibody to a globular protein. Significantly, amino acid residues that make critical contacts with antigen in the crystal structure of the Ab3-antigen complex are highly conserved in Ab1, suggesting that the epitopes of the Ab2-beta recognized by the Ab3 do indeed resemble the bound structure of the antigen.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia, K C -- Desiderio, S V -- Ronco, P M -- Verroust, P J -- Amzel, L M -- 6M 44692/PHS HHS/ -- New York, N.Y. -- Science. 1992 Jul 24;257(5069):528-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins University Medical School, Baltimore, MD 21205.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1636087" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Angiotensin II/chemistry/*immunology ; Animals ; Antibodies, Anti-Idiotypic/chemistry/genetics/*immunology ; Antibodies, Monoclonal/chemistry/genetics/*immunology ; Antigen-Antibody Complex ; Base Sequence ; Cell Line ; Hybridomas/immunology ; Immunoglobulin Heavy Chains/genetics/immunology ; Immunoglobulin Light Chains/genetics/immunology ; Immunoglobulin Variable Region/chemistry/genetics/immunology ; Mice ; Mice, Inbred BALB C/immunology ; Models, Molecular ; Molecular Sequence Data ; Plasmacytoma ; Protein Conformation
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    Protein solvation in allosteric regulation: a water effect on hemoglobin (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-05-01
    Description: The oxygen affinity of hemoglobin varies linearly with the chemical potential of water in the bathing medium, as seen from the osmotic effect of several neutral solutes, namely sucrose, stachyose, and two polyethyleneglycols (molecular weights of 150 and 400). The data, analyzed either by Wyman linkage equations or by Gibbs-Duhem relations, show that approximately 60 extra water molecules bind to hemoglobin during the transition from the fully deoxygenated tense (T) state to the fully oxygenated relaxed (R) state. This number, independent of the nature of the solute, agrees with the difference in water-accessible surface areas previously computed for the two conformations. The work of solvation in allosteric regulation can no longer go unrecognized.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Colombo, M F -- Rau, D C -- Parsegian, V A -- New York, N.Y. -- Science. 1992 May 1;256(5057):655-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Biochemistry and Metabolism, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1585178" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation/physiology ; Chemistry, Physical ; Hemoglobins/*chemistry/metabolism ; Oligosaccharides/pharmacology ; Osmotic Pressure ; Oxygen/metabolism ; Physicochemical Phenomena ; Polyethylene Glycols/pharmacology ; Protein Conformation ; Sucrose/pharmacology ; Thermodynamics ; Water/metabolism/*pharmacology
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    The location of bound lipid in the lipovitellin complex (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-07-31
    Description: The location of the bound lipid in the soluble lipoprotein lipovitellin has been determined by neutron crystallographic techniques. With the use of the contrast variation method, whereby the crystals are soaked in different H2O-D2O mixtures, the lipid has been found to occupy a large cavity in the protein whose structure had previously been determined by x-ray crystallography. The lipid appears to be bound in the form of a bilayer with the major protein-lipid interactions being hydrophobic and with the lipid headgroups projecting into the bulk solvent and into a solvent-filled space in the cavity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Timmins, P A -- Poliks, B -- Banaszak, L -- New York, N.Y. -- Science. 1992 Jul 31;257(5070):652-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Laue-Langevin, Grenoble, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1496377" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chemistry, Physical ; Crystallography ; Deuterium ; Egg Proteins ; Egg Proteins, Dietary/*chemistry/metabolism ; *Lipid Metabolism ; Lipids/analysis ; Macromolecular Substances ; Molecular Structure ; Neutrons ; Physicochemical Phenomena ; Protein Conformation ; Water ; X-Ray Diffraction
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    Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-09-18
    Description: The nitrogenase enzyme system catalyzes the ATP (adenosine triphosphate)-dependent reduction of dinitrogen to ammonia during the process of nitrogen fixation. Nitrogenase consists of two proteins: the iron (Fe)-protein, which couples hydrolysis of ATP to electron transfer, and the molybdenum-iron (MoFe)-protein, which contains the dinitrogen binding site. In order to address the role of ATP in nitrogen fixation, the crystal structure of the nitrogenase Fe-protein from Azotobacter vinelandii has been determined at 2.9 angstrom (A) resolution. Fe-protein is a dimer of two identical subunits that coordinate a single 4Fe:4S cluster. Each subunit folds as a single alpha/beta type domain, which together symmetrically ligate the surface exposed 4Fe:4S cluster through two cysteines from each subunit. A single bound ADP (adenosine diphosphate) molecule is located in the interface region between the two subunits. Because the phosphate groups of this nucleotide are approximately 20 A from the 4Fe:4S cluster, it is unlikely that ATP hydrolysis and electron transfer are directly coupled. Instead, it appears that interactions between the nucleotide and cluster sites must be indirectly coupled by allosteric changes occurring at the subunit interface. The coupling between protein conformation and nucleotide hydrolysis in Fe-protein exhibits general similarities to the H-Ras p21 and recA proteins that have been recently characterized structurally. The Fe-protein structure may be relevant to the functioning of other biochemical energy-transducing systems containing two nucleotide-binding sites, including membrane transport proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Georgiadis, M M -- Komiya, H -- Chakrabarti, P -- Woo, D -- Kornuc, J J -- Rees, D C -- GM45162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Sep 18;257(5077):1653-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Columbia University, New York, NY 10032.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1529353" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism/pharmacology ; Amino Acid Sequence ; Azotobacter vinelandii/*enzymology ; Binding Sites ; Chemistry, Physical ; Crystallization ; Electron Transport ; Hydrolysis ; Iron-Sulfur Proteins/*chemistry ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Molybdoferredoxin/chemistry ; Nitrogenase/*chemistry/metabolism ; Physicochemical Phenomena ; Protein Conformation ; X-Ray Diffraction
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  • 79
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    Getting some "backbone": how MHC binds peptides (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-08-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barinaga, M -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):880-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1502554" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Histocompatibility Antigens Class I/*chemistry/metabolism ; Humans ; Hydrogen Bonding ; Major Histocompatibility Complex ; Models, Molecular ; Protein Binding ; Protein Conformation ; Proteins/chemistry/metabolism ; T-Lymphocytes/immunology
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  • 80
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    Identification of heregulin, a specific activator of p185erbB2 (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-05-22
    Description: The proto-oncogene designated erbB2 or HER2 encodes a 185-kilodalton transmembrane tyrosine kinase (p185erbB2), whose overexpression has been correlated with a poor prognosis in several human malignancies. A 45-kilodalton protein heregulin-alpha (HRG-alpha) that specifically induced phosphorylation of p185erbB2 was purified from the conditioned medium of a human breast tumor cell line. Several complementary DNA clones encoding related HRGs were identified, all of which are similar to proteins in the epidermal growth factor family. Scatchard analysis of the binding of recombinant HRG to a breast tumor cell line expressing p185erbB2 showed a single high affinity binding site [dissociation constant (Kd) = 105 +/- 15 picomolar]. Heregulin transcripts were identified in several normal tissues and cancer cell lines. The HRGs may represent the natural ligands for p185erbB2.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holmes, W E -- Sliwkowski, M X -- Akita, R W -- Henzel, W J -- Lee, J -- Park, J W -- Yansura, D -- Abadi, N -- Raab, H -- Lewis, G D -- New York, N.Y. -- Science. 1992 May 22;256(5060):1205-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA 94080.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1350381" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Breast Neoplasms/genetics ; Cell Line ; Chromatography, High Pressure Liquid ; Codon ; Culture Media ; DNA-Binding Proteins/genetics/isolation & purification/*metabolism ; Epidermal Growth Factor/genetics ; Female ; Glycoproteins/*metabolism ; Humans ; Kinetics ; Molecular Sequence Data ; Neuregulins ; Oligonucleotide Probes ; Phosphorylation ; Protein Conformation ; Protein-Tyrosine Kinases/*genetics ; Proto-Oncogene Proteins/*genetics ; *Proto-Oncogenes ; Receptor, ErbB-2 ; Sequence Homology, Nucleic Acid ; Transfection
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  • 81
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    The disulfide folding pathway of BPTI (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Creighton, T E -- New York, N.Y. -- Science. 1992 Apr 3;256(5053):111-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1373519" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Aprotinin/*chemistry ; Cattle ; *Cysteine ; *Disulfides ; Kinetics ; Models, Molecular ; Protein Conformation
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  • 82
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    NMR determination of residual structure in a urea-denatured protein, the 434-repressor (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-09-11
    Description: A nuclear magnetic resonance (NMR) structure determination is reported for the polypeptide chain of a globular protein in strongly denaturing solution. Nuclear Overhauser effect (NOE) measurements with a 7 molar urea solution of the amino-terminal 63-residue domain of the 434-repressor and distance geometry calculations showed that the polypeptide segment 54 to 59 forms a hydrophobic cluster containing the side chains of Val54, Val56, Trp58, and Leu59. This residual structure in the urea-unfolded protein is related to the corresponding region of the native, folded protein by simple rearrangements of the residues 58 to 60. Based on these observations a model for the early phase of refolding of the 434-repressor(1-63) is proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neri, D -- Billeter, M -- Wider, G -- Wuthrich, K -- New York, N.Y. -- Science. 1992 Sep 11;257(5076):1559-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Molekularbiologie und Biophysik, ETH-Honggerberg, Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1523410" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Denaturation ; Repressor Proteins/*chemistry/pharmacology ; Urea/*pharmacology ; Viral Proteins
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  • 83
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    A mutant of TTX-resistant cardiac sodium channels with TTX-sensitive properties (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-05-22
    Description: The cardiac sodium channel alpha subunit (RHI) is less sensitive to tetrodotoxin (TTX) and saxitoxin (STX) and more sensitive to cadmium than brain and skeletal muscle (microliter) isoforms. An RHI mutant, with Tyr substituted for Cys at position 374 (as in microliter) confers three properties of TTX-sensitive channels: (i) greater sensitivity to TTX (730-fold); (ii) lower sensitivity to cadmium (28-fold); and (iii) altered additional block by toxin upon repetitive stimulation. Thus, the primary determinant of high-affinity TTX-STX binding is a critical aromatic residue at position 374, and the interaction may take place possibly through an ionized hydrogen bond. This finding requires revision of the sodium channel pore structure that has been previously suggested by homology with the potassium channel.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Satin, J -- Kyle, J W -- Chen, M -- Bell, P -- Cribbs, L L -- Fozzard, H A -- Rogart, R B -- HL-20592/HL/NHLBI NIH HHS/ -- HL-37217/HL/NHLBI NIH HHS/ -- NS 23360/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1992 May 22;256(5060):1202-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, University of Chicago, IL 60637.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1375397" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Brain/physiology ; Cadmium/pharmacology ; Cell Membrane/physiology ; Cloning, Molecular ; Drug Resistance/genetics ; Genetic Vectors ; Heart/*physiology ; Kinetics ; Molecular Sequence Data ; Muscles/physiology ; *Mutagenesis, Site-Directed ; Oocytes/drug effects/*physiology ; Polymerase Chain Reaction ; Protein Conformation ; RNA/genetics ; Rats ; Restriction Mapping ; Saxitoxin/pharmacology ; Sodium Channels/drug effects/genetics/*physiology ; Tetrodotoxin/*pharmacology ; Xenopus
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  • 84
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    Solution structure of a calmodulin-target peptide complex by multidimensional NMR (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-05-01
    Description: The three-dimensional solution structure of the complex between calcium-bound calmodulin (Ca(2+)-CaM) and a 26-residue synthetic peptide comprising the CaM binding domain (residues 577 to 602) of skeletal muscle myosin light chain kinase, has been determined using multidimensional heteronuclear filtered and separated nuclear magnetic resonance spectroscopy. The two domains of CaM (residues 6 to 73 and 83 to 146) remain essentially unchanged upon complexation. The long central helix (residues 65 to 93), however, which connects the two domains in the crystal structure of Ca(2+)-CaM, is disrupted into two helices connected by a long flexible loop (residues 74 to 82), thereby enabling the two domains to clamp residues 3 to 21 of the bound peptide, which adopt a helical conformation. The overall structure of the complex is globular, approximating an ellipsoid of dimensions 47 by 32 by 30 angstroms. The helical peptide is located in a hydrophobic channel that passes through the center of the ellipsoid at an angle of approximately 45 degrees with its long axis. The complex is mainly stabilized by hydrophobic interactions which, from the CaM side, involve an unusually large number of methionines. Key residues of the peptide are Trp4 and Phe17, which serve to anchor the amino- and carboxyl-terminal halves of the peptide to the carboxyl- and amino-terminal domains of CaM, respectively. Sequence comparisons indicate that a number of peptides that bind CaM with high affinity share this common feature containing either aromatic residues or long-chain hydrophobic ones separated by a stretch of 12 residues, suggesting that they interact with CaM in a similar manner.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ikura, M -- Clore, G M -- Gronenborn, A M -- Zhu, G -- Klee, C B -- Bax, A -- New York, N.Y. -- Science. 1992 May 1;256(5057):632-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1585175" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Calcium/metabolism ; Calmodulin/*chemistry/metabolism ; Drosophila melanogaster ; Hydrogen Bonding ; *Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Muscles/enzymology ; Myosin-Light-Chain Kinase/chemistry/metabolism ; Peptide Fragments/*chemistry/metabolism ; Protein Conformation ; Rabbits
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  • 85
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    A phosphorylation site in the Na+ channel required for modulation by protein kinase C (1991)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1991-11-08
    Description: Voltage-gated sodium channels are responsible for generation of action potentials in excitable cells. Activation of protein kinase C slows inactivation of sodium channels and reduces peak sodium currents. Phosphorylation of a single residue, serine 1506, that is located in the conserved intracellular loop between domains III and IV and is involved in inactivation of the sodium channel, is required for both modulatory effects. Mutant sodium channels lacking this phosphorylation site have normal functional properties in unstimulated cells but do not respond to activation of protein kinase C. Phosphorylation of this conserved site in sodium channel alpha subunits may regulate electrical activity in a wide range of excitable cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉West, J W -- Numann, R -- Murphy, B J -- Scheuer, T -- Catterall, W A -- GM07270/GM/NIGMS NIH HHS/ -- NS15751/NS/NINDS NIH HHS/ -- NS25704/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1991 Nov 8;254(5033):866-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Washington, Seattle 98195.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1658937" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cell Membrane/physiology ; Cells, Cultured ; Membrane Potentials ; Models, Structural ; Molecular Sequence Data ; Phosphorylation ; Protein Conformation ; Protein Kinase C/*metabolism ; Sodium Channels/metabolism/*physiology
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  • 86
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    Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase (1991)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1991-07-26
    Description: The structure of a 20-amino acid peptide inhibitor bound to the catalytic subunit of cyclic AMP-dependent protein kinase, and its interactions with the enzyme, are described. The x-ray crystal structure of the complex is the basis of the analysis. The peptide inhibitor, derived from a naturally occurring heat-stable protein kinase inhibitor, contains an amphipathic helix that is followed by a turn and an extended conformation. The extended region occupies the cleft between the two lobes of the enzyme and contains a five-residue consensus recognition sequence common to all substrates and peptide inhibitors of the catalytic subunit. The helical portion of the peptide binds to a hydrophobic groove and conveys high affinity binding. Loops from both domains converge at the active site and contribute to a network of conserved residues at the sites of magnesium adenosine triphosphate binding and catalysis. Amino acids associated with peptide recognition, nonconserved, extend over a large surface area.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knighton, D R -- Zheng, J H -- Ten Eyck, L F -- Xuong, N H -- Taylor, S S -- Sowadski, J M -- RR01644/RR/NCRR NIH HHS/ -- T32CA09523/CA/NCI NIH HHS/ -- T32DK07233/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1991 Jul 26;253(5018):414-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, San Diego, La Jolla 92093-0654.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1862343" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Carrier Proteins/*chemistry/metabolism ; Computer Simulation ; Enzyme Inhibitors/*chemistry ; *Intracellular Signaling Peptides and Proteins ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Kinases/*chemistry/metabolism ; X-Ray Diffraction
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  • 87
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    Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein (1991)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1991-08-23
    Description: The three-dimensional structure of acetylcholinesterase from Torpedo californica electric organ has been determined by x-ray analysis to 2.8 angstrom resolution. The form crystallized is the glycolipid-anchored homodimer that was purified subsequent to solubilization with a bacterial phosphatidylinositol-specific phospholipase C. The enzyme monomer is an alpha/beta protein that contains 537 amino acids. It consists of a 12-stranded mixed beta sheet surrounded by 14 alpha helices and bears a striking resemblance to several hydrolase structures including dienelactone hydrolase, serine carboxypeptidase-II, three neutral lipases, and haloalkane dehalogenase. The active site is unusual because it contains Glu, not Asp, in the Ser-His-acid catalytic triad and because the relation of the triad to the rest of the protein approximates a mirror image of that seen in the serine proteases. Furthermore, the active site lies near the bottom of a deep and narrow gorge that reaches halfway into the protein. Modeling of acetylcholine binding to the enzyme suggests that the quaternary ammonium ion is bound not to a negatively charged "anionic" site, but rather to some of the 14 aromatic residues that line the gorge.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sussman, J L -- Harel, M -- Frolow, F -- Oefner, C -- Goldman, A -- Toker, L -- Silman, I -- New York, N.Y. -- Science. 1991 Aug 23;253(5022):872-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Chemistry, Weizmann Institute of Science, Rehovot, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1678899" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylcholine/*metabolism ; Acetylcholinesterase/*chemistry/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Cell Membrane/enzymology ; Chemistry, Physical ; Crystallization ; Electric Organ/*enzymology ; Glutamates ; Glutamic Acid ; Macromolecular Substances ; Molecular Sequence Data ; Molecular Structure ; Phosphatidylinositols/metabolism ; Physicochemical Phenomena ; Protein Conformation ; Sequence Homology, Nucleic Acid ; *Torpedo ; X-Ray Diffraction
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  • 88
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    Three-dimensional structures of the ligand-binding domain of the bacterial aspartate receptor with and without a ligand (1991)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1991-12-09
    Description: The three-dimensional structure of an active, disulfide cross-linked dimer of the ligand-binding domain of the Salmonella typhimurium aspartate receptor and that of an aspartate complex have been determined by x-ray crystallographic methods at 2.4 and 2.0 angstrom (A) resolution, respectively. A single subunit is a four-alpha-helix bundle with two long amino-terminal and carboxyl-terminal helices and two shorter helices that form a cylinder 20 A in diameter and more than 70 A long. The two subunits in the disulfide-bonded dimer are related by a crystallographic twofold axis in the apo structure, but by a noncrystallographic twofold axis in the aspartate complex structure. The latter structure reveals that the ligand binding site is located more than 60 A from the presumed membrane surface and is at the interface of the two subunits. Aspartate binds between two alpha helices from one subunit and one alpha helix from the other in a highly charged pocket formed by three arginines. The comparison of the apo and aspartate complex structures shows only small structural changes in the individual subunits, except for one loop region that is disordered, but the subunits appear to change orientation relative to each other. The structures of the two forms of this protein provide a step toward understanding the mechanisms of transmembrane signaling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Milburn, M V -- Prive, G G -- Milligan, D L -- Scott, W G -- Yeh, J -- Jancarik, J -- Koshland, D E Jr -- Kim, S H -- AI 30725/AI/NIAID NIH HHS/ -- DK09765/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1991 Nov 29;254(5036):1342-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1660187" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Aspartic Acid/metabolism ; Binding Sites ; Disulfides/analysis ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; *Receptors, Amino Acid ; Receptors, Cell Surface/*chemistry/metabolism ; Salmonella typhimurium/metabolism ; X-Ray Diffraction
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  • 89
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    Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization (1991)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1991-03-22
    Description: Defensins (molecular weight 3500 to 4000) act in the mammalian immune response by permeabilizing the plasma membranes of a broad spectrum of target organisms, including bacteria, fungi, and enveloped viruses. The high-resolution crystal structure of defensin HNP-3 (1.9 angstrom resolution, R factor 0.19) reveals a dimeric beta sheet that has an architecture very different from other lytic peptides. The dimeric assembly suggests mechanisms by which defensins might bind to and permeabilize the lipid bilayer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hill, C P -- Yee, J -- Selsted, M E -- Eisenberg, D -- New York, N.Y. -- Science. 1991 Mar 22;251(5000):1481-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Eisenberg, Molecular Biology Institute, Los Angeles, CA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2006422" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Blood Proteins/chemistry/*ultrastructure ; Cell Membrane Permeability ; Crystallography ; Defensins ; Guinea Pigs ; Humans ; Macromolecular Substances ; Membrane Proteins/chemistry/ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Protein Conformation ; Rabbits ; Rats ; Structure-Activity Relationship ; X-Ray Diffraction ; *alpha-Defensins
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  • 90
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    Similarity of protein G and ubiquitin (1991)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1991-10-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kraulis, P J -- New York, N.Y. -- Science. 1991 Oct 25;254(5031):581-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1658931" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites, Antibody ; Immunoglobulin G ; Models, Molecular ; Molecular Sequence Data ; Nerve Tissue Proteins/*chemistry/genetics/immunology ; Protein Conformation ; Sequence Homology, Nucleic Acid ; Ubiquitins/*chemistry/genetics
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  • 91
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    Specific DNA binding by c-Myb: evidence for a double helix-turn-helix-related motif (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-09-06
    Description: The c-Myb protein is a sequence-specific DNA binding protein that activates transcription in hematopoietic cells. Three imperfect repeats (R1, R2, and R3) that contain regularly spaced tryptophan residues form the DNA binding domain of c-Myb. A fragment of c-Myb that contained the R2 and R3 regions bound specifically to a DNA sequence recognized by c-Myb plus ten additional base pairs at the 3' end of the element. The R2R3 fragment was predicted to contain two consecutive helix-turn-helix (HTH) motifs with unconventional turns. Mutagenesis of amino acids in R2R3 at positions that correspond to DNA-contacting amino acids in other HTH-containing proteins abolished specific DNA binding without affecting nonspecific DNA interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gabrielsen, O S -- Sentenac, A -- Fromageot, P -- New York, N.Y. -- Science. 1991 Sep 6;253(5024):1140-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire d'Ingenierie des Proteines, Centre d'Etudes de Saclay, Gif-sur-Yvette, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1887237" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Chickens ; DNA/*metabolism ; DNA-Binding Proteins/*metabolism ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Oligonucleotide Probes ; Oncogenes ; Polymerase Chain Reaction ; Protein Conformation ; Proto-Oncogene Proteins/genetics/*metabolism ; Proto-Oncogene Proteins c-myb ; Recombinant Proteins/metabolism ; Restriction Mapping ; Sequence Homology, Nucleic Acid ; Transcription Factors/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 92
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    Engineered metal-binding proteins: purification to protein folding (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-06-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arnold, F H -- Haymore, B L -- New York, N.Y. -- Science. 1991 Jun 28;252(5014):1796-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1648261" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carrier Proteins/*chemical synthesis/chemistry/isolation & purification ; Cytochrome c Group/chemistry ; Histidine ; Ligands ; Metals/*metabolism ; Models, Molecular ; Protein Conformation ; *Protein Engineering
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 93
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    A component of calcium-activated potassium channels encoded by the Drosophila slo locus (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-08-02
    Description: Calcium-activated potassium channels mediate many biologically important functions in electrically excitable cells. Despite recent progress in the molecular analysis of voltage-activated K+ channels, Ca(2+)-activated K+ channels have not been similarly characterized. The Drosophila slowpoke (slo) locus, mutations of which specifically abolish a Ca(2+)-activated K+ current in muscles and neurons, provides an opportunity for molecular characterization of these channels. Genomic and complementary DNA clones from the slo locus were isolated and sequenced. The polypeptide predicted by slo is similar to voltage-activated K+ channel polypeptides in discrete domains known to be essential for function. Thus, these results indicate that slo encodes a structural component of Ca(2+)-activated K+ channels.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Atkinson, N S -- Robertson, G A -- Ganetzky, B -- NS15390/NS/NINDS NIH HHS/ -- T32 GM07131/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1991 Aug 2;253(5019):551-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Genetics, University of Wisconsin, Madison 53706.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1857984" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Calcium/pharmacology ; Chromosome Aberrations ; Chromosome Deletion ; Cloning, Molecular ; DNA/genetics/isolation & purification ; Drosophila/*genetics/physiology ; Exons ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phenotype ; Potassium Channels/drug effects/*genetics/physiology ; Protein Conformation ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; Translocation, Genetic
    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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  • 94
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    First protein kinase structure (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-07-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoffman, M -- New York, N.Y. -- Science. 1991 Jul 26;253(5018):383.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1862341" target="_blank"〉PubMed〈/a〉
    Keywords: Carrier Proteins/chemistry/metabolism ; Enzyme Inhibitors/chemistry ; *Intracellular Signaling Peptides and Proteins ; Models, Molecular ; Protein Conformation ; Protein Kinases/*chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 95
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    Critical structural elements of the VP16 transcriptional activation domain (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-01-04
    Description: Virion protein 16 (VP16) of herpes simplex virus type 1 contains an acidic transcriptional activation domain. Missense mutations within this domain have provided insights into the structural elements critical for its function. Net negative charge contributed to, but was not sufficient for, transcriptional activation by VP16. A putative amphipathic alpha helix did not appear to be an important structural component of the activation domain. A phenylalanine residue at position 442 was exquisitely sensitive to mutation. Transcriptional activators of several classes contain hydrophobic amino acids arranged in patterns resembling that of VP16. Therefore, the mechanism of transcriptional activation by VP16 and other proteins may involve both ionic and specific hydrophobic interactions with target molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cress, W D -- Triezenberg, S J -- AI 27323/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1991 Jan 4;251(4989):87-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Michigan State University, East Lansing 48824-1319.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1846049" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Immediate-Early Proteins ; Molecular Sequence Data ; Mutation ; Protein Conformation ; *Simplexvirus ; Structure-Activity Relationship ; Transcription Factors/*chemistry/genetics/pharmacology ; Transcription, Genetic/*drug effects ; Transfection ; Viral Proteins/*genetics ; Virion
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 96
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    Membrane-mediated assembly of filamentous bacteriophage Pf1 coat protein (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-05-31
    Description: Filamentous bacteriophage Pf1 assembles by a membrane-mediated process during which the viral DNA is secreted through the membrane while being encapsulated by the major coat protein. Neutron diffraction studies showed that in the virus most of the coat protein consists of two alpha-helical segments arranged end-to-end with an intervening mobile surface loop. Nuclear magnetic resonance studies of the coat protein in the membrane-bound form have shown that the secondary structure is essentially identical to that in the intact virus. A comparison indicates that during membrane-mediated viral assembly, while the secondary structure of the coat protein is largely conserved, its tertiary structure changes substantially.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nambudripad, R -- Stark, W -- Opella, S J -- Makowski, L -- New York, N.Y. -- Science. 1991 May 31;252(5010):1305-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Boston University, MA 02215.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1925543" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophages/chemistry ; Capsid/*chemistry/metabolism ; *Capsid Proteins ; Cell Membrane/*metabolism ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Structure ; Neutrons ; Protein Conformation
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 97
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    Three-dimensional structure of the LDL receptor-binding domain of human apolipoprotein E (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-06-28
    Description: Human apolipoprotein E, a blood plasma protein, mediates the transport and uptake of cholesterol and lipid by way of its high affinity interaction with different cellular receptors, including the low-density lipoprotein (LDL) receptor. The three-dimensional structure of the LDL receptor-binding domain of apoE has been determined at 2.5 angstrom resolution by x-ray crystallography. The protein forms an unusually elongated (65 angstroms) four-helix bundle, with the helices apparently stabilized by a tightly packed hydrophobic core that includes leucine zipper-type interactions and by numerous salt bridges on the mostly charged surface. Basic amino acids important for LDL receptor binding are clustered into a surface patch on one long helix. This structure provides the basis for understanding the behavior of naturally occurring mutants that can lead to atherosclerosis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, C -- Wardell, M R -- Weisgraber, K H -- Mahley, R W -- Agard, D A -- HL-41633/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1991 Jun 28;252(5014):1817-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, San Francisco 94143-0448.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2063194" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Apolipoproteins E/*chemistry/genetics/metabolism ; Binding Sites ; Computer Graphics ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Receptors, LDL/*metabolism ; X-Ray Diffraction
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  • 98
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    Structure of a legume lectin with an ordered N-linked carbohydrate in complex with lactose (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-11-08
    Description: The three-dimensional structure of the lactose complex of the Erythrina corallodendron lectin (EcorL), a dimer of N-glycosylated subunits, was determined crystallographically and refined at 2.0 angstrom resolution to an R value of 0.19. The tertiary structure of the subunit is similar to that of other legume lectins, but interference by the bulky N-linked heptasaccharide, which is exceptionally well ordered in the crystal, forces the EcorL dimer into a drastically different quaternary structure. Only the galactose moiety of the lactose ligand resides within the combining site. The galactose moiety is oriented differently from ligands in the mannose-glucose specific legume lectins and is held by hydrophobic interactions with Ala88, Tyr106, Phe131, and Ala218 and by seven hydrogen bonds, four of which are to the conserved Asp89, Asn133, and NH of Gly107. The specificity of legume lectins toward the different C-4 epimers appears to be associated with extensive variations in the outline of the variable parts of the binding sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shaanan, B -- Lis, H -- Sharon, N -- New York, N.Y. -- Science. 1991 Nov 8;254(5033):862-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1948067" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Carbohydrate Conformation ; Carbohydrate Sequence ; Computer Simulation ; Erythrina ; Glycosylation ; Hydrogen Bonding ; Lectins/*chemistry ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Oligosaccharides ; Plant Lectins ; Plants, Medicinal ; Protein Conformation ; X-Ray Diffraction
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 99
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    Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-05-31
    Description: The crystal structure of a murine adenosine deaminase complexed with 6-hydroxyl-1,6-dihydropurine ribonucleoside, a nearly ideal transition-state analog, has been determined and refined at 2.4 angstrom resolution. The structure is folded as an eight-stranded parallel alpha/beta barrel with a deep pocket at the beta-barrel COOH-terminal end wherein the inhibitor and a zinc are bound and completely sequestered. The presence of the zinc cofactor and the precise structure of the bound analog were not previously known. The 6R isomer of the analog is very tightly held in place by the coordination of the 6-hydroxyl to the zinc and the formation of nine hydrogen bonds. On the basis of the structure of the complex a stereoselective addition-elimination or SN2 mechanism of the enzyme is proposed with the zinc atom and the Glu and Asp residues playing key roles. A molecular explanation of a hereditary disease caused by several point mutations of an enzyme is also presented.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, D K -- Rudolph, F B -- Quiocho, F A -- CA14030/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1991 May 31;252(5010):1278-84.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1925539" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Deaminase/*chemistry/deficiency/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Catalysis ; Crystallization ; Immunologic Deficiency Syndromes/*enzymology/genetics ; Mice ; Models, Molecular ; Molecular Structure ; Mutation ; Protein Conformation ; Purine Nucleosides/chemistry/*metabolism ; Ribonucleosides/chemistry/*metabolism ; Zinc/metabolism
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  • 100
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    Refined structure of charybdotoxin: common motifs in scorpion toxins and insect defensins (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-12-06
    Description: Conflicting three-dimensional structures of charybdotoxin (Chtx), a blocker of K+ channels, have been previously reported. A high-resolution model depicting the tertiary structure of Chtx has been obtained by DIANA and X-PLOR calculations from new proton nuclear magnetic resonance (NMR) data. The protein possesses a small triple-stranded antiparallel beta sheet linked to a short helix by two disulfides and to an extended fragment by one disulfide, respectively. This motif also exists in all known structures of scorpion toxins, irrespective of their size, sequence, and function. Strikingly, antibacterial insect defensins also adopt this folding pattern.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bontems, F -- Roumestand, C -- Gilquin, B -- Menez, A -- Toma, F -- New York, N.Y. -- Science. 1991 Dec 6;254(5037):1521-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departement d'Ingenierie et d'Etudes des Proteines, Gif sur Yvette, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1720574" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Blood Proteins/*ultrastructure ; Charybdotoxin ; Defensins ; Magnetic Resonance Spectroscopy ; Molecular Sequence Data ; Neurotoxins/*chemistry ; Potassium Channels/drug effects ; Protein Conformation ; Scorpion Venoms/*chemistry ; Scorpions ; Sequence Alignment
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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