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  • Models, Molecular  (108)
  • American Association for the Advancement of Science (AAAS)  (108)
  • Blackwell Publishing Ltd
  • 1995-1999  (108)
  • 1999  (49)
  • 1996  (59)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (108)
  • Blackwell Publishing Ltd
Years
  • 1995-1999  (108)
Year
  • 1
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    Evolution of a protein fold in vitro (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-04-09
    Description: A "switch" mutant of the Arc repressor homodimer was constructed by interchanging the sequence positions of a hydrophobic core residue, leucine 12, and an adjacent surface polar residue, asparagine 11, in each strand of an intersubunit beta sheet. The mutant protein adopts a fold in which each beta strand is replaced by a right-handed helix and side chains in this region undergo significant repacking. The observed structural changes allow the protein to maintain solvent exposure of polar side chains and optimal burial of hydrophobic side chains. These results suggest that new protein folds can evolve from existing folds without drastic or large-scale mutagenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cordes, M H -- Walsh, N P -- McKnight, C J -- Sauer, R T -- AI-15706/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1999 Apr 9;284(5412):325-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10195898" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Asparagine/chemistry ; Circular Dichroism ; Hydrogen Bonding ; Leucine/chemistry ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Insertional ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; *Protein Folding ; *Protein Structure, Secondary ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry ; Viral Proteins/*chemistry ; Viral Regulatory and Accessory Proteins
    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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    Crystal structure of invasin: a bacterial integrin-binding protein (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-09
    Description: The Yersinia pseudotuberculosis invasin protein promotes bacterial entry by binding to host cell integrins with higher affinity than natural substrates such as fibronectin. The 2.3 angstrom crystal structure of the invasin extracellular region reveals five domains that form a 180 angstrom rod with structural similarities to tandem fibronectin type III domains. The integrin-binding surfaces of invasin and fibronectin include similarly located key residues, but in the context of different folds and surface shapes. The structures of invasin and fibronectin provide an example of convergent evolution, in which invasin presents an optimized surface for integrin binding, in comparison with host substrates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hamburger, Z A -- Brown, M S -- Isberg, R R -- Bjorkman, P J -- New York, N.Y. -- Science. 1999 Oct 8;286(5438):291-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology 156-29, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10514372" target="_blank"〉PubMed〈/a〉
    Keywords: *Adhesins, Bacterial ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Crystallography, X-Ray ; Evolution, Molecular ; Fibronectins/chemistry/metabolism ; Hydrogen Bonding ; Integrins/*metabolism ; Ligands ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Yersinia pseudotuberculosis/*chemistry/metabolism
    Print ISSN: 0036-8075
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  • 3
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    Perspectives: protein structure. Class-conscious TCR? (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, I A -- New York, N.Y. -- Science. 1999 Dec 3;286(5446):1867-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. wilson@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10610577" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens/*chemistry/immunology/metabolism ; Binding Sites ; CD4-Positive T-Lymphocytes/immunology/metabolism ; CD8-Positive T-Lymphocytes/immunology/metabolism ; Crystallography, X-Ray ; Histocompatibility Antigens Class I/chemistry/immunology/metabolism ; Histocompatibility Antigens Class II/*chemistry/immunology/metabolism ; Mice ; Models, Molecular ; Peptides/chemistry/immunology/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/immunology/metabolism
    Print ISSN: 0036-8075
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  • 4
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    Chaperonin function: folding by forced unfolding (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-04-30
    Description: The ability of the GroEL chaperonin to unfold a protein trapped in a misfolded condition was detected and studied by hydrogen exchange. The GroEL-induced unfolding of its substrate protein is only partial, requires the complete chaperonin system, and is accomplished within the 13 seconds required for a single system turnover. The binding of nucleoside triphosphate provides the energy for a single unfolding event; multiple turnovers require adenosine triphosphate hydrolysis. The substrate protein is released on each turnover even if it has not yet refolded to the native state. These results suggest that GroEL helps partly folded but blocked proteins to fold by causing them first to partially unfold. The structure of GroEL seems well suited to generate the nonspecific mechanical stretching force required for forceful protein unfolding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427652/" 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/PMC3427652/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shtilerman, M -- Lorimer, G H -- Englander, S W -- GM31847/GM/NIGMS NIH HHS/ -- R01 GM031847/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Apr 30;284(5415):822-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10221918" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Adenylyl Imidodiphosphate/metabolism ; Binding Sites ; Chaperonin 10/chemistry/metabolism/physiology ; Chaperonin 60/chemistry/metabolism/*physiology ; Hydrogen/chemistry/metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; Ribulose-Bisphosphate Carboxylase/*chemistry/metabolism
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  • 5
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    Evolution of shape complementarity and catalytic efficiency from a primordial antibody template (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-22
    Description: The crystal structure of an efficient Diels-Alder antibody catalyst at 1.9 angstrom resolution reveals almost perfect shape complementarity with its transition state analog. Comparison with highly related progesterone and Diels-Alderase antibodies that arose from the same primordial germ line template shows the relatively subtle mutational steps that were able to evolve both structural complementarity and catalytic efficiency.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, J -- Deng, Q -- Chen, J -- Houk, K N -- Bartek, J -- Hilvert, D -- Wilson, I A -- CA27489/CA/NCI NIH HHS/ -- GM38273/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Dec 17;286(5448):2345-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10600746" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Catalytic/*chemistry/genetics/*metabolism ; Binding Sites, Antibody ; Catalysis ; Chemistry, Physical ; Crystallography, X-Ray ; *Evolution, Molecular ; Haptens/chemistry/metabolism ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/chemistry/metabolism ; Ligands ; Models, Molecular ; Mutation ; Physicochemical Phenomena ; Progesterone/immunology ; Protein Conformation ; Solubility ; Temperature ; Templates, Genetic
    Print ISSN: 0036-8075
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  • 6
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    Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-08-14
    Description: Isoleucyl-transfer RNA (tRNA) synthetase (IleRS) joins Ile to tRNA(Ile) at its synthetic active site and hydrolyzes incorrectly acylated amino acids at its editing active site. The 2.2 angstrom resolution crystal structure of Staphylococcus aureus IleRS complexed with tRNA(Ile) and Mupirocin shows the acceptor strand of the tRNA(Ile) in the continuously stacked, A-form conformation with the 3' terminal nucleotide in the editing active site. To position the 3' terminus in the synthetic active site, the acceptor strand must adopt the hairpinned conformation seen in tRNA(Gln) complexed with its synthetase. The amino acid editing activity of the IleRS may result from the incorrect products shuttling between the synthetic and editing active sites, which is reminiscent of the editing mechanism of DNA polymerases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Silvian, L F -- Wang, J -- Steitz, T A -- GM22778/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Aug 13;285(5430):1074-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics, Yale University, and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10446055" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Adenosine Monophosphate/analogs & derivatives/metabolism ; Amino Acids/metabolism ; Binding Sites ; Crystallography, X-Ray ; DNA-Directed DNA Polymerase/metabolism ; Glutamate-tRNA Ligase/chemistry/metabolism ; Isoleucine/metabolism ; Isoleucine-tRNA Ligase/*chemistry/*metabolism ; Models, Molecular ; Mupirocin/chemistry/*metabolism ; Nucleic Acid Conformation ; Oligopeptides/metabolism ; Protein Conformation ; Protein Structure, Secondary ; RNA, Transfer, Gln/chemistry/metabolism ; RNA, Transfer, Ile/*chemistry/*metabolism ; Staphylococcus aureus/enzymology ; Substrate Specificity
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  • 7
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    Crystallographic evidence for preformed dimers of erythropoietin receptor before ligand activation (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-02-12
    Description: Erythropoietin receptor (EPOR) is thought to be activated by ligand-induced homodimerization. However, structures of agonist and antagonist peptide complexes of EPOR, as well as an EPO-EPOR complex, have shown that the actual dimer configuration is critical for the biological response and signal efficiency. The crystal structure of the extracellular domain of EPOR in its unliganded form at 2.4 angstrom resolution has revealed a dimer in which the individual membrane-spanning and intracellular domains would be too far apart to permit phosphorylation by JAK2. This unliganded EPOR dimer is formed from self-association of the same key binding site residues that interact with EPO-mimetic peptide and EPO ligands. This model for a preformed dimer on the cell surface provides insights into the organization, activation, and plasticity of recognition of hematopoietic cell surface receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Livnah, O -- Stura, E A -- Middleton, S A -- Johnson, D L -- Jolliffe, L K -- Wilson, I A -- GM49497/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Feb 12;283(5404):987-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9974392" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/chemistry ; Crystallography, X-Ray ; Dimerization ; Erythropoietin/metabolism ; Humans ; Hydrogen Bonding ; Janus Kinase 2 ; Ligands ; Models, Molecular ; Peptide Fragments/*chemistry/metabolism ; Peptides, Cyclic/metabolism ; Protein Conformation ; Protein-Tyrosine Kinases/metabolism ; *Proto-Oncogene Proteins ; Receptors, Erythropoietin/*chemistry/metabolism
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  • 8
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    Structure of the VHL-ElonginC-ElonginB complex: implications for VHL tumor suppressor function (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-04-16
    Description: Mutation of the VHL tumor suppressor is associated with the inherited von Hippel-Lindau (VHL) cancer syndrome and the majority of kidney cancers. VHL binds the ElonginC-ElonginB complex and regulates levels of hypoxia-inducible proteins. The structure of the ternary complex at 2.7 angstrom resolution shows two interfaces, one between VHL and ElonginC and another between ElonginC and ElonginB. Tumorigenic mutations frequently occur in a 35-residue domain of VHL responsible for ElonginC binding. A mutational patch on a separate domain of VHL indicates a second macromolecular binding site. The structure extends the similarities to the SCF (Skp1-Cul1-F-box protein) complex that targets proteins for degradation, supporting the hypothesis that VHL may function in an analogous pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stebbins, C E -- Kaelin, W G Jr -- Pavletich, N P -- New York, N.Y. -- Science. 1999 Apr 16;284(5413):455-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Structural Biology, Joan and Sanford I. Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10205047" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Cell Cycle Proteins/chemistry/metabolism ; Cloning, Molecular ; Crystallography, X-Ray ; *Genes, Tumor Suppressor ; Humans ; Hydrogen Bonding ; *Ligases ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Mutation, Missense ; Neoplasms/genetics ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry/genetics/metabolism ; S-Phase Kinase-Associated Proteins ; Surface Properties ; Transcription Factors/*chemistry/metabolism ; *Tumor Suppressor Proteins ; *Ubiquitin-Protein Ligases ; Von Hippel-Lindau Tumor Suppressor Protein ; von Hippel-Lindau Disease/*genetics
    Print ISSN: 0036-8075
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  • 9
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    Molecular architecture of the rotary motor in ATP synthase (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-11-27
    Description: Adenosine triphosphate (ATP) synthase contains a rotary motor involved in biological energy conversion. Its membrane-embedded F0 sector has a rotation generator fueled by the proton-motive force, which provides the energy required for the synthesis of ATP by the F1 domain. An electron density map obtained from crystals of a subcomplex of yeast mitochondrial ATP synthase shows a ring of 10 c subunits. Each c subunit forms an alpha-helical hairpin. The interhelical loops of six to seven of the c subunits are in close contact with the gamma and delta subunits of the central stalk. The extensive contact between the c ring and the stalk suggests that they may rotate as an ensemble during catalysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stock, D -- Leslie, A G -- Walker, J E -- New York, N.Y. -- Science. 1999 Nov 26;286(5445):1700-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10576729" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Catalysis ; Crystallization ; Crystallography, X-Ray ; Hydrogen Bonding ; Mitochondria/enzymology ; Models, Molecular ; Molecular Motor Proteins/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proton-Motive Force ; Proton-Translocating ATPases/*chemistry/metabolism ; Protons ; Saccharomyces cerevisiae/enzymology
    Print ISSN: 0036-8075
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  • 10
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    X-ray crystallographic structure of the Norwalk virus capsid (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-09
    Description: Norwalk virus, a noncultivatable human calicivirus, is the major cause of epidemic gastroenteritis in humans. The first x-ray structure of a calicivirus capsid, which consists of 180 copies of a single protein, has been determined by phase extension from a low-resolution electron microscopy structure. The capsid protein has a protruding (P) domain connected by a flexible hinge to a shell (S) domain that has a classical eight-stranded beta-sandwich motif. The structure of the P domain is unlike that of any other viral protein with a subdomain exhibiting a fold similar to that of the second domain in the eukaryotic translation elongation factor-Tu. This subdomain, located at the exterior of the capsid, has the largest sequence variation among Norwalk-like human caliciviruses and is likely to contain the determinants of strain specificity and cell binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prasad, B V -- Hardy, M E -- Dokland, T -- Bella, J -- Rossmann, M G -- Estes, M K -- New York, N.Y. -- Science. 1999 Oct 8;286(5438):287-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Verna and Marrs Mclean Department of Biochemistry, Division of Molecular Virology, Baylor College of Medicine, Houston, TX 77030, USA. bprasad@bcm.tmc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10514371" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Capsid/*chemistry/metabolism ; *Capsid Proteins ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Dimerization ; Genome, Viral ; Humans ; Hydrogen Bonding ; Image Processing, Computer-Assisted ; Models, Molecular ; Molecular Sequence Data ; Norwalk virus/*chemistry/genetics/physiology ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins/chemistry ; Virus Assembly
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  • 11
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    Chemical etiology of nucleic acid structure (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-06-26
    Description: Systematic chemical studies indicate that the capability of Watson-Crick base-pairing is widespread among potentially natural nucleic acid alternatives taken from RNA's close structural neighborhood. A comparison of RNA and such alternatives with regard to chemical properties that are fundamental to the biological function of RNA provides chemical facts that may contain clues to RNA's origin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eschenmoser, A -- New York, N.Y. -- Science. 1999 Jun 25;284(5423):2118-24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Skaggs Institute for Chemical Biology at The Scripps Research Institute (TSRI), 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10381870" target="_blank"〉PubMed〈/a〉
    Keywords: *Base Pairing ; DNA/chemistry ; *Evolution, Chemical ; Isomerism ; Models, Molecular ; Nucleic Acid Conformation ; Oligonucleotides/*chemistry ; RNA/*chemistry ; Structure-Activity Relationship ; Templates, Genetic
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  • 12
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    Structural basis of Smad2 recognition by the Smad anchor for receptor activation (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-30
    Description: The Smad proteins mediate transforming growth factor-beta (TGFbeta) signaling from the transmembrane serine-threonine receptor kinases to the nucleus. The Smad anchor for receptor activation (SARA) recruits Smad2 to the TGFbeta receptors for phosphorylation. The crystal structure of a Smad2 MH2 domain in complex with the Smad-binding domain (SBD) of SARA has been determined at 2.2 angstrom resolution. SARA SBD, in an extended conformation comprising a rigid coil, an alpha helix, and a beta strand, interacts with the beta sheet and the three-helix bundle of Smad2. Recognition between the SARA rigid coil and the Smad2 beta sheet is essential for specificity, whereas interactions between the SARA beta strand and the Smad2 three-helix bundle contribute significantly to binding affinity. Comparison of the structures between Smad2 and a comediator Smad suggests a model for how receptor-regulated Smads are recognized by the type I receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, G -- Chen, Y G -- Ozdamar, B -- Gyuricza, C A -- Chong, P A -- Wrana, J L -- Massague, J -- Shi, Y -- CA85171/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2000 Jan 7;287(5450):92-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, NJ 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10615055" target="_blank"〉PubMed〈/a〉
    Keywords: *Activin Receptors, Type I ; Amino Acid Sequence ; Binding Sites ; Carrier Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phosphorylation ; Point Mutation ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/chemistry/genetics/metabolism ; Receptors, Transforming Growth Factor beta/chemistry/genetics/metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Signal Transduction ; Smad2 Protein ; Trans-Activators/*chemistry/genetics/*metabolism ; Zinc Fingers
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  • 13
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    The rotary enzyme of the cell: the rotation of F1-ATPase (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-01-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Noji, H -- New York, N.Y. -- Science. 1998 Dec 4;282(5395):1844-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉"Genetic Programming" Team 13, Teikyo Unmiversity Biotechnology Center, Nogawa, Kawasaki, Japan. noji@phys.keio.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9874637" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/chemistry/metabolism ; Adenosine Triphosphate/metabolism ; *Awards and Prizes ; *Biochemistry/history ; Catalytic Domain ; History, 20th Century ; Japan ; Microscopy, Fluorescence ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Proton-Translocating ATPases/*chemistry/*metabolism ; Protons ; Thermodynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 14
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    Crystal structure of the ectodomain of human transferrin receptor (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-26
    Description: The transferrin receptor (TfR) undergoes multiple rounds of clathrin-mediated endocytosis and reemergence at the cell surface, importing iron-loaded transferrin (Tf) and recycling apotransferrin after discharge of iron in the endosome. The crystal structure of the dimeric ectodomain of the human TfR, determined here to 3.2 angstroms resolution, reveals a three-domain subunit. One domain closely resembles carboxy- and aminopeptidases, and features of membrane glutamate carboxypeptidase can be deduced from the TfR structure. A model is proposed for Tf binding to the receptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lawrence, C M -- Ray, S -- Babyonyshev, M -- Galluser, R -- Borhani, D W -- Harrison, S C -- New York, N.Y. -- Science. 1999 Oct 22;286(5440):779-82.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Children's Hospital Laboratory of Molecular Medicine, 320 Longwood Avenue, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10531064" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; CHO Cells ; Carboxypeptidases/chemistry ; Cell Membrane/chemistry ; Conserved Sequence ; Cricetinae ; Crystallography, X-Ray ; Dimerization ; Ferric Compounds/metabolism ; Glycosylation ; Humans ; Hydrogen-Ion Concentration ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Transferrin/*chemistry/metabolism ; Transferrin/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 15
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    Evolutionarily conserved pathways of energetic connectivity in protein families (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-09
    Description: For mapping energetic interactions in proteins, a technique was developed that uses evolutionary data for a protein family to measure statistical interactions between amino acid positions. For the PDZ domain family, this analysis predicted a set of energetically coupled positions for a binding site residue that includes unexpected long-range interactions. Mutational studies confirm these predictions, demonstrating that the statistical energy function is a good indicator of thermodynamic coupling in proteins. Sets of interacting residues form connected pathways through the protein fold that may be the basis for efficient energy conduction within proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lockless, S W -- Ranganathan, R -- New York, N.Y. -- Science. 1999 Oct 8;286(5438):295-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75235-9050, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10514373" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/chemistry/metabolism ; Binding Sites ; Conserved Sequence ; *Evolution, Molecular ; Models, Molecular ; Mutation ; Probability ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Proteins/*chemistry/*metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Sequence Alignment ; Statistics as Topic ; Thermodynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 16
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    Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-11-13
    Description: The E6AP ubiquitin-protein ligase (E3) mediates the human papillomavirus-induced degradation of the p53 tumor suppressor in cervical cancer and is mutated in Angelman syndrome, a neurological disorder. The crystal structure of the catalytic hect domain of E6AP reveals a bilobal structure with a broad catalytic cleft at the junction of the two lobes. The cleft consists of conserved residues whose mutation interferes with ubiquitin-thioester bond formation and is the site of Angelman syndrome mutations. The crystal structure of the E6AP hect domain bound to the UbcH7 ubiquitin-conjugating enzyme (E2) reveals the determinants of E2-E3 specificity and provides insights into the transfer of ubiquitin from the E2 to the E3.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, L -- Kinnucan, E -- Wang, G -- Beaudenon, S -- Howley, P M -- Huibregtse, J M -- Pavletich, N P -- New York, N.Y. -- Science. 1999 Nov 12;286(5443):1321-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular Biochemistry and Biophysics Program, Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10558980" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Angelman Syndrome/genetics ; Binding Sites ; Catalytic Domain ; Conserved Sequence ; Crystallography, X-Ray ; Cysteine/chemistry ; Humans ; Ligases/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Structure, Secondary ; Substrate Specificity ; Ubiquitin-Conjugating Enzymes ; Ubiquitin-Protein Ligases ; Ubiquitins/*metabolism
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  • 17
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    Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-11-24
    Description: Binding of virus particles to specific host cell surface receptors is known to be an obligatory step in infection even though the molecular basis for these interactions is not well characterized. The crystal structure of the adenovirus fiber knob domain in complex with domain I of its human cellular receptor, coxsackie and adenovirus receptor (CAR), is presented here. Surface-exposed loops on knob contact one face of CAR, forming a high-affinity complex. Topology mismatches between interacting surfaces create interfacial solvent-filled cavities and channels that may be targets for antiviral drug therapy. The structure identifies key determinants of binding specificity, which may suggest ways to modify the tropism of adenovirus-based gene therapy vectors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bewley, M C -- Springer, K -- Zhang, Y B -- Freimuth, P -- Flanagan, J M -- 1P41 RR12408-01A1/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1999 Nov 19;286(5444):1579-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10567268" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviruses, Human/chemistry/*metabolism ; Amino Acid Substitution ; Binding Sites ; Capsid/*chemistry/*metabolism ; *Capsid Proteins ; Coxsackie and Adenovirus Receptor-Like Membrane Protein ; Crystallization ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Mutagenesis ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Virus/*chemistry/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Thermodynamics
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  • 18
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    Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-09
    Description: Crystal structures of the Asp96 to Asn mutant of the light-driven proton pump bacteriorhodopsin and its M photointermediate produced by illumination at ambient temperature have been determined to 1.8 and 2.0 angstroms resolution, respectively. The trapped photoproduct corresponds to the late M state in the transport cycle-that is, after proton transfer to Asp85 and release of a proton to the extracellular membrane surface, but before reprotonation of the deprotonated retinal Schiff base. Its density map describes displacements of side chains near the retinal induced by its photoisomerization to 13-cis,15-anti and an extensive rearrangement of the three-dimensional network of hydrogen-bonded residues and bound water that accounts for the changed pKa values (where Ka is the acid constant) of the Schiff base and Asp85. The structural changes detected suggest the means for conserving energy at the active site and for ensuring the directionality of proton translocation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Luecke, H -- Schobert, B -- Richter, H T -- Cartailler, J P -- Lanyi, J K -- R01-GM29498/GM/NIGMS NIH HHS/ -- R01-GM56445/GM/NIGMS NIH HHS/ -- R01-GM59970/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Oct 8;286(5438):255-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA. hudel@uci.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10514362" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/*chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Cytoplasm/chemistry ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Ion Transport ; Isomerism ; Light ; Models, Molecular ; Photolysis ; Photons ; Point Mutation ; Protein Conformation ; Protein Structure, Secondary ; Proton Pumps/*chemistry/*metabolism ; Protons ; Retinaldehyde/chemistry/metabolism ; Schiff Bases ; Thermodynamics ; Water
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  • 19
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    Two-metal-Ion catalysis in adenylyl cyclase (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-07-31
    Description: Adenylyl cyclase (AC) converts adenosine triphosphate (ATP) to cyclic adenosine monophosphate, a ubiquitous second messenger that regulates many cellular functions. Recent structural studies have revealed much about the structure and function of mammalian AC but have not fully defined its active site or catalytic mechanism. Four crystal structures were determined of the catalytic domains of AC in complex with two different ATP analogs and various divalent metal ions. These structures provide a model for the enzyme-substrate complex and conclusively demonstrate that two metal ions bind in the active site. The similarity of the active site of AC to those of DNA polymerases suggests that the enzymes catalyze phosphoryl transfer by the same two-metal-ion mechanism and likely have evolved from a common ancestor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tesmer, J J -- Sunahara, R K -- Johnson, R A -- Gosselin, G -- Gilman, A G -- Sprang, S R -- DK38828/DK/NIDDK NIH HHS/ -- DK46371/DK/NIDDK NIH HHS/ -- GM34497/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Jul 30;285(5428):756-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75235-9050, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10427002" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Adenylyl Cyclase Inhibitors ; Adenylyl Cyclases/chemistry/genetics/*metabolism ; Animals ; Aspartic Acid/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Deoxyadenine Nucleotides/metabolism/pharmacology ; Dideoxynucleotides ; Dimerization ; Enzyme Inhibitors/metabolism ; Hydrogen Bonding ; Ligands ; Magnesium/*metabolism ; Manganese/*metabolism ; Models, Molecular ; Mutation ; Protein Conformation ; Protein Folding ; Rats ; Thionucleotides/metabolism/pharmacology ; Zinc/*metabolism
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    The race to the ribosome structure (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 1999 Sep 24;285(5436):2048-51.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10523195" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry ; Cryoelectron Microscopy ; Crystallization ; Crystallography, X-Ray ; Image Processing, Computer-Assisted ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Ribosomal/chemistry ; RNA, Transfer/chemistry/metabolism ; Ribosomal Proteins/chemistry ; Ribosomes/*chemistry/*ultrastructure
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  • 21
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    Ribosome finally begins to yield its complete structure (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-09-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 1999 Aug 27;285(5432):1343.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10490407" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Haloarcula marismortui/ultrastructure ; Models, Molecular ; Neutrons ; Nucleic Acid Conformation ; Protein Conformation ; RNA, Ribosomal/*chemistry ; Ribosomal Proteins/*chemistry ; Ribosomes/*chemistry/*ultrastructure ; Scattering, Radiation ; Thermus thermophilus/ultrastructure
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  • 22
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    The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-07-03
    Description: The electrostatic influence of the central cavity and pore alpha helices in the potassium ion channel from Streptomyces lividans (KcsA K+ channel) was analyzed by solving the finite difference Poisson equation. The cavity and helices overcome the destabilizing influence of the membrane and stabilize a cation at the membrane center. The electrostatic effect of the pore helices is large compared to that described for water-soluble proteins because of the low dielectric membrane environment. The combined contributions of the ion self-energy and the helix electrostatic field give rise to selectivity for monovalent cations in the water-filled cavity. Thus, the K+ channel uses simple electrostatic principles to solve the fundamental problem of ion destabilization by the cell membrane lipid bilayer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roux, B -- MacKinnon, R -- GM47400/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Jul 2;285(5424):100-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉GRTM, Dipartements de Physique et Chimie, Universite de Montreal, Case Postal 6128, succursale Centre-Ville, Montreal, Canada H3C 3J7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10390357" target="_blank"〉PubMed〈/a〉
    Keywords: *Bacterial Proteins ; Cations, Monovalent/*metabolism ; Cell Membrane/*chemistry/metabolism ; Crystallography, X-Ray ; Ion Transport ; Lipid Bilayers ; Models, Molecular ; Potassium/*metabolism ; Potassium Channels/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Static Electricity ; Streptomyces/*chemistry ; Thermodynamics ; Water
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  • 23
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    Structure of a transcribing T7 RNA polymerase initiation complex (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-22
    Description: The structure of a T7 RNA polymerase (T7 RNAP) initiation complex captured transcribing a trinucleotide of RNA from a 17-base pair promoter DNA containing a 5-nucleotide single-strand template extension was determined at a resolution of 2.4 angstroms. Binding of the upstream duplex portion of the promoter occurs in the same manner as that in the open promoter complex, but the single-stranded template is repositioned to place the +4 base at the catalytic active site. Thus, synthesis of RNA in the initiation phase leads to accumulation or "scrunching" of the template in the enclosed active site pocket of T7 RNAP. Only three base pairs of heteroduplex are formed before the RNA peels off the template.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheetham, G M -- Steitz, T A -- GM-22778/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Dec 17;286(5448):2305-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10600732" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacteriophage T7/enzymology ; Catalytic Domain ; Conserved Sequence ; Crystallography, X-Ray ; DNA, Single-Stranded/*chemistry/genetics/metabolism ; DNA-Directed DNA Polymerase/chemistry/metabolism ; DNA-Directed RNA Polymerases/*chemistry/*metabolism ; Hydrogen Bonding ; Models, Molecular ; N-Acetylmuramoyl-L-alanine Amidase/metabolism ; Nucleic Acid Conformation ; Nucleic Acid Heteroduplexes/chemistry/metabolism ; Oligoribonucleotides/chemistry/metabolism ; *Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Messenger/biosynthesis/*chemistry/genetics ; Substrate Specificity ; Templates, Genetic ; *Transcription, Genetic ; Viral Proteins
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  • 24
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    Structural basis of chaperone function and pilus biogenesis (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-08-14
    Description: Many Gram-negative pathogens assemble architecturally and functionally diverse adhesive pili on their surfaces by the chaperone-usher pathway. Immunoglobulin-like periplasmic chaperones escort pilus subunits to the usher, a large protein complex that facilitates the translocation and assembly of subunits across the outer membrane. The crystal structure of the PapD-PapK chaperone-subunit complex, determined at 2.4 angstrom resolution, reveals that the chaperone functions by donating its G(1) beta strand to complete the immunoglobulin-like fold of the subunit via a mechanism termed donor strand complementation. The structure of the PapD-PapK complex also suggests that during pilus biogenesis, every subunit completes the immunoglobulin-like fold of its neighboring subunit via a mechanism termed donor strand exchange.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sauer, F G -- Futterer, K -- Pinkner, J S -- Dodson, K W -- Hultgren, S J -- Waksman, G -- R01AI29549/AI/NIAID NIH HHS/ -- R01DK51406/DK/NIDDK NIH HHS/ -- R01GM54033/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Aug 13;285(5430):1058-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10446050" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; Escherichia coli ; *Escherichia coli Proteins ; Fimbriae Proteins ; Fimbriae, Bacterial/chemistry/*metabolism/ultrastructure ; Models, Molecular ; Molecular Chaperones/*chemistry/*metabolism ; Molecular Sequence Data ; *Periplasmic Proteins ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Sequence Alignment
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  • 25
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    Oxidative phosphorylation at the fin de siecle (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-03-05
    Description: Mitochondria produce most of the energy in animal cells by a process called oxidative phosphorylation. Electrons are passed along a series of respiratory enzyme complexes located in the inner mitochondrial membrane, and the energy released by this electron transfer is used to pump protons across the membrane. The resultant electrochemical gradient enables another complex, adenosine 5'-triphosphate (ATP) synthase, to synthesize the energy carrier ATP. Important new mechanistic insights into oxidative phosphorylation have emerged from recent three-dimensional structural analyses of ATP synthase and two of the respiratory enzyme complexes, cytochrome bc1 and cytochrome c oxidase. This work, and new enzymological studies of ATP synthase's unusual catalytic mechanism, are reviewed here.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saraste, M -- New York, N.Y. -- Science. 1999 Mar 5;283(5407):1488-93.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 102209, D-69012, Heidelberg, Germany. Saraste@EMBL-Heidelberg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10066163" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Electron Transport Complex II ; Electron Transport Complex III/chemistry/metabolism ; Electron Transport Complex IV/chemistry/metabolism ; Mitochondria/enzymology/*metabolism ; Models, Molecular ; Molecular Motor Proteins ; Multienzyme Complexes/chemistry/metabolism ; NAD(P)H Dehydrogenase (Quinone)/chemistry/metabolism ; *Oxidative Phosphorylation ; Oxidoreductases/chemistry/metabolism ; Proton Pumps ; Proton-Translocating ATPases/chemistry/genetics/*metabolism ; Succinate Dehydrogenase/chemistry/metabolism
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  • 26
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    Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-06-12
    Description: The editing enzyme double-stranded RNA adenosine deaminase includes a DNA binding domain, Zalpha, which is specific for left-handed Z-DNA. The 2.1 angstrom crystal structure of Zalpha complexed to DNA reveals that the substrate is in the left-handed Z conformation. The contacts between Zalpha and Z-DNA are made primarily with the "zigzag" sugar-phosphate backbone, which provides a basis for the specificity for the Z conformation. A single base contact is observed to guanine in the syn conformation, characteristic of Z-DNA. Intriguingly, the helix-turn-helix motif, frequently used to recognize B-DNA, is used by Zalpha to contact Z-DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schwartz, T -- Rould, M A -- Lowenhaupt, K -- Herbert, A -- Rich, A -- New York, N.Y. -- Science. 1999 Jun 11;284(5421):1841-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10364558" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Deaminase/*chemistry/metabolism ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; Helix-Turn-Helix Motifs ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; RNA-Binding Proteins ; Substrate Specificity ; Water/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-22
    Description: Ribosome recycling factor (RRF), together with elongation factor G (EF-G), catalyzes recycling of ribosomes after one round of protein synthesis. The crystal structure of RRF was determined at 2.55 angstrom resolution. The protein has an unusual fold where domain I is a long three-helix bundle and domain II is a three-layer beta/alpha/beta sandwich. The molecule superimposes almost perfectly with a transfer RNA (tRNA) except that the amino acid-binding 3' end is missing. The mimicry suggests that RRF interacts with the posttermination ribosomal complex in a similar manner to a tRNA, leading to disassembly of the complex. The structural arrangement of this mimicry is entirely different from that of other cases of less pronounced mimicry of tRNA so far described.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Selmer, M -- Al-Karadaghi, S -- Hirokawa, G -- Kaji, A -- Liljas, A -- New York, N.Y. -- Science. 1999 Dec 17;286(5448):2349-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biophysics, Center for Chemistry and Chemical Engineering, Lund University, Post Office Box 124, SE-22100 Lund, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10600747" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Models, Molecular ; *Molecular Mimicry ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptide Elongation Factor G/chemistry ; Protein Biosynthesis ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry/*metabolism ; RNA, Bacterial/chemistry/metabolism ; RNA, Fungal/chemistry/metabolism ; RNA, Transfer/*chemistry/metabolism ; RNA, Transfer, Phe/chemistry/metabolism ; Ribosomal Proteins ; Ribosomes/*metabolism ; Sequence Alignment ; Thermotoga maritima/*chemistry/metabolism
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    A glycyl radical site in the crystal structure of a class III ribonucleotide reductase (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-03-05
    Description: Ribonucleotide reductases catalyze the reduction of ribonucleotides to deoxyribonucleotides. Three classes have been identified, all using free-radical chemistry but based on different cofactors. Classes I and II have been shown to be evolutionarily related, whereas the origin of anaerobic class III has remained elusive. The structure of a class III enzyme suggests a common origin for the three classes but shows differences in the active site that can be understood on the basis of the radical-initiation system and source of reductive electrons, as well as a unique protein glycyl radical site. A possible evolutionary relationship between early deoxyribonucleotide metabolism and primary anaerobic metabolism is suggested.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Logan, D T -- Andersson, J -- Sjoberg, B M -- Nordlund, P -- New York, N.Y. -- Science. 1999 Mar 5;283(5407):1499-504.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Department of Molecular Biology, Stockholm University, S-106 91 Stockholm, Sweden. derek@biokemi.su.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10066165" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyltransferases/chemistry/metabolism ; Amino Acid Sequence ; Anaerobiosis ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Glycine/*chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Ribonucleotide Reductases/*chemistry/genetics/metabolism ; Viral Proteins/chemistry
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    Structural rearrangements underlying K+-channel activation gating (1999)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1999-07-03
    Description: The intramembrane molecular events underlying activation gating in the Streptomyces K+ channel were investigated by site-directed spin-labeling methods and electron paramagnetic resonance spectroscopy. A comparison of the closed and open conformations of the channel revealed periodic changes in spin-label mobility and intersubunit spin-spin interaction consistent with rigid-body movements of the two transmembrane helices TM1 and TM2. These changes involve translations and counterclockwise rotations of both helices relative to the center of symmetry of the channel. The movement of TM2 increases the diameter of the permeation pathway along the point of convergence of the four subunits, thus opening the pore. Although the extracellular residues flanking the selectivity filter remained immobile during gating, small movements were detected at the C-terminal end of the pore helix, with possible implications to the gating mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perozo, E -- Cortes, D M -- Cuello, L G -- GM54690/GM/NIGMS NIH HHS/ -- GM57846/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Jul 2;285(5424):73-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Physiology and Biological Physics and Center for Structural Biology, University of Virginia Health Sciences Center, Charlottesville, VA 22906-0011, USA. eperozo@virginia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10390363" target="_blank"〉PubMed〈/a〉
    Keywords: *Bacterial Proteins ; Binding Sites ; Circular Dichroism ; Cysteine/chemistry ; Electron Spin Resonance Spectroscopy ; Hydrogen-Ion Concentration ; *Ion Channel Gating ; Models, Molecular ; Potassium/*metabolism ; Potassium Channels/*chemistry/*physiology ; Protein Conformation ; Protein Structure, Secondary ; Rubidium/metabolism ; Sequence Deletion ; Streptomyces/chemistry/physiology
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  • 30
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    Implication of tubby proteins as transcription factors by structure-based functional analysis (1999)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1999-12-11
    Description: Tubby-like proteins (TULPs) are found in a broad range of multicellular organisms. In mammals, genetic mutation of tubby or other TULPs can result in one or more of three disease phenotypes: obesity (from which the name "tubby" is derived), retinal degeneration, and hearing loss. These disease phenotypes indicate a vital role for tubby proteins; however, no biochemical function has yet been ascribed to any member of this protein family. A structure-directed approach was employed to investigate the biological function of these proteins. The crystal structure of the core domain from mouse tubby was determined at a resolution of 1.9 angstroms. From primarily structural clues, experiments were devised, the results of which suggest that TULPs are a unique family of bipartite transcription factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boggon, T J -- Shan, W S -- Santagata, S -- Myers, S C -- Shapiro, L -- New York, N.Y. -- Science. 1999 Dec 10;286(5447):2119-25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Department of Physiology and Biophysics, Ruttenberg Cancer Center, Mount Sinai School of Medicine of New York University, New York, NY 10029, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10591637" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing ; Alternative Splicing ; Amino Acid Sequence ; Animals ; Cell Line ; Cell Nucleus/chemistry ; Crystallography, X-Ray ; DNA/metabolism ; Eye Proteins/*chemistry/genetics/*metabolism ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry/genetics/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Sequence Alignment ; Transcription Factors/*chemistry/genetics/*metabolism ; Transcriptional Activation
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    Oligomeric structure of the human EphB2 receptor SAM domain (1999)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1999-02-05
    Description: The sterile alpha motif (SAM) domain is a protein interaction module that is present in diverse signal-transducing proteins. SAM domains are known to form homo- and hetero-oligomers. The crystal structure of the SAM domain from an Eph receptor tyrosine kinase, EphB2, reveals two large interfaces. In one interface, adjacent monomers exchange amino-terminal peptides that insert into a hydrophobic groove on each neighbor. A second interface is composed of the carboxyl-terminal helix and a nearby loop. A possible oligomer, constructed from a combination of these binding modes, may provide a platform for the formation of larger protein complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thanos, C D -- Goodwill, K E -- Bowie, J U -- New York, N.Y. -- Science. 1999 Feb 5;283(5403):833-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UCLA-DOE Laboratory of Structural Biology and Molecular Medicine and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9933164" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Dimerization ; GRB10 Adaptor Protein ; Humans ; Hydrogen Bonding ; Kinesin/metabolism ; Models, Molecular ; Myosins/metabolism ; Phosphorylation ; *Protein Conformation ; Protein Structure, Secondary ; Protein Tyrosine Phosphatases/metabolism ; Proteins/metabolism ; Receptor Aggregation ; Receptor Protein-Tyrosine Kinases/*chemistry/metabolism ; Receptor, EphB2 ; Recombinant Proteins/chemistry/metabolism ; Surface Properties
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    Three-dimensional structure of a recombinant gap junction membrane channel (1999)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1999-02-19
    Description: Gap junction membrane channels mediate electrical and metabolic coupling between adjacent cells. The structure of a recombinant cardiac gap junction channel was determined by electron crystallography at resolutions of 7.5 angstroms in the membrane plane and 21 angstroms in the vertical direction. The dodecameric channel was formed by the end-to-end docking of two hexamers, each of which displayed 24 rods of density in the membrane interior, which is consistent with an alpha-helical conformation for the four transmembrane domains of each connexin subunit. The transmembrane alpha-helical rods contrasted with the double-layered appearance of the extracellular domains. Although not indicative for a particular type of secondary structure, the protein density that formed the extracellular vestibule provided a tight seal to exclude the exchange of substances with the extracellular milieu.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Unger, V M -- Kumar, N M -- Gilula, N B -- Yeager, M -- New York, N.Y. -- Science. 1999 Feb 19;283(5405):1176-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Scripps Research Institute, Department of Cell Biology, 10550 North Torrey Pines Road, Division of Cardiovascular Diseases, Scripps Clinic, 10666 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10024245" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Connexin 43/*chemistry ; Cricetinae ; Crystallography ; Gap Junctions/*chemistry/ultrastructure ; Lipid Bilayers/chemistry ; Models, Molecular ; Mutation ; Myocardium/*chemistry/ultrastructure ; Protein Conformation ; *Protein Structure, Secondary ; Recombinant Proteins/chemistry
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    X-ray crystal structures of 70S ribosome functional complexes (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-09-25
    Description: Structures of 70S ribosome complexes containing messenger RNA and transfer RNA (tRNA), or tRNA analogs, have been solved by x-ray crystallography at up to 7.8 angstrom resolution. Many details of the interactions between tRNA and the ribosome, and of the packing arrangements of ribosomal RNA (rRNA) helices in and between the ribosomal subunits, can be seen. Numerous contacts are made between the 30S subunit and the P-tRNA anticodon stem-loop; in contrast, the anticodon region of A-tRNA is much more exposed. A complex network of molecular interactions suggestive of a functional relay is centered around the long penultimate stem of 16S rRNA at the subunit interface, including interactions involving the "switch" helix and decoding site of 16S rRNA, and RNA bridges from the 50S subunit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cate, J H -- Yusupov, M M -- Yusupova, G Z -- Earnest, T N -- Noller, H F -- GM-17129/GM/NIGMS NIH HHS/ -- GM-59140/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Sep 24;285(5436):2095-104.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA. cate@wi.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10497122" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon/metabolism ; Bacterial Proteins/chemistry/metabolism ; Base Pairing ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Fourier Analysis ; Models, Molecular ; Nucleic Acid Conformation ; Peptide Elongation Factors/metabolism ; Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Ribosomal/*chemistry/metabolism ; RNA, Ribosomal, 16S/chemistry ; RNA, Ribosomal, 23S/chemistry ; RNA, Transfer/*chemistry/metabolism ; Ribosomal Proteins/chemistry/metabolism ; Ribosomes/*chemistry/*physiology/ultrastructure ; Thermus thermophilus/*chemistry/ultrastructure
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    Crystal structure of human ZAG, a fat-depleting factor related to MHC molecules (1999)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1999-04-17
    Description: Zn-alpha2-glycoprotein (ZAG) is a soluble protein that is present in serum and other body fluids. ZAG stimulates lipid degradation in adipocytes and causes the extensive fat losses associated with some advanced cancers. The 2.8 angstrom crystal structure of ZAG resembles a class I major histocompatibility complex (MHC) heavy chain, but ZAG does not bind the class I light chain beta2-microglobulin. The ZAG structure includes a large groove analogous to class I MHC peptide binding grooves. Instead of a peptide, the ZAG groove contains a nonpeptidic compound that may be implicated in lipid catabolism under normal or pathological conditions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanchez, L M -- Chirino, A J -- Bjorkman, P j -- New York, N.Y. -- Science. 1999 Mar 19;283(5409):1914-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10206894" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Glycoproteins/blood/*chemistry/isolation & purification/metabolism ; Glycosylation ; HLA-A2 Antigen/chemistry/metabolism ; Histocompatibility Antigens Class I/*chemistry ; Humans ; Hydrogen Bonding ; Ligands ; Lipid Metabolism ; Models, Molecular ; Peptides/metabolism ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Seminal Plasma Proteins ; beta 2-Microglobulin/metabolism
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    Structure of human pro-matrix metalloproteinase-2: activation mechanism revealed (1999)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1999-06-05
    Description: Matrix metalloproteinases (MMPs) catalyze extracellular matrix degradation. Control of their activity is a promising target for therapy of diseases characterized by abnormal connective tissue turnover. MMPs are expressed as latent proenzymes that are activated by proteolytic cleavage that triggers a conformational change in the propeptide (cysteine switch). The structure of proMMP-2 reveals how the propeptide shields the catalytic cleft and that the cysteine switch may operate through cleavage of loops essential for propeptide stability.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morgunova, E -- Tuuttila, A -- Bergmann, U -- Isupov, M -- Lindqvist, Y -- Schneider, G -- Tryggvason, K -- New York, N.Y. -- Science. 1999 Jun 4;284(5420):1667-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10356396" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Catalytic Domain ; Enzyme Activation ; Enzyme Precursors/*chemistry/metabolism ; Fibronectins/chemistry ; Gelatinases/*chemistry/metabolism ; Hemopexin/chemistry ; Humans ; Hydrogen Bonding ; Matrix Metalloproteinase 2 ; Metalloendopeptidases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary
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    Crystal structure of a conserved ribosomal protein-RNA complex (1999)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1999-05-15
    Description: The structure of a highly conserved complex between a 58-nucleotide domain of large subunit ribosomal RNA and the RNA-binding domain of ribosomal protein L11 has been solved at 2.8 angstrom resolution. It reveals a precisely folded RNA structure that is stabilized by extensive tertiary contacts and contains an unusually large core of stacked bases. A bulge loop base from one hairpin of the RNA is intercalated into the distorted major groove of another helix; the protein locks this tertiary interaction into place by binding to the intercalated base from the minor groove side. This direct interaction with a key ribosomal RNA tertiary interaction suggests that part of the role of L11 is to stabilize an unusual RNA fold within the ribosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Conn, G L -- Draper, D E -- Lattman, E E -- Gittis, A G -- R37 GM29048/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 May 14;284(5417):1171-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10325228" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/metabolism ; Base Pairing ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Peptide Elongation Factor G ; Peptide Elongation Factors/metabolism ; Phylogeny ; Protein Conformation ; RNA, Bacterial/*chemistry/metabolism ; RNA, Ribosomal/*chemistry/metabolism ; Ribosomal Proteins/*chemistry/metabolism
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    New leads to cancer, arthritis therapies (1999)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1999-06-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hagmann, M -- New York, N.Y. -- Science. 1999 Jun 4;284(5420):1600-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10383332" target="_blank"〉PubMed〈/a〉
    Keywords: ADAM Proteins ; Animals ; Antineoplastic Agents ; Antirheumatic Agents ; Arthritis/*drug therapy ; Binding Sites ; Cloning, Molecular ; Enzyme Precursors/chemistry/metabolism ; Gelatinases/antagonists & inhibitors/*chemistry/metabolism ; Humans ; Matrix Metalloproteinase 2 ; Metalloendopeptidases/antagonists & inhibitors/*chemistry/genetics/metabolism ; Mice ; Models, Molecular ; Neoplasms/*drug therapy ; Procollagen N-Endopeptidase ; Protease Inhibitors/*pharmacology ; Protein Conformation ; Protein Structure, Secondary
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    Crystal structure of the human papillomavirus type 18 E2 activation domain (1999)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1999-06-05
    Description: The papillomavirus E2 protein regulates viral transcription and DNA replication through interactions with cellular and viral proteins. The amino-terminal activation domain, which represents a protein class whose structural themes are poorly understood, contains key residues that mediate these functional contacts. The crystal structure of a protease-resistant core of the human papillomavirus type 18 E2 activation domain reveals a novel fold creating a cashew-shaped form with a glutamine-rich alpha helix packed against a beta-sheet framework. The protein surface shows extensive overlap of determinants for replication and transcription. The structure broadens the concept of activators to include proteins with potentially malleable, but certainly ordered, structures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harris, S F -- Botchan, M R -- CA30490/CA/NCI NIH HHS/ -- CA42414/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1999 Jun 4;284(5420):1673-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10356398" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Crystallization ; Crystallography, X-Ray ; DNA Replication ; Evolution, Molecular ; Humans ; Models, Molecular ; Molecular Sequence Data ; Oncogene Proteins, Viral/*chemistry/physiology ; Papillomaviridae/*chemistry/physiology ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Trans-Activators/*chemistry/physiology ; Virus Replication
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    Genetic engineers aim to soup up crop photosynthesis (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-01-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mann, C C -- New York, N.Y. -- Science. 1999 Jan 15;283(5400):314-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9925484" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Dioxide/metabolism ; Crops, Agricultural/enzymology/genetics/*metabolism ; Energy Metabolism ; *Genetic Engineering ; Models, Molecular ; Phosphoenolpyruvate Carboxylase/genetics/metabolism ; *Photosynthesis ; Ribulose-Bisphosphate Carboxylase/chemistry/*genetics/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    How chaperones protect virgin proteins (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-09-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eisenberg, D -- New York, N.Y. -- Science. 1999 Aug 13;285(5430):1021-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉DOE Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles, CA 90095, USA. david@mbi.ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10475844" target="_blank"〉PubMed〈/a〉
    Keywords: Adhesins, Bacterial/chemistry/metabolism ; *Adhesins, Escherichia coli ; Bacterial Outer Membrane Proteins/chemistry/metabolism ; Bacterial Proteins/chemistry/*metabolism ; Crystallography, X-Ray ; Escherichia coli/metabolism/ultrastructure ; *Escherichia coli Proteins ; Fimbriae Proteins ; Fimbriae, Bacterial/*metabolism/ultrastructure ; Membrane Proteins/chemistry/*metabolism ; Models, Molecular ; Molecular Chaperones/*chemistry/*metabolism ; *Periplasmic Proteins ; Protein Folding ; Protein Structure, Secondary ; Thermodynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Structure of the Escherichia coli fumarate reductase respiratory complex (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-06-18
    Description: The integral membrane protein fumarate reductase catalyzes the final step of anaerobic respiration when fumarate is the terminal electron acceptor. The homologous enzyme succinate dehydrogenase also plays a prominent role in cellular energetics as a member of the Krebs cycle and as complex II of the aerobic respiratory chain. Fumarate reductase consists of four subunits that contain a covalently linked flavin adenine dinucleotide, three different iron-sulfur clusters, and at least two quinones. The crystal structure of intact fumarate reductase has been solved at 3.3 angstrom resolution and demonstrates that the cofactors are arranged in a nearly linear manner from the membrane-bound quinone to the active site flavin. Although fumarate reductase is not associated with any proton-pumping function, the two quinones are positioned on opposite sides of the membrane in an arrangement similar to that of the Q-cycle organization observed for cytochrome bc1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Iverson, T M -- Luna-Chavez, C -- Cecchini, G -- Rees, D C -- New York, N.Y. -- Science. 1999 Jun 18;284(5422):1961-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Option in Biochemistry, 147-75CH, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10373108" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Anaerobiosis ; Binding Sites ; Cell Membrane/enzymology ; Crystallization ; Crystallography, X-Ray ; Electron Transport ; Energy Metabolism ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Fumarates/metabolism ; Iron-Sulfur Proteins/chemistry/metabolism ; Models, Molecular ; Oxidation-Reduction ; Oxygen Consumption ; Protein Conformation ; Protein Folding ; Quinones/chemistry/metabolism ; Succinate Dehydrogenase/*chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Quaternary structure of the insulin-insulin receptor complex (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-08-14
    Description: The three-dimensional (3D) structure of the intrinsically dimeric insulin receptor bound to its ligand, insulin, was determined by electron cryomicroscopy. Gold-labeled insulin served to locate the insulin-binding domain. The 3D structure was then fitted with available known high-resolution domain substructures to obtain a detailed contiguous model for this heterotetrameric transmembrane receptor. The 3D reconstruction indicates that the two alpha subunits jointly participate in insulin binding and that the kinase domains in the two beta subunits are in a juxtaposition that permits autophosphorylation of tyrosine residues in the first step of insulin receptor activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Luo, R Z -- Beniac, D R -- Fernandes, A -- Yip, C C -- Ottensmeyer, F P -- New York, N.Y. -- Science. 1999 Aug 13;285(5430):1077-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10446056" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Dimerization ; Gold ; Image Processing, Computer-Assisted ; Insulin/*chemistry/metabolism ; Ligands ; Microscopy, Electron, Scanning Transmission ; Models, Molecular ; Phosphorylation ; Protein Conformation ; Protein-Tyrosine Kinases/chemistry/metabolism ; Receptor, Insulin/*chemistry/metabolism
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    The crystal structure of a T cell receptor in complex with peptide and MHC class II (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-03
    Description: The crystal structure of a complex involving the D10 T cell receptor (TCR), 16-residue foreign peptide antigen, and the I-Ak self major histocompatibility complex (MHC) class II molecule is reported at 3.2 angstrom resolution. The D10 TCR is oriented in an orthogonal mode relative to its peptide-MHC (pMHC) ligand, necessitated by the amino-terminal extension of peptide residues projecting from the MHC class II antigen-binding groove as part of a mini beta sheet. Consequently, the disposition of D10 complementarity-determining region loops is altered relative to that of most pMHCI-specific TCRs; the latter TCRs assume a diagonal orientation, although with substantial variability. Peptide recognition, which involves P-1 to P8 residues, is dominated by the Valpha domain, which also binds to the class II MHC beta1 helix. That docking is limited to one segment of MHC-bound peptide offers an explanation for epitope recognition and altered peptide ligand effects, suggests a structural basis for alloreactivity, and illustrates how bacterial superantigens can span the TCR-pMHCII surface.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reinherz, E L -- Tan, K -- Tang, L -- Kern, P -- Liu, J -- Xiong, Y -- Hussey, R E -- Smolyar, A -- Hare, B -- Zhang, R -- Joachimiak, A -- Chang, H C -- Wagner, G -- Wang, J -- AI/CA37581/AI/NIAID NIH HHS/ -- AI19807/AI/NIAID NIH HHS/ -- GM56008/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Dec 3;286(5446):1913-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Immunobiology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10583947" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens/*chemistry/immunology/metabolism ; Binding Sites ; CD4-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/immunology ; Conalbumin/chemistry/immunology ; Crystallization ; Crystallography, X-Ray ; Histocompatibility Antigens Class I/immunology ; Histocompatibility Antigens Class II/*chemistry/immunology/metabolism ; Hydrogen Bonding ; Ligands ; Mice ; Mice, Inbred AKR ; Models, Molecular ; Oligopeptides/chemistry/immunology/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/immunology/metabolism ; Superantigens/immunology/metabolism ; Thymus Gland/cytology/immunology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    A steric mechanism for inhibition of CO binding to heme proteins (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-04-16
    Description: The crystal structures of myoglobin in the deoxy- and carbon monoxide-ligated states at a resolution of 1.15 angstroms show that carbon monoxide binding at ambient temperatures requires concerted motions of the heme, the iron, and helices E and F for relief of steric inhibition. These steps constitute the main mechanism by which heme proteins lower the affinity of the heme group for the toxic ligand carbon monoxide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kachalova, G S -- Popov, A N -- Bartunik, H D -- New York, N.Y. -- Science. 1999 Apr 16;284(5413):473-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Arbeitsgruppen fur Strukturelle Molekularbiologie, Arbeitsgruppe Proteindynamik, Notkestrabetae 85, 22603 Hamburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10205052" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Carbon Monoxide/chemistry/*metabolism ; Crystallography, X-Ray ; Heme/chemistry/metabolism ; Histidine/chemistry/metabolism ; Hydrogen Bonding ; Iron/chemistry/metabolism ; Ligands ; Metmyoglobin/chemistry ; Models, Molecular ; Myoglobin/*analogs & derivatives/*chemistry/metabolism ; Nitrogen/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Temperature ; Valine/chemistry/metabolism
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    Domain movement in gelsolin: a calcium-activated switch (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-03
    Description: The actin-binding protein gelsolin is involved in remodeling the actin cytoskeleton during growth-factor signaling, apoptosis, cytokinesis, and cell movement. Calcium-activated gelsolin severs and caps actin filaments. The 3.4 angstrom x-ray structure of the carboxyl-terminal half of gelsolin (G4-G6) in complex with actin reveals the basis for gelsolin activation. Calcium binding induces a conformational rearrangement in which domain G6 is flipped over and translated by about 40 angstroms relative to G4 and G5. The structural reorganization tears apart the continuous beta sheet core of G4 and G6. This exposes the actin-binding site on G4, enabling severing and capping of actin filaments to proceed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Robinson, R C -- Mejillano, M -- Le, V P -- Burtnick, L D -- Yin, H L -- Choe, S -- New York, N.Y. -- Science. 1999 Dec 3;286(5446):1939-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Laboratory, Salk Institute for Biological Studies, Post Office Box 85800, San Diego, CA 92186-5800, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10583954" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Gelsolin/*chemistry/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 46
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    A copper cofactor for the ethylene receptor ETR1 from Arabidopsis (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-02-12
    Description: The ETR1 receptor from Arabidopsis binds the gaseous hormone ethylene. A copper ion associated with the ethylene-binding domain is required for high-affinity ethylene-binding activity. A missense mutation in the domain that renders the plant insensitive to ethylene eliminates both ethylene binding and the interaction of copper with the receptor. A sequence from the genome of the cyanobacterium Synechocystis sp. strain 6803 that shows homology to the ethylene-binding domain of ETR1 encodes a functional ethylene-binding protein. On the basis of sequence conservation between the Arabidopsis and the cyanobacterial ethylene-binding domains and on in vitro mutagenesis of ETR1, a structural model for this copper-based ethylene sensor domain is presented.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rodriguez, F I -- Esch, J J -- Hall, A E -- Binder, B M -- Schaller, G E -- Bleecker, A B -- New York, N.Y. -- Science. 1999 Feb 12;283(5404):996-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Botany, 430 Lincoln Drive, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9974395" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Arabidopsis/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics ; Binding Sites ; Conserved Sequence ; Copper/analysis/*metabolism ; Copper Sulfate/pharmacology ; Cyanobacteria/genetics/metabolism ; Dimerization ; Ethylenes/*metabolism ; Models, Molecular ; Mutagenesis ; Open Reading Frames ; Plant Proteins/chemistry/genetics/isolation & purification/*metabolism ; Receptors, Cell Surface/chemistry/genetics/isolation & purification/*metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Saccharomyces cerevisiae ; Silver/metabolism/pharmacology
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  • 47
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    Identification of a conserved receptor-binding site on the fiber proteins of CAR-recognizing adenoviridae (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-11-24
    Description: The human adenovirus serotype 5 (Ad5) is used widely for applications in human gene therapy. Cellular attachment of Ad5 is mediated by binding of the carboxyl-terminal knob of its fiber coat protein to the Coxsackie adenovirus receptor (CAR) protein. However, Ad5 binding to CAR hampers the development of adenovirus vectors capable of specifically targeting (diseased) tissues or organs. Through sequence analysis and mutagenesis, a conserved receptor-binding region was identified on the side of three divergent CAR-binding knobs. The feasibility of simultaneous CAR ablation and redirection of an adenovirus to a new receptor is demonstrated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roelvink, P W -- Mi Lee, G -- Einfeld, D A -- Kovesdi, I -- Wickham, T J -- New York, N.Y. -- Science. 1999 Nov 19;286(5444):1568-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Research and Development, GenVec Inc., 65 West Watkins Mill Road, Gaithersburg, MD 20879, USA. genecloner@genvec.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10567265" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviruses, Human/*chemistry/metabolism ; Amino Acid Sequence ; Binding Sites ; Capsid/*chemistry/genetics/*metabolism ; *Capsid Proteins ; Cell Line ; Conserved Sequence ; Coxsackie and Adenovirus Receptor-Like Membrane Protein ; Genetic Vectors ; Humans ; Models, Molecular ; Mutagenesis, Site-Directed ; Point Mutation ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Virus/*metabolism ; Sequence Deletion ; Transfection ; Tumor Cells, Cultured
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    How serpins are shaping up (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carrell, R W -- New York, N.Y. -- Science. 1999 Sep 17;285(5435):1861.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 2XY, UK. rwc1000@cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10515791" target="_blank"〉PubMed〈/a〉
    Keywords: Antithrombin III/chemistry/*metabolism/pharmacology ; Heparin/metabolism ; Models, Molecular ; Neoplasms/blood supply/drug therapy ; Neovascularization, Pathologic/prevention & control ; Plasminogen Activator Inhibitor 1/metabolism ; Protein Binding ; Protein Conformation ; Serpins/chemistry/*metabolism/pharmacology ; Structure-Activity Relationship ; Vitronectin/metabolism
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    X-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-08-14
    Description: Type 1 pili-adhesive fibers expressed in most members of the Enterobacteriaceae family-mediate binding to mannose receptors on host cells through the FimH adhesin. Pilus biogenesis proceeds by way of the chaperone/usher pathway. The x-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli at 2.5 angstrom resolution reveals the basis for carbohydrate recognition and for pilus assembly. The carboxyl-terminal pilin domain of FimH has an immunoglobulin-like fold, except that the seventh strand is missing, leaving part of the hydrophobic core exposed. A donor strand complementation mechanism in which the chaperone donates a strand to complete the pilin domain explains the basis for both chaperone function and pilus biogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choudhury, D -- Thompson, A -- Stojanoff, V -- Langermann, S -- Pinkner, J -- Hultgren, S J -- Knight, S D -- R01AI29549/AI/NIAID NIH HHS/ -- R01DK51406/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1999 Aug 13;285(5430):1061-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Uppsala Biomedical Center, Swedish University of Agricultural Sciences, Box 590, S-753 24 Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10446051" target="_blank"〉PubMed〈/a〉
    Keywords: Adhesins, Bacterial/*chemistry/metabolism ; *Adhesins, Escherichia coli ; Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/metabolism ; *Bacterial Proteins ; Chlorpropamide/analogs & derivatives/metabolism ; Crystallography, X-Ray ; Escherichia coli/*chemistry/metabolism/pathogenicity ; *Escherichia coli Proteins ; Fimbriae Proteins ; Fimbriae, Bacterial/chemistry/*metabolism/ultrastructure ; Hydrogen Bonding ; Membrane Proteins/*chemistry ; Models, Molecular ; Molecular Chaperones/*chemistry/metabolism ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Sequence Alignment
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    Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-12-13
    Description: The structure of the Staphylococcus aureus alpha-hemolysin pore has been determined to 1.9 A resolution. Contained within the mushroom-shaped homo-oligomeric heptamer is a solvent-filled channel, 100 A in length, that runs along the sevenfold axis and ranges from 14 A to 46 A in diameter. The lytic, transmembrane domain comprises the lower half of a 14-strand antiparallel beta barrel, to which each protomer contributes two beta strands, each 65 A long. The interior of the beta barrel is primarily hydrophilic, and the exterior has a hydrophobic belt 28 A wide. The structure proves the heptameric subunit stoichiometry of the alpha-hemolysin oligomer, shows that a glycine-rich and solvent-exposed region of a water-soluble protein can self-assemble to form a transmembrane pore of defined structure, and provides insight into the principles of membrane interaction and transport activity of beta barrel pore-forming toxins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, L -- Hobaugh, M R -- Shustak, C -- Cheley, S -- Bayley, H -- Gouaux, J E -- New York, N.Y. -- Science. 1996 Dec 13;274(5294):1859-66.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Chicago, 920 East 58 Street, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8943190" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Toxins/*chemistry/metabolism ; Cell Membrane/chemistry/metabolism ; Crystallography, X-Ray ; Hemolysin Proteins/*chemistry/metabolism ; Hydrogen Bonding ; Lipid Bilayers/*chemistry ; Membrane Potentials ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Staphylococcus aureus/*chemistry
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  • 51
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    Solution structure of a two-base DNA bulge complexed with an enediyne cleaving analog (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-06-28
    Description: Nucleic acid bulges have been implicated in a number of biological processes and are specific cleavage targets for the enediyne antitumor antibiotic neocarzinostatin chromophore in a base-catalyzed, radical-mediated reaction. The solution structure of the complex between an analog of the bulge-specific cleaving species and an oligodeoxynucleotide containing a two-base bulge was elucidated by nuclear magnetic resonance. An unusual binding mode involves major groove recognition by the drug carbohydrate unit and tight fitting of the wedge-shaped drug in the triangular prism pocket formed by the two looped-out bulge bases and the neighboring base pairs. The two drug rings mimic helical DNA bases, complementing the bent DNA structure. The putative abstracting drug radical is 2.2 +/- 0.1 angstroms from the pro-S H5' of the target bulge nucleotide. This structure clarifies the mechanism of bulge recognition and cleavage by a drug and provides insight into the design of bulge-specific nucleic acid binding molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stassinopoulos, A -- Ji, J -- Gao, X -- Goldberg, I H -- CA44257/CA/NCI NIH HHS/ -- GM53793/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jun 28;272(5270):1943-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658168" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; DNA/chemistry/*metabolism ; Enediynes ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/*metabolism ; Zinostatin/analogs & derivatives/chemistry/metabolism
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    Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-05-31
    Description: In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy. Both aptamers contain two asymmetrical internal loops that are not well ordered in the free RNA but that fold into a compact structure upon ligand binding. Those nucleotides common to both RNAs include a conserved cluster of purine residues, three of which form an uneven plane containing a G:G pair, and two other residues nearly perpendicular to that surface. Two of the three variant nucleotides are stacked on the cluster of purines and form a triple contact to the amino acid side chain, whereas the edge of the third variant nucleotide is capping the binding pocket.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Y -- Kochoyan, M -- Burgstaller, P -- Westhof, E -- Famulok, M -- New York, N.Y. -- Science. 1996 May 31;272(5266):1343-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre de Biochimie Structurale (CBS), Unite Mixte de Recherche, CNRS 9955, Montpellier, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8650546" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/chemistry/*metabolism ; Base Composition ; Base Sequence ; Citrulline/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Ligands ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Nucleic Acid Conformation ; RNA/*chemistry/genetics/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 53
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    Crystal structure of a group I ribozyme domain: principles of RNA packing (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-09-20
    Description: Group I self-splicing introns catalyze their own excision from precursor RNAs by way of a two-step transesterification reaction. The catalytic core of these ribozymes is formed by two structural domains. The 2.8-angstrom crystal structure of one of these, the P4-P6 domain of the Tetrahymena thermophila intron, is described. In the 160-nucleotide domain, a sharp bend allows stacked helices of the conserved core to pack alongside helices of an adjacent region. Two specific long-range interactions clamp the two halves of the domain together: a two-Mg2+-coordinated adenosine-rich corkscrew plugs into the minor groove of a helix, and a GAAA hairpin loop binds to a conserved 11-nucleotide internal loop. Metal- and ribose-mediated backbone contacts further stabilize the close side-by-side helical packing. The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cate, J H -- Gooding, A R -- Podell, E -- Zhou, K -- Golden, B L -- Kundrot, C E -- Cech, T R -- Doudna, J A -- 5T32GM08283-07/GM/NIGMS NIH HHS/ -- GM22778-21/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Sep 20;273(5282):1678-85.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. doudna@csb.yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8781224" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/chemistry ; Animals ; Base Composition ; Base Sequence ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Hydrogen Bonding ; *Introns ; Magnesium/chemistry ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phosphates/chemistry ; Phylogeny ; RNA Splicing ; RNA, Catalytic/*chemistry/metabolism ; RNA, Protozoan/*chemistry/metabolism ; Ribose/chemistry ; Tetrahymena thermophila/genetics
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    Structure of the amino-terminal core domain of the HIV-1 capsid protein (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-07-12
    Description: The three-dimensional structure of the amino-terminal core domain (residues 1 through 151) of the human immunodeficiency virus-type 1 (HIV-1) capsid protein has been solved by multidimensional heteronuclear magnetic resonance spectroscopy. The structure is unlike those of previously characterized viral coat proteins and is composed of seven alpha helices, two beta hairpins, and an exposed partially ordered loop. The domain is shaped like an arrowhead, with the beta hairpins and loop exposed at the trailing edge and the carboxyl-terminal helix projecting from the tip. The proline residue Pro1 forms a salt bridge with a conserved, buried aspartate residue (Asp51), which suggests that the amino terminus of the protein rearranges upon proteolytic maturation. The binding site for cyclophilin A, a cellular rotamase that is packaged into the HIV-1 virion, is located on the exposed loop and encompasses the essential proline residue Pro90. In the free monomeric domain, Pro90 adopts kinetically trapped cis and trans conformations, raising the possibility that cyclophilin A catalyzes interconversion of the cis- and trans-Pro90 loop structures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gitti, R K -- Lee, B M -- Walker, J -- Summers, M F -- Yoo, S -- Sundquist, W I -- AI30917/AI/NIAID NIH HHS/ -- CA 42014/CA/NCI NIH HHS/ -- GM 42561/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 12;273(5272):231-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21228, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662505" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Isomerases/metabolism ; Amino Acid Sequence ; Aspartic Acid/chemistry ; Binding Sites ; Capsid/*chemistry/metabolism ; Carrier Proteins/metabolism ; HIV Core Protein p24/*chemistry/metabolism ; HIV-1/*chemistry ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Peptidylprolyl Isomerase ; Proline/chemistry ; Protein Conformation ; Protein Processing, Post-Translational ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Virion/chemistry
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  • 55
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    Catalytic role of 2'-hydroxyl groups within a group II intron active site (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-03-08
    Description: Domain 5 is an essential active-site component of group II intron ribozymes. The role of backbone substituents in D5 function was explored through synthesis of a series of derivatives containing deoxynucleotides at each position along the D5 strand. Kinetic screens revealed that eight 2'-hydroxyl groups were likely to be critical for activity of D5. Through two separate methods, including competitive inhibition and direct kinetic analysis, effects on binding and chemistry were distinguished. Depending on their function, important 2'-hydroxyl groups lie on opposite faces of the molecule, defining distinct loci for molecular recognition and catalysis by D5.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abramovitz, D L -- Friedman, R A -- Pyle, A M -- GM41371/GM/NIGMS NIH HHS/ -- GM50313/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Mar 8;271(5254):1410-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8596912" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Binding Sites ; Catalysis ; Exons ; Hydrogen Bonding ; Hydroxyl Radical/chemistry ; *Introns ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligoribonucleotides/chemistry/metabolism ; RNA/metabolism ; RNA, Catalytic/chemistry/*metabolism
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  • 56
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    Structure of the FKBP12-rapamycin complex interacting with the binding domain of human FRAP (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-07-12
    Description: Rapamycin, a potent immunosuppressive agent, binds two proteins: the FK506-binding protein (FKBP12) and the FKBP-rapamycin-associated protein (FRAP). A crystal structure of the ternary complex of human FKBP12, rapamycin, and the FKBP12-rapamycin-binding (FRB) domain of human FRAP at a resolution of 2.7 angstroms revealed the two proteins bound together as a result of the ability of rapamycin to occupy two different hydrophobic binding pockets simultaneously. The structure shows extensive interactions between rapamycin and both proteins, but fewer interactions between the proteins. The structure of the FRB domain of FRAP clarifies both rapamycin-independent and -dependent effects observed for mutants of FRAP and its homologs in the family of proteins related to the ataxia-telangiectasia mutant gene product, and it illustrates how a small cell-permeable molecule can mediate protein dimerization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choi, J -- Chen, J -- Schreiber, S L -- Clardy, J -- CA59021/CA/NCI NIH HHS/ -- GM38625/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 12;273(5272):239-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Baker Laboratory, Cornell University, Ithaca, NY 14853-1301, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662507" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carrier Proteins/chemistry/genetics/*metabolism ; Crystallography, X-Ray ; DNA-Binding Proteins/chemistry/*metabolism ; Heat-Shock Proteins/chemistry/*metabolism ; Humans ; *Immunophilins ; Models, Molecular ; Mutation ; *Phosphotransferases (Alcohol Group Acceptor) ; Polyenes/*chemistry/*metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Sirolimus ; TOR Serine-Threonine Kinases ; Tacrolimus Binding Proteins
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  • 57
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    A mechanism of drug action revealed by structural studies of enoyl reductase (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-12-20
    Description: Enoyl reductase (ENR), an enzyme involved in fatty acid biosynthesis, is the target for antibacterial diazaborines and the front-line antituberculosis drug isoniazid. Analysis of the structures of complexes of Escherichia coli ENR with nicotinamide adenine dinucleotide and either thienodiazaborine or benzodiazaborine revealed the formation of a covalent bond between the 2' hydroxyl of the nicotinamide ribose and a boron atom in the drugs to generate a tight, noncovalently bound bisubstrate analog. This analysis has implications for the structure-based design of inhibitors of ENR, and similarities to other oxidoreductases suggest that mimicking this molecular linkage may have generic applications in other areas of medicinal chemistry.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baldock, C -- Rafferty, J B -- Sedelnikova, S E -- Baker, P J -- Stuitje, A R -- Slabas, A R -- Hawkes, T R -- Rice, D W -- New York, N.Y. -- Science. 1996 Dec 20;274(5295):2107-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK. D.Rice@sheffield.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8953047" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/*metabolism/pharmacology ; Binding Sites ; Boron Compounds/*metabolism/pharmacology ; Crystallography, X-Ray ; Drug Design ; Drug Resistance, Microbial ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH) ; Enzyme Inhibitors/*metabolism/pharmacology ; Escherichia coli/enzymology ; Escherichia coli Proteins ; Fatty Acid Synthase, Type II ; Fatty Acid Synthases/antagonists & inhibitors/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; NAD/*metabolism ; Oxidoreductases/antagonists & inhibitors/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary
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    Transcription factor IIA: a structure with multiple functions (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacobson, R H -- Tjian, R -- New York, N.Y. -- Science. 1996 May 10;272(5263):827-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, Berkeley 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8629011" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallography, X-Ray ; DNA/*chemistry/metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Humans ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; TATA Box ; TATA-Box Binding Protein ; Transcription Factor TFIIA ; Transcription Factor TFIID ; Transcription Factors/*chemistry/genetics/*metabolism ; *Transcription, Genetic
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  • 59
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    Another twist to MHC-peptide recognition (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-05-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, I A -- New York, N.Y. -- Science. 1996 May 17;272(5264):973-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8638141" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigen Presentation ; Antigens/chemistry/*metabolism ; Antigens, Differentiation, B-Lymphocyte/chemistry/*metabolism ; HLA-DR1 Antigen/chemistry/metabolism ; Histocompatibility Antigens Class II/chemistry/immunology/*metabolism ; Humans ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Mice ; Models, Molecular ; Protein Conformation
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  • 60
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    Molecular orientation and two-component nature of the crystalline fraction of spider dragline silk (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-01-05
    Description: The molecular origin of the exceptional mechanical properties of spider silk is unclear. This paper presents solid-state 2H nuclear magnetic resonance data from unoriented, oriented, and supercontracted fibers, indicating that the crystalline fraction of dragline silk consists of two types of alanine-rich regions, one that is highly oriented and one that is poorly oriented and less densely packed. A new model for the molecular-level structure of individual silk molecules and their arrangement in the fibers is proposed. These data suggest that it will be necessary to control the secondary structure of individual polymer molecules in order to obtain optimum properties in bio-inspired polymers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simmons, A H -- Michal, C A -- Jelinski, L W -- New York, N.Y. -- Science. 1996 Jan 5;271(5245):84-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Advanced Technology in Biotechnology, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8539605" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/analysis ; Algorithms ; Amino Acid Sequence ; Animals ; Crystallization ; Crystallography, X-Ray ; *Fibroins ; Glycine/analysis ; *Insect Proteins ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Peptides/analysis ; Protein Conformation ; Protein Structure, Secondary ; Proteins/*chemistry ; Silk ; Spiders/*chemistry
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  • 61
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    Direct observation of protein solvation and discrete disorder with experimental crystallographic phases (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-01-05
    Description: A complete and accurate set of experimental crystallographic phases to a resolution of 1.8 angstroms was obtained for a 230-residue dimeric fragment of rat mannose-binding protein A with the use of multiwavelength anomalous dispersion (MAD) phasing. An accurate image of the crystal structure could thus be obtained without resort to phases calculated from a model. Partially reduced disulfide bonds, local disorder, and differences in the mobility of chemically equivalent molecules are apparent in the experimental electron density map. A solvation layer is visible that includes well-ordered sites of hydration around polar and charged protein atoms, as well as diffuse, partially disordered solvent shells around exposed hydrophobic groups. Because the experimental phases and the resulting electron density map are free from the influence of a model, they provide a stringent test of theoretical models of macromolecular solvation, motion, and conformational heterogeneity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burling, F T -- Weis, W I -- Flaherty, K M -- Brunger, A T -- GM50565/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jan 5;271(5245):72-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8539602" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carrier Proteins/*chemistry ; Chemistry, Physical ; Crystallization ; *Crystallography, X-Ray ; Hydrogen Bonding ; Mannose/*metabolism ; *Mannose-Binding Lectin ; Models, Molecular ; Molecular Sequence Data ; Physicochemical Phenomena ; *Protein Conformation ; Rats ; Solvents ; Water
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  • 62
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    Tricorn protease--the core of a modular proteolytic system (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-11-22
    Description: Large macromolecular assemblies have evolved as a means of compartmentalizing reactions in organisms lacking membrane-bounded compartments. A tricorn-shaped protease was isolated from the archaeon Thermoplasma and was shown to form a multisubunit proteolytic complex. The 120-kilodalton monomer assembled to form a hexameric toroid that could assemble further into a capsid structure. Tricorn protease appeared to act as the core of a proteolytic system; when it interacted with several smaller proteins, it displayed multicatalytic activities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tamura, T -- Tamura, N -- Cejka, Z -- Hegerl, R -- Lottspeich, F -- Baumeister, W -- New York, N.Y. -- Science. 1996 Nov 22;274(5291):1385-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institute for Biochemistry, D-82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8910281" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cloning, Molecular ; Cysteine Endopeptidases/metabolism ; Endopeptidases/*chemistry/genetics/isolation & purification/*metabolism ; Genes, Bacterial ; Microscopy, Electron ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Multienzyme Complexes/metabolism ; Peptides/metabolism ; Proteasome Endopeptidase Complex ; *Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Substrate Specificity ; Thermoplasma/*enzymology
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  • 63
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    Structure of the p53 tumor suppressor bound to the ankyrin and SH3 domains of 53BP2 (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-11-08
    Description: Mutations in the p53 tumor suppressor are among the most frequently observed genetic alterations in human cancer and map to the 200-amino acid core domain of the protein. The core domain contains the sequence-specific DNA binding activity and the in vitro 53BP2 protein binding activity of p53. The crystal structure of the p53 core domain bound to the 53BP2 protein, which contains an SH3 (Src homology 3) domain and four ankyrin repeats, revealed that (i) the SH3 domain binds the L3 loop of p53 in a manner distinct from that of previously characterized SH3-polyproline peptide complexes, and (ii) an ankyrin repeat, which forms an L-shaped structure consisting of a beta hairpin and two alpha helices, binds the L2 loop of p53. The structure of the complex shows that the 53BP2 binding site on the p53 core domain consists of evolutionarily conserved regions that are frequently mutated in cancer and that it overlaps the site of DNA binding. The six most frequently observed p53 mutations disrupt 53BP2 binding in vitro. The structure provides evidence that the 53BP2-p53 complex forms in vivo and may have a critical role in the p53 pathway of tumor suppression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gorina, S -- Pavletich, N P -- CA65698/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1996 Nov 8;274(5289):1001-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8875926" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Ankyrins/*chemistry ; Apoptosis Regulatory Proteins ; Binding Sites ; Carrier Proteins/*chemistry/metabolism ; Crystallography, X-Ray ; DNA/metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Neoplasms/genetics ; Protein Binding ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Tumor Suppressor Protein p53/*chemistry/genetics/metabolism ; *src Homology Domains
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  • 64
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    Iron metabolism in eukaryotes: Mars and Venus at it again (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-03-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaplan, J -- O'Halloran, T V -- R01 GM038784/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Mar 15;271(5255):1510-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, University of Utah School of Medicine, Salt Lake City, 84132, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8599104" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Biological Transport ; Carrier Proteins/genetics/*metabolism ; Ceruloplasmin/chemistry/*metabolism ; Copper/metabolism ; Ferric Compounds/metabolism ; Ferrous Compounds/metabolism ; Iron/*metabolism ; Membrane Transport Proteins/genetics/*metabolism ; Models, Molecular ; Oxidation-Reduction ; Oxidoreductases/*metabolism ; Protein Conformation ; Saccharomyces cerevisiae/genetics/*metabolism ; *Saccharomyces cerevisiae Proteins
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    The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-05-24
    Description: The crystal structure of bovine heart cytochrome c oxidase at 2.8 A resolution with an R value of 19.9 percent reveals 13 subunits, each different from the other, five phosphatidyl ethanolamines, three phosphatidyl glycerols and two cholates, two hemes A, and three copper, one magnesium, and one zinc. Of 3606 amino acid residues in the dimer, 3560 have been converged to a reasonable structure by refinement. A hydrogen-bonded system, including a propionate of a heme A (heme a), part of peptide backbone, and an imidazole ligand of CuA, could provide an electron transfer pathway between CuA and heme a. Two possible proton pathways for pumping, each spanning from the matrix to the cytosolic surfaces, were identified, including hydrogen bonds, internal cavities likely to contain water molecules, and structures that could form hydrogen bonds with small possible conformational change of amino acid side chains. Possible channels for chemical protons to produce H2O, for removing the produced water, and for O2, respectively, were identified.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsukihara, T -- Aoyama, H -- Yamashita, E -- Tomizaki, T -- Yamaguchi, H -- Shinzawa-Itoh, K -- Nakashima, R -- Yaono, R -- Yoshikawa, S -- New York, N.Y. -- Science. 1996 May 24;272(5265):1136-44.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Protein Research, Osaka University, Suita, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8638158" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cattle ; Cell Nucleus/genetics ; Copper/analysis ; Crystallography, X-Ray ; Electron Transport ; Electron Transport Complex IV/*chemistry/genetics/metabolism ; Heme/analogs & derivatives/analysis ; Hydrogen Bonding ; Iron/analysis ; Membrane Proteins/chemistry ; Mitochondria, Heart/genetics ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Myocardium/enzymology ; Nucleotides/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Phospholipids/analysis ; *Protein Conformation ; Protein Structure, Secondary ; Proton Pumps ; Water/metabolism
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    Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-09-13
    Description: The solution structure of a human immunodeficiency virus type-1 (HIV-1) Rev peptide bound to stem-loop IIB of the Rev response element (RRE) RNA was solved by nuclear magnetic resonance spectroscopy. The Rev peptide has an alpha-helical conformation and binds in the major groove of the RNA near a purine-rich internal loop. Several arginine side chains make base-specific contacts, and an asparagine residue contacts a G.A base pair. The phosphate backbone adjacent to a G.G base pair adopts an unusual structure that allows the peptide to access a widened major groove. The structure formed by the two purine-purine base pairs of the RRE creates a distinctive binding pocket that the peptide can use for specific recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Battiste, J L -- Mao, H -- Rao, N S -- Tan, R -- Muhandiram, D R -- Kay, L E -- Frankel, A D -- Williamson, J R -- GM-08344/GM/NIGMS NIH HHS/ -- GM-39589/GM/NIGMS NIH HHS/ -- GM-53320/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Sep 13;273(5281):1547-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8703216" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/chemistry ; Asparagine/chemistry ; Base Composition ; Base Sequence ; *DNA-Binding Proteins ; Fungal Proteins/chemistry ; Gene Products, rev/*chemistry/*metabolism ; *Genes, env ; HIV-1/*chemistry ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Protein Kinases/chemistry ; *Protein Structure, Secondary ; RNA, Viral/*chemistry/genetics/metabolism ; *Saccharomyces cerevisiae Proteins ; Threonine/chemistry ; rev Gene Products, Human Immunodeficiency Virus
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    Site-directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S5 (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-06-14
    Description: Cysteine residues were introduced into three different positions distributed on the surface of ribosomal protein S5, to serve as targets for derivatization with an Fe(II)-ethyl-enediaminetetraacetic acid linker. Hydroxyl radicals generated locally from the tethered Fe(II) in intermediate ribonucleoprotein particles or in 30S ribosomal subunits reconstituted from derivatized S5 caused cleavage of the RNA, resulting in characteristically different cleavage patterns for the three different tethering positions. These findings provide constraints for the three-dimensional folding of 16S ribosomal RNA (rRNA) and for the orientation of S5 in the 30S subunit, and they further suggest that antibiotic resistance and accuracy mutations in S5 may involve perturbation of 16S rRNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heilek, G M -- Noller, H F -- New York, N.Y. -- Science. 1996 Jun 14;272(5268):1659-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658142" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/pharmacology ; Cloning, Molecular ; Cysteine/chemistry ; Edetic Acid/analogs & derivatives ; Escherichia coli ; Ferrous Compounds/chemistry ; Hydroxyl Radical/*chemistry ; Models, Molecular ; Molecular Probes ; Mutagenesis, Site-Directed ; Nucleic Acid Conformation ; Organometallic Compounds ; Protein Conformation ; RNA, Ribosomal/*chemistry ; RNA, Ribosomal, 16S/chemistry/drug effects ; Ribosomal Proteins/*chemistry/genetics ; Spectinomycin/pharmacology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Crystal structure of DMSO reductase: redox-linked changes in molybdopterin coordination (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-06-14
    Description: The molybdoenzyme dimethylsulfoxide (DMSO) reductase contributes to the release of dimethylsulfide, a compound that has been implicated in cloud nucleation and global climate regulation. The crystal structure of DMSO reductase from Rhodobacter sphaeroides reveals a monooxo molybdenum cofactor containing two molybdopterin guanine dinucleotides that asymmetrically coordinate the molybdenum through their dithiolene groups. One of the pterins exhibits different coordination modes to the molybdenum between the oxidized and reduced states, whereas the side chain oxygen of Ser147 coordinates the metal in both states. The change in pterin coordination between the Mo(VI) and Mo(IV) forms suggests a mechanism for substrate binding and reduction by this enzyme. Sequence comparisons of DMSO reductase with a family of bacterial oxotransferases containing molybdopterin guanine dinucleotide indicate a similar polypeptide fold and active site with two molybdopterins within this family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schindelin, H -- Kisker, C -- Hilton, J -- Rajagopalan, K V -- Rees, D C -- GM00091/GM/NIGMS NIH HHS/ -- GM50775/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jun 14;272(5268):1615-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658134" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Coenzymes/*chemistry ; Crystallography, X-Ray ; *Iron-Sulfur Proteins ; Metalloproteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/*chemistry/metabolism ; Protein Conformation ; Pteridines/*chemistry ; Rhodobacter sphaeroides/*enzymology ; Sequence Homology, Amino Acid
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    Hats off to the tricorn protease (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-11-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schneider, C -- Hartl, F U -- New York, N.Y. -- Science. 1996 Nov 22;274(5291):1323-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. f-hartl@ski.mskcc.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8966603" target="_blank"〉PubMed〈/a〉
    Keywords: Cysteine Endopeptidases/chemistry/metabolism ; Endopeptidases/chemistry/*metabolism ; Models, Molecular ; Multienzyme Complexes/chemistry/metabolism ; Proteasome Endopeptidase Complex ; *Protein Conformation ; Thermoplasma/*enzymology
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    Nanosecond crystallographic snapshots of protein structural changes (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-12-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eaton, W A -- Henry, E R -- Hofrichter, J -- New York, N.Y. -- Science. 1996 Dec 6;274(5293):1631-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA. eaton@helix.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8984630" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Monoxide/chemistry/metabolism ; Computer Simulation ; Crystallography, X-Ray/*methods ; Heme/chemistry ; Ligands ; Models, Molecular ; Myoglobin/*chemistry/metabolism ; Photolysis ; *Protein Conformation ; Time Factors
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    Bio-molecular dynamics comes of age (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-02-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berendsen, H J -- New York, N.Y. -- Science. 1996 Feb 16;271(5251):954-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysical Chemistry, University of Groningen, Netherlands. berendsen@chem.rug.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8584930" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry ; Biotin/*chemistry ; Chemistry, Physical ; Computer Graphics ; *Computer Simulation ; Hydrogen Bonding ; Microscopy, Atomic Force ; *Models, Chemical ; Models, Molecular ; Molecular Conformation ; Physicochemical Phenomena ; Protein Conformation ; Streptavidin ; Thermodynamics
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    Crystal structure of the lactose operon repressor and its complexes with DNA and inducer (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-03-01
    Description: The lac operon of Escherichia coli is the paradigm for gene regulation. Its key component is the lac repressor, a product of the lacI gene. The three-dimensional structures of the intact lac repressor, the lac repressor bound to the gratuitous inducer isopropyl-beta-D-1-thiogalactoside (IPTG) and the lac repressor complexed with a 21-base pair symmetric operator DNA have been determined. These three structures show the conformation of the molecule in both the induced and repressed states and provide a framework for understanding a wealth of biochemical and genetic information. The DNA sequence of the lac operon has three lac repressor recognition sites in a stretch of 500 base pairs. The crystallographic structure of the complex with DNA suggests that the tetrameric repressor functions synergistically with catabolite gene activator protein (CAP) and participates in the quaternary formation of repression loops in which one tetrameric repressor interacts simultaneously with two sites on the genomic DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewis, M -- Chang, G -- Horton, N C -- Kercher, M A -- Pace, H C -- Schumacher, M A -- Brennan, R G -- Lu, P -- 2-T32-GM082745/GM/NIGMS NIH HHS/ -- GM44617/GM/NIGMS NIH HHS/ -- P41-RR06017/RR/NCRR NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1996 Mar 1;271(5253):1247-54.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Johnson Research Foundation, University of Pennsylvania, Philadelphia 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8638105" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Bacterial Proteins/*chemistry/genetics/metabolism ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Cyclic AMP Receptor Protein/metabolism ; DNA, Bacterial/chemistry/*metabolism ; *Escherichia coli Proteins ; Hydrogen Bonding ; Isopropyl Thiogalactoside/*metabolism ; *Lac Operon ; Lac Repressors ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Operator Regions, Genetic ; Point Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Repressor Proteins/*chemistry/genetics/metabolism
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    The galvanization of biology: a growing appreciation for the roles of zinc (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-02-23
    Description: Zinc ions are key structural components of a large number of proteins. The binding of zinc stabilizes the folded conformations of domains so that they may facilitate interactions between the proteins and other macromolecules such as DNA. The modular nature of some of these zinc-containing proteins has allowed the rational design of site-specific DNA binding proteins. The ability of zinc to be bound specifically within a range of tetrahedral sites appears to be responsible for the evolution of the side range of zinc-stabilized structural domains now known to exist. The lack of redox activity for the zinc ion and its binding and exchange kinetics also may be important in the use of zinc for specific functional roles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berg, J M -- Shi, Y -- New York, N.Y. -- Science. 1996 Feb 23;271(5252):1081-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8599083" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; DNA/metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Engineering ; Transcription Factors/chemistry/*metabolism ; Zinc/chemistry/metabolism/*physiology ; Zinc Fingers/*physiology
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    Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-12-20
    Description: The crystal structure of an unmodified hammerhead RNA in the absence of divalent metal ions has been solved, and it was shown that this ribozyme can cleave itself in the crystal when divalent metal ions are added. This biologically active RNA fold is the same as that found previously for two modified hammerhead ribozymes. Addition of divalent cations at low pH makes it possible to capture the uncleaved RNA in metal-bound form. A conformational intermediate, having an additional Mg(II) bound to the cleavage-site phosphate, was captured by freeze-trapping the RNA at an active pH prior to cleavage. The most significant conformational changes were limited to the active site of the ribozyme, and the changed conformation requires only small additional movements to reach a proposed transition-state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, W G -- Murray, J B -- Arnold, J R -- Stoddard, B L -- Klug, A -- GM-49857/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Dec 20;274(5295):2065-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8953035" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Crystallization ; Crystallography, X-Ray ; Freezing ; Hydrogen-Ion Concentration ; Magnesium/metabolism ; Manganese/metabolism ; Models, Molecular ; *Nucleic Acid Conformation ; RNA, Catalytic/*chemistry/metabolism
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    Structural basis of light harvesting by carotenoids: peridinin-chlorophyll-protein from Amphidinium carterae (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-06-21
    Description: Peridinin-chlorophyll-protein, a water-soluble light-harvesting complex that has a blue-green absorbing carotenoid as its main pigment, is present in most photosynthetic dinoflagellates. Its high-resolution (2.0 angstrom) x-ray structure reveals a noncrystallographic trimer in which each polypeptide contains an unusual jellyroll fold of the alpha-helical amino- and carboxyl-terminal domains. These domains constitute a scaffold with pseudo-twofold symmetry surrounding a hydrophobic cavity filled by two lipid, eight peridinin, and two chlorophyll a molecules. The structural basis for efficient excitonic energy transfer from peridinin to chlorophyll is found in the clustering of peridinins around the chlorophylls at van der Waals distances.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hofmann, E -- Wrench, P M -- Sharples, F P -- Hiller, R G -- Welte, W -- Diederichs, K -- New York, N.Y. -- Science. 1996 Jun 21;272(5269):1788-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Fakultat fur Biologie, Universitat Konstanz, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8650577" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carotenoids/*chemistry ; Chlorophyll/chemistry ; Crystallography, X-Ray ; Dinoflagellida/*chemistry/metabolism ; Energy Transfer ; Hydrogen Bonding ; Models, Molecular ; Molecular Conformation ; Photosynthesis ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protozoan Proteins/*chemistry
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    Organization of diphtheria toxin T domain in bilayers: a site-directed spin labeling study (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-08-09
    Description: The diphtheria toxin transmembrane (T) domain was spin-labeled at consecutive residues in a helical segment, TH9. After binding of the T domain to membranes at low pH, the nitroxide side chains generated by spin labeling were measured with respect to their frequency of collision with polar and nonpolar reagents. The data showed that the helical structure of TH9 in solution is conserved, with one face exposed to water and the other to the hydrophobic interior of the bilayer. Measurement of the depth of the nitroxide side chains from the membrane surfaces revealed an incremental change of about 5 angstroms per turn, which is consistent with a transmembrane orientation of an alpha helix. These results indicate that the helix forms the lining of a transmembrane water-filled channel.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oh, K J -- Zhan, H -- Cui, C -- Hideg, K -- Collier, R J -- Hubbell, W L -- AI-22021/AI/NIAID NIH HHS/ -- AI-22848/AI/NIAID NIH HHS/ -- EY-05216/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 1996 Aug 9;273(5276):810-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-7008, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8670424" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Diphtheria Toxin/*chemistry/genetics ; Edetic Acid/analogs & derivatives ; Electron Spin Resonance Spectroscopy ; Hydrogen-Ion Concentration ; *Lipid Bilayers ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nickel ; Oxygen ; Phospholipids ; *Protein Structure, Secondary ; *Protein Structure, Tertiary ; Spin Labels
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    A protein phosphorylation switch at the conserved allosteric site in GP (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-09-13
    Description: A phosphorylation-initiated mechanism of local protein refolding activates yeast glycogen phosphorylase (GP). Refolding of the phosphorylated amino-terminus was shown to create a hydrophobic cluster that wedges into the subunit interface of the enzyme to trigger activation. The phosphorylated threonine is buried in the allosteric site. The mechanism implicates glucose 6-phosphate, the allosteric inhibitor, in facilitating dephosphorylation by dislodging the buried covalent phosphate through binding competition. Thus, protein phosphorylation-dephosphorylation may also be controlled through regulation of the accessibility of the phosphorylation site to kinases and phosphatases. In mammalian glycogen phosphorylase, phosphorylation occurs at a distinct locus. The corresponding allosteric site binds a ligand activator, adenosine monophosphate, which triggers activation by a mechanism analogous to that of phosphorylation in the yeast enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, K -- Rath, V L -- Dai, S C -- Fletterick, R J -- Hwang, P K -- DK32822/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1996 Sep 13;273(5281):1539-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California at San Francisco, 513 Parnassus, San Francisco, CA 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8703213" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/metabolism ; Allosteric Site ; Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Enzyme Activation ; Enzyme Inhibitors/metabolism/pharmacology ; Glucose-6-Phosphate ; Glucosephosphates/metabolism/pharmacology ; Models, Molecular ; Molecular Sequence Data ; Phosphorylases/antagonists & inhibitors/*chemistry/*metabolism ; Phosphorylation ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Saccharomyces cerevisiae/enzymology
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    Close-up of a killer (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-10-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 1996 Oct 11;274(5285):176-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8927977" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cells, Cultured ; Crystallography, X-Ray ; Drosophila melanogaster ; H-2 Antigens/*chemistry/immunology/metabolism ; Killer Cells, Natural/immunology ; *Major Histocompatibility Complex ; Models, Molecular ; Peptides/immunology/metabolism ; Protein Conformation ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/immunology/metabolism ; Recombinant Proteins/chemistry ; T-Lymphocytes, Cytotoxic/*immunology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 79
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    Structural analysis of substrate binding by the molecular chaperone DnaK (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-06-14
    Description: DnaK and other members of the 70-kilodalton heat-shock protein (hsp70) family promote protein folding, interaction, and translocation, both constitutively and in response to stress, by binding to unfolded polypeptide segments. These proteins have two functional units: a substrate-binding portion binds the polypeptide, and an adenosine triphosphatase portion facilitates substrate exchange. The crystal structure of a peptide complex with the substrate-binding unit of DnaK has now been determined at 2.0 angstroms resolution. The structure consists of a beta-sandwich subdomain followed by alpha-helical segments. The peptide is bound to DnaK in an extended conformation through a channel defined by loops from the beta sandwich. An alpha-helical domain stabilizes the complex, but does not contact the peptide directly. This domain is rotated in the molecules of a second crystal lattice, which suggests a model of conformation-dependent substrate binding that features a latch mechanism for maintaining long lifetime complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, X -- Zhao, X -- Burkholder, W F -- Gragerov, A -- Ogata, C M -- Gottesman, M E -- Hendrickson, W A -- GM 34102/GM/NIGMS NIH HHS/ -- GM 37219/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jun 14;272(5268):1606-14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658133" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chaperonins/chemistry/*metabolism ; Crystallography, X-Ray ; Escherichia coli ; *Escherichia coli Proteins ; HSP70 Heat-Shock Proteins/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Peptides/metabolism ; Protein Binding ; Protein Conformation ; Sequence Homology, Amino Acid
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 80
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    DNA: an extensible molecule (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-02-09
    Description: The force-displacement response of a single duplex DNA molecule was measured. The force saturates at a plateau around 70 piconewtons, which ends when the DNA has been stretched about 1.7 times its contour length. This behavior reveals a highly cooperative transition to a state here termed S-DNA. Addition of an intercalator suppresses this transition. Molecular modeling of the process also yields a force plateau and suggests a structure for the extended form. These results may shed light on biological processes involving DNA extension and open the route for mechanical studies on individual molecules in a previously unexplored range.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cluzel, P -- Lebrun, A -- Heller, C -- Lavery, R -- Viovy, J L -- Chatenay, D -- Caron, F -- New York, N.Y. -- Science. 1996 Feb 9;271(5250):792-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Curie URA Centre National de la Recherche Scientifique (CNRS), Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8628993" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; DNA/*chemistry ; Models, Molecular ; *Nucleic Acid Conformation ; Physicochemical Phenomena ; Software
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  • 81
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    Direct visualization of A-, P-, and E-site transfer RNAs in the Escherichia coli ribosome (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-02-16
    Description: Transfer RNA (tRNA) molecules play a crucial role in protein biosynthesis in all organisms. Their interactions with ribosomes mediate the translation of genetic messages into polypeptides. Three tRNAs bound to the Escherichia coli 70S ribosome were visualized directly with cryoelectron microscopy and three-dimensional reconstruction. The detailed arrangement of A- and P-site tRNAs inferred from this study allows localization of the sites for anticodon interaction and peptide bond formation on the ribosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Agrawal, R K -- Penczek, P -- Grassucci, R A -- Li, Y -- Leith, A -- Nierhaus, K H -- Frank, J -- 1R01 GM29169/GM/NIGMS NIH HHS/ -- P41 RR01219/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1996 Feb 16;271(5251):1000-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wadsworth Center, New York State Department of Health, Albany 12201-0509, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8584922" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon ; Binding Sites ; Codon ; Escherichia coli/*metabolism ; Image Processing, Computer-Assisted ; Microscopy, Electron ; Models, Molecular ; Nucleic Acid Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Transfer/*chemistry/metabolism ; RNA, Transfer, Amino Acyl/*chemistry/metabolism ; RNA, Transfer, Phe/*chemistry/metabolism ; Ribosomes/*metabolism
    Print ISSN: 0036-8075
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  • 82
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    Design of a monomeric 23-residue polypeptide with defined tertiary structure (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-01-19
    Description: Small proteins or protein domains generally require disulfide bridges or metal sites for their stabilization. Here it is shown that the beta beta alpha architecture of zinc fingers can be reproduced in a 23-residue polypeptide in the absence of metal ions. The sequence was obtained through an iterative design process. A key feature of the final design is the incorporation of a type II' beta turn to aid in beta-hairpin formation. Nuclear magnetic resonance analysis reveals that the alpha helix and beta hairpin are held together by a defined hydrophobic core. The availability of this structural template has implications for the development of functional polypeptides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Struthers, M D -- Cheng, R P -- Imperiali, B -- New York, N.Y. -- Science. 1996 Jan 19;271(5247):342-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8553067" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Circular Dichroism ; DNA-Binding Proteins/chemistry ; *Genes, Synthetic ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Peptides/*chemistry ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Proteins/*chemistry ; Transcription Factors/chemistry ; Zinc Fingers
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  • 83
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    Crystal structure of the dual specificity protein phosphatase VHR (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-05-31
    Description: Dual specificity protein phosphatases (DSPs) regulate mitogenic signal transduction and control the cell cycle. Here, the crystal structure of a human DSP, vaccinia H1-related phosphatase (or VHR), was determined at 2.1 angstrom resolution. A shallow active site pocket in VHR allows for the hydrolysis of phosphorylated serine, threonine, or tyrosine protein residues, whereas the deeper active site of protein tyrosine phosphatases (PTPs) restricts substrate specificity to only phosphotyrosine. Positively charged crevices near the active site may explain the enzyme's preference for substrates with two phosphorylated residues. The VHR structure defines a conserved structural scaffold for both DSPs and PTPs. A "recognition region," connecting helix alpha1 to strand beta1, may determine differences in substrate specificity between VHR, the PTPs, and other DSPs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yuvaniyama, J -- Denu, J M -- Dixon, J E -- Saper, M A -- AI 34095/AI/NIAID NIH HHS/ -- DK18024/DK/NIDDK NIH HHS/ -- DK18849/DK/NIDDK NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1996 May 31;272(5266):1328-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Research Division and Department of Biological Chemistry, University of Michigan, Ann Arbor 48109-1055, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8650541" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Dual Specificity Phosphatase 3 ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Phosphorylation ; Phosphoserine/metabolism ; Phosphothreonine/metabolism ; Phosphotyrosine/metabolism ; *Protein Conformation ; Protein Folding ; *Protein Structure, Secondary ; Protein Tyrosine Phosphatases/*chemistry/metabolism ; Sequence Alignment ; Substrate Specificity ; Water/metabolism ; Yersinia/enzymology
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  • 84
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    An asymmetric model for the nucleosome: a binding site for linker histones inside the DNA gyres (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-10-25
    Description: Histone-DNA contacts within a nucleosome influence the function of trans-acting factors and the molecular machines required to activate the transcription process. The internal architecture of a positioned nucleosome has now been probed with the use of photoactivatable cross-linking reagents to determine the placement of histones along the DNA molecule. A model for the nucleosome is proposed in which the winged-helix domain of the linker histone is asymmetrically located inside the gyres of DNA that also wrap around the core histones. This domain extends the path of the protein superhelix to one side of the core particle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pruss, D -- Bartholomew, B -- Persinger, J -- Hayes, J -- Arents, G -- Moudrianakis, E N -- Wolffe, A P -- New York, N.Y. -- Science. 1996 Oct 25;274(5287):614-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2710, USA. awlme@helix.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8849453" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Cross-Linking Reagents ; DNA/*chemistry/metabolism ; Histones/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleosomes/*chemistry ; Protein Conformation ; Protein Structure, Secondary ; RNA, Ribosomal/genetics ; Recombinant Proteins/chemistry ; Xenopus
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  • 85
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    Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-10-18
    Description: The Escherichia coli DNA binding protein RuvA acts in concert with the helicase RuvB to drive branch migration of Holliday intermediates during recombination and DNA repair. The atomic structure of RuvA was determined at a resolution of 1.9 angstroms. Four monomers of RuvA are related by fourfold symmetry in a manner reminiscent of a four-petaled flower. The four DNA duplex arms of a Holliday junction can be modeled in a square planar configuration and docked into grooves on the concave surface of the protein around a central pin that may facilitate strand separation during the migration reaction. The model presented reveals how a RuvAB-junction complex may also accommodate the resolvase RuvC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rafferty, J B -- Sedelnikova, S E -- Hargreaves, D -- Artymiuk, P J -- Baker, P J -- Sharples, G J -- Mahdi, A A -- Lloyd, R G -- Rice, D W -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 1996 Oct 18;274(5286):415-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK. d.rice@sheffield.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8832889" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Base Composition ; Crystallography, X-Ray ; DNA Helicases/metabolism ; DNA, Bacterial/chemistry/*metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Endodeoxyribonucleases/metabolism ; Escherichia coli ; *Escherichia coli Proteins ; Hydrogen Bonding ; Models, Molecular ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Recombination, Genetic
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  • 86
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    Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-11-08
    Description: The MDM2 oncoprotein is a cellular inhibitor of the p53 tumor suppressor in that it can bind the transactivation domain of p53 and downregulate its ability to activate transcription. In certain cancers, MDM2 amplification is a common event and contributes to the inactivation of p53. The crystal structure of the 109-residue amino-terminal domain of MDM2 bound to a 15-residue transactivation domain peptide of p53 revealed that MDM2 has a deep hydrophobic cleft on which the p53 peptide binds as an amphipathic alpha helix. The interface relies on the steric complementarity between the MDM2 cleft and the hydrophobic face of the p53 alpha helix and, in particular, on a triad of p53 amino acids-Phe19, Trp23, and Leu26-which insert deep into the MDM2 cleft. These same p53 residues are also involved in transactivation, supporting the hypothesis that MDM2 inactivates p53 by concealing its transactivation domain. The structure also suggests that the amphipathic alpha helix may be a common structural motif in the binding of a diverse family of transactivation factors to the TATA-binding protein-associated factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kussie, P H -- Gorina, S -- Marechal, V -- Elenbaas, B -- Moreau, J -- Levine, A J -- Pavletich, N P -- CA65698/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1996 Nov 8;274(5289):948-53.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. nikola@xray2.mskcc.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8875929" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; *Nuclear Proteins ; Protein Binding ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proto-Oncogene Proteins/*chemistry/metabolism ; Proto-Oncogene Proteins c-mdm2 ; Transcription Factors/chemistry/metabolism ; *Transcriptional Activation ; Tumor Suppressor Protein p53/*chemistry/metabolism
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  • 87
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    Parallel and antiparallel (G.GC)2 triple helix fragments in a crystal structure (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-09-20
    Description: Nucleic acid triplexes are formed by sequence-specific interactions between single-stranded polynucleotides and the double helix. These triplexes are implicated in genetic recombination in vivo and have application to areas that include genome analysis and antigene therapy. Despite the importance of the triple helix, only limited high-resolution structural information is available. The x-ray crystal structure of the oligonucleotide d(GGCCAATTGG) is described; it was designed to contain the d(G middle dotGC)2 fragment and thus provide the basic repeat unit of a DNA triple helix. Parameters derived from this crystal structure have made it possible to construct models of both parallel and antiparallel triple helices.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vlieghe, D -- Van Meervelt, L -- Dautant, A -- Gallois, B -- Precigoux, G -- Kennard, O -- New York, N.Y. -- Science. 1996 Sep 20;273(5282):1702-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Heverlee, Belgium. Structurale, EP CNRS, Universite de Bordeaux.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8781231" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Crystallography, X-Ray ; DNA/*chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/*chemistry
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  • 88
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    Flexing muscle with just one amino acid (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-01-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 1996 Jan 5;271(5245):31.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8539593" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Calcium/*metabolism ; Glutamic Acid/*physiology ; Humans ; Magnetic Resonance Spectroscopy ; Models, Molecular ; *Muscle Contraction ; Muscle, Skeletal/chemistry ; Mutation ; Myocardium/chemistry ; *Protein Conformation ; Protein Structure, Secondary ; Troponin/*chemistry/genetics/metabolism ; Troponin C
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  • 89
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    Bipartite Ca2+-binding motif in C2 domains of synaptotagmin and protein kinase C (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-07-12
    Description: C2 domains are found in many proteins involved in membrane traffic or signal transduction. Although C2 domains are thought to bind calcium ions, the structural basis for calcium binding is unclear. Analysis of calcium binding to C2 domains of synaptotagmin I and protein kinase C-beta by nuclear magnetic resonance spectroscopy revealed a bipartite calcium-binding motif that involves the coordination of two calcium ions by five aspartate residues located on two separate loops. Sequence comparisons indicated that this may be a widely used calcium-binding motif, designated here as the C2 motif.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shao, X -- Davletov, B A -- Sutton, R B -- Sudhof, T C -- Rizo, J -- R01-MH52804-01/MH/NIMH NIH HHS/ -- R29 NS33731-01A1/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 12;273(5272):248-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75235, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662510" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid/chemistry ; Base Sequence ; Calcium/*metabolism ; *Calcium-Binding Proteins ; Crystallography, X-Ray ; Hydrogen-Ion Concentration ; Magnetic Resonance Spectroscopy ; Membrane Glycoproteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Nerve Tissue Proteins/*chemistry/*metabolism ; Phospholipids/metabolism ; Protein Conformation ; Protein Folding ; Protein Kinase C/chemistry/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Synaptotagmin I ; Synaptotagmins ; Temperature
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  • 90
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    The crystal structure of a five-stranded coiled coil in COMP: a prototype ion channel? (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-11-01
    Description: Oligomerization by the formation of alpha-helical bundles is common in many proteins. The crystal structure of a parallel pentameric coiled coil, constituting the oligomerization domain in the cartilage oligomeric matrix protein (COMP), was determined at 2.05 angstroms resolution. The same structure probably occurs in two other extracellular matrix proteins, thrombospondins 3 and 4. Complementary hydrophobic interactions and conserved disulfide bridges between the alpha helices result in a thermostable structure with unusual properties. The long hydrophobic axial pore is filled with water molecules but can also accommodate small apolar groups. An "ion trap" is formed inside the pore by a ring of conserved glutamines, which binds chloride and probably other monatomic anions. The oligomerization domain of COMP has marked similarities with proposed models of the pentameric transmembrane ion channels in phospholamban and the acetylcholine receptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Malashkevich, V N -- Kammerer, R A -- Efimov, V P -- Schulthess, T -- Engel, J -- New York, N.Y. -- Science. 1996 Nov 1;274(5288):761-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8864111" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cartilage Oligomeric Matrix Protein ; Chloride Channels/chemistry ; Chlorides/chemistry ; Crystallography, X-Ray ; Disulfides/chemistry ; Extracellular Matrix Proteins/*chemistry ; Glutamine/chemistry ; Glycoproteins/*chemistry ; Humans ; Hydrogen Bonding ; Ion Channels/*chemistry ; Matrilin Proteins ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; *Protein Structure, Secondary ; Sequence Alignment
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  • 91
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    Bioinformatics. Working the Web with a virtual lab and some Java (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-08-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fischman, J -- New York, N.Y. -- Science. 1996 Aug 2;273(5275):591-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8701313" target="_blank"〉PubMed〈/a〉
    Keywords: *Amino Acid Sequence ; *Base Sequence ; *Computer Communication Networks ; DNA/*genetics ; *Information Systems ; Models, Molecular ; *Programming Languages ; Protein Conformation ; Proteins/chemistry
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  • 92
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    Linker histones, DNA's protein custodians, gain new respect (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-10-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 1996 Oct 25;274(5287):503-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8928004" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; Gene Expression Regulation ; Histones/chemistry/*metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Nucleosomes/*chemistry/genetics ; Tetrahymena thermophila/genetics ; Xenopus
    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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  • 93
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    Tumor-killer made; how does it work? (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-12-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 1996 Dec 20;274(5295):2009.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8984658" target="_blank"〉PubMed〈/a〉
    Keywords: *Alkanes ; Antineoplastic Agents/*chemical synthesis/chemistry/metabolism/*pharmacology ; *Carbamates ; Computer Simulation ; *Epothilones ; Epoxy Compounds/*chemical synthesis/chemistry/metabolism/*pharmacology ; Lactones/chemical synthesis/chemistry/pharmacology ; Microtubules/drug effects/metabolism ; Models, Molecular ; Molecular Conformation ; Paclitaxel/chemistry/pharmacology ; Pyrones ; Thiazoles/*chemical synthesis/chemistry/metabolism/*pharmacology ; Tumor Cells, Cultured
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 94
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    Crystal structure of the Aequorea victoria green fluorescent protein (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-09-06
    Description: The green fluorescent protein (GFP) from the Pacific Northwest jellyfish Aequorea victoria has generated intense interest as a marker for gene expression and localization of gene products. The chromophore, resulting from the spontaneous cyclization and oxidation of the sequence -Ser65 (or Thr65)-Tyr66-Gly67-, requires the native protein fold for both formation and fluorescence emission. The structure of Thr65 GFP has been determined at 1.9 angstrom resolution. The protein fold consists of an 11-stranded beta barrel with a coaxial helix, with the chromophore forming from the central helix. Directed mutagenesis of one residue adjacent to the chromophore, Thr203, to Tyr or His results in significantly red-shifted excitation and emission maxima.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ormo, M -- Cubitt, A B -- Kallio, K -- Gross, L A -- Tsien, R Y -- Remington, S J -- New York, N.Y. -- Science. 1996 Sep 6;273(5280):1392-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Department of Physics, University of Oregon, Eugene, OR 97403-1226, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8703075" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Green Fluorescent Proteins ; Hydrogen Bonding ; Luminescent Proteins/*chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Spectrometry, Fluorescence
    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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  • 95
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    Functional mimicry of a protein hormone by a peptide agonist: the EPO receptor complex at 2.8 A (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-07-26
    Description: The functional mimicry of a protein by an unrelated small molecule has been a formidable challenge. Now, however, the biological activity of a 166-residue hematopoietic growth hormone, erythropoietin (EPO), with its class 1 cytokine receptor has been mimicked by a 20-residue cyclic peptide unrelated in sequence to the natural ligand. The crystal structure at 2.8 A resolution of a complex of this agonist peptide with the extracellular domain of EPO receptor reveals that a peptide dimer induces an almost perfect twofold dimerization of the receptor. The dimer assembly differs from that of the human growth hormone (hGH) receptor complex and suggests that more than one mode of dimerization may be able to induce signal transduction and cell proliferation. The EPO receptor binding site, defined by peptide interaction, corresponds to the smaller functional epitope identified for hGH receptor. Similarly, the EPO mimetic peptide ligand can be considered as a minimal hormone, and suggests the design of nonpeptidic small molecule mimetics for EPO and other cytokines may indeed be achievable.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Livnah, O -- Stura, E A -- Johnson, D L -- Middleton, S A -- Mulcahy, L S -- Wrighton, N C -- Dower, W J -- Jolliffe, L K -- Wilson, I A -- GM-49497/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 26;273(5274):464-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10666 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662530" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Drug Design ; Erythropoietin/*chemistry/*metabolism ; Growth Hormone/chemistry/metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; *Molecular Mimicry ; Molecular Sequence Data ; Peptides, Cyclic/*chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Erythropoietin/*agonists/chemistry/metabolism ; Receptors, Somatotropin/chemistry/metabolism
    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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  • 96
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    Intercalation, DNA kinking, and the control of transcription (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-02-09
    Description: Biological processes involved in the control and regulation of transcription are dependent on protein-induced distortions in DNA structure that enhance the recruitment of proteins to their specific DNA targets. This function is often accomplished by accessory factors that bind sequence specifically and locally bend or kink the DNA. The recent determination of the three-dimensional structures of several protein-DNA complexes, involving proteins that perform such architectural tasks, brings to light a common theme of side chain intercalation as a mechanism capable of driving the deformation of the DNA helix. The protein scaffolds orienting the intercalating side chain (or side chains) are structurally diverse, presently comprising four distinct topologies that can accomplish the same task. The intercalating side chain (or side chains), however, is exclusively hydrophobic. Intercalation can either kink or bend the DNA, unstacking one or more adjacent base pairs and locally unwinding the DNA over as much as a full turn of helix. Despite these distortions, the return to B-DNA helical parameters generally occurs within the adjacent half-turns of DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Werner, M H -- Gronenborn, A M -- Clore, G M -- New York, N.Y. -- Science. 1996 Feb 9;271(5250):778-84.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8628992" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; DNA/*chemistry/metabolism ; DNA Helicases/chemistry/metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Hydrogen Bonding ; Intercalating Agents/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Transcription Factors/chemistry/*metabolism ; *Transcription, Genetic
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 97
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    Heparin structure and interactions with basic fibroblast growth factor (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-02-23
    Description: Crystal structures of heparin-derived tetra- and hexasaccharides complexed with basic fibroblast growth factor (bFGF) were determined at resolutions of 1.9 and 2.2 angstroms, respectively. The heparin structure may be approximated as a helical polymer with a disaccharide rotation of 174 degrees and a translation of 8.6 angstroms along the helix axis. Both molecules bound similarly to a region of the bFGF surface containing residues asparagine-28, arginine-121, lysine-126, and glutamine-135, the hexasaccharide also interacted with an additional binding site formed by lysine-27, asparagine-102, and lysine-136. No significant conformational change in bFGF occurred upon heparin oligosaccharide binding, which suggests that heparin primarily serves to juxtapose components of the FGF signal transduction pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Faham, S -- Hileman, R E -- Fromm, J R -- Linhardt, R J -- Rees, D C -- GM38060/GM/NIGMS NIH HHS/ -- GM45162/GM/NIGMS NIH HHS/ -- T32 GM08346/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Feb 23;271(5252):1116-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8599088" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbohydrate Conformation ; Carbohydrate Sequence ; Crystallization ; Crystallography, X-Ray ; Fibroblast Growth Factor 2/*metabolism ; Heparin/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Oligosaccharides/chemistry/metabolism ; Protein Conformation
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 98
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    An alphabeta T cell receptor structure at 2.5 A and its orientation in the TCR-MHC complex (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-10-11
    Description: The central event in the cellular immune response to invading microorganisms is the specific recognition of foreign peptides bound to major histocompatibility complex (MHC) molecules by the alphabeta T cell receptor (TCR). The x-ray structure of the complete extracellular fragment of a glycosylated alphabeta TCR was determined at 2.5 angstroms, and its orientation bound to a class I MHC-peptide (pMHC) complex was elucidated from crystals of the TCR-pMHC complex. The TCR resembles an antibody in the variable Valpha and Vbeta domains but deviates in the constant Calpha domain and in the interdomain pairing of Calpha with Cbeta. Four of seven possible asparagine-linked glycosylation sites have ordered carbohydrate moieties, one of which lies in the Calpha-Cbeta interface. The TCR combining site is relatively flat except for a deep hydrophobic cavity between the hypervariable CDR3s (complementarity-determining regions) of the alpha and beta chains. The 2C TCR covers the class I MHC H-2Kb binding groove so that the Valpha CDRs 1 and 2 are positioned over the amino-terminal region of the bound dEV8 peptide, the Vbeta chain CDRs 1 and 2 are over the carboxyl-terminal region of the peptide, and the Valpha and Vbeta CDR3s straddle the peptide between the helices around the central position of the peptide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia, K C -- Degano, M -- Stanfield, R L -- Brunmark, A -- Jackson, M R -- Peterson, P A -- Teyton, L -- Wilson, I A -- R01 CA58896/CA/NCI NIH HHS/ -- T32-A107244/PHS HHS/ -- New York, N.Y. -- Science. 1996 Oct 11;274(5285):209-19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute of Chemical Biology, Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8824178" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carbohydrate Sequence ; Cells, Cultured ; Crystallization ; Crystallography, X-Ray ; Drosophila melanogaster ; Glycosylation ; H-2 Antigens/*chemistry/immunology/metabolism ; Hydrogen Bonding ; Major Histocompatibility Complex ; Mice ; Models, Molecular ; Molecular Sequence Data ; Peptides/*chemistry/immunology/metabolism ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/immunology/metabolism ; Recombinant Proteins ; T-Lymphocytes, Cytotoxic/*immunology
    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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  • 99
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    RNA tertiary structure mediation by adenosine platforms (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-09-20
    Description: The crystal structure of a group I intron domain reveals an unexpected motif that mediates both intra- and intermolecular interactions. At three separate locations in the 160-nucleotide domain, adjacent adenosines in the sequence lie side-by-side and form a pseudo-base pair within a helix. This adenosine platform opens the minor groove for base stacking or base pairing with nucleotides from a noncontiguous RNA strand. The platform motif has a distinctive chemical modification signature that may enable its detection in other structured RNAs. The ability of this motif to facilitate higher order folding provides one explanation for the abundance of adenosine residues in internal loops of many RNAs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cate, J H -- Gooding, A R -- Podell, E -- Zhou, K -- Golden, B L -- Szewczak, A A -- Kundrot, C E -- Cech, T R -- Doudna, J A -- 5T32GM08283-07/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Sep 20;273(5282):1696-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8781229" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/*chemistry ; Animals ; Base Composition ; Hydrogen Bonding ; *Introns ; Models, Molecular ; *Nucleic Acid Conformation ; RNA, Catalytic/*chemistry ; RNA, Protozoan/*chemistry ; Tetrahymena thermophila/genetics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 100
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    Computational molecular biology. Software matchmakers help make sense of sequences (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-08-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Taubes, G -- New York, N.Y. -- Science. 1996 Aug 2;273(5275):588-90.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8701312" target="_blank"〉PubMed〈/a〉
    Keywords: *Algorithms ; *Amino Acid Sequence ; Base Sequence ; Computer Communication Networks ; *Databases, Factual ; Evolution, Molecular ; Markov Chains ; Models, Molecular ; Molecular Sequence Data ; Neural Networks (Computer) ; *Protein Conformation ; Sequence Alignment
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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