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  • 1
    Publikationsdatum: 1997-04-18
    Beschreibung: The crystal structure of the adenine nucleotide exchange factor GrpE in complex with the adenosine triphosphatase (ATPase) domain of Escherichia coli DnaK [heat shock protein 70 (Hsp70)] was determined at 2.8 angstrom resolution. A dimer of GrpE binds asymmetrically to a single molecule of DnaK. The structure of the nucleotide-free ATPase domain in complex with GrpE resembles closely that of the nucleotide-bound mammalian Hsp70 homolog, except for an outward rotation of one of the subdomains of the protein. This conformational change is not consistent with tight nucleotide binding. Two long alpha helices extend away from the GrpE dimer and suggest a role for GrpE in peptide release from DnaK.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harrison, C J -- Hayer-Hartl, M -- Di Liberto, M -- Hartl, F -- Kuriyan, J -- New York, N.Y. -- Science. 1997 Apr 18;276(5311):431-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratories of Molecular Biophysics and Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9103205" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Adenosine Diphosphate/metabolism ; Adenosine Triphosphatases/*chemistry/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; *Escherichia coli Proteins ; HSP70 Heat-Shock Proteins/*chemistry/metabolism ; Heat-Shock Proteins/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Chaperones/*chemistry/metabolism ; Molecular Sequence Data ; *Protein Conformation ; Protein Structure, Secondary
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 2
    Publikationsdatum: 1997-11-21
    Beschreibung: Many neuropeptides and peptide hormones require amidation at the carboxyl terminus for activity. Peptidylglycine alpha-amidating monooxygenase (PAM) catalyzes the amidation of these diverse physiological regulators. The amino-terminal domain of the bifunctional PAM protein is a peptidylglycine alpha-hydroxylating monooxygenase (PHM) with two coppers that cycle through cupric and cuprous oxidation states. The anomalous signal of the endogenous coppers was used to determine the structure of the catalytic core of oxidized rat PHM with and without bound peptide substrate. These structures strongly suggest that the PHM reaction proceeds via activation of substrate by a copper-bound oxygen species. The mechanistic and structural insight gained from the PHM structures can be directly extended to dopamine beta-monooxygenase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prigge, S T -- Kolhekar, A S -- Eipper, B A -- Mains, R E -- Amzel, L M -- DK32949/DK/NIDDK NIH HHS/ -- GM44692/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Nov 14;278(5341):1300-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9360928" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Binding Sites ; Catalysis ; Copper/chemistry/metabolism ; Crystallography, X-Ray ; Dipeptides/metabolism ; Dopamine beta-Hydroxylase/chemistry/metabolism ; Electrons ; Hydroxylation ; Ligands ; Mixed Function Oxygenases/*chemistry/metabolism ; Models, Molecular ; *Multienzyme Complexes ; Oxidation-Reduction ; Oxygen/metabolism ; Peptides/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Rats
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 3
    Publikationsdatum: 1997-06-13
    Beschreibung: The crystal structures of a germline antibody Fab fragment and its complex with hapten have been solved at 2.1 A resolution. These structures are compared with the corresponding crystal structures of the affinity-matured antibody, 48G7, which has a 30,000 times higher affinity for hapten as a result of nine replacement somatic mutations. Significant changes in the configuration of the combining site occur upon binding of hapten to the germline antibody, whereas hapten binds to the mature antibody by a lock-and-key fit mechanism. The reorganization of the combining site that was nucleated by hapten binding is further optimized by somatic mutations that occur up to 15 from bound hapten. These results suggest that the binding potential of the primary antibody repertoire may be significantly expanded by the ability of germline antibodies to adopt more than one combining-site configuration, with both antigen binding and somatic mutation stabilizing the configuration with optimal hapten complementarity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wedemayer, G J -- Patten, P A -- Wang, L H -- Schultz, P G -- Stevens, R C -- R01 AI39089/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1997 Jun 13;276(5319):1665-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9180069" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Antibodies, Catalytic/*chemistry/genetics/immunology ; Antibody Affinity ; Antibody Diversity ; Antigen-Antibody Complex ; Antigen-Antibody Reactions ; Binding Sites ; *Binding Sites, Antibody ; Crystallography, X-Ray ; *Evolution, Molecular ; Haptens/immunology ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/*chemistry/genetics/immunology ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Structure, Secondary
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 4
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1997-10-06
    Beschreibung: The first fully automated design and experimental validation of a novel sequence for an entire protein is described. A computational design algorithm based on physical chemical potential functions and stereochemical constraints was used to screen a combinatorial library of 1.9 x 10(27) possible amino acid sequences for compatibility with the design target, a betabetaalpha protein motif based on the polypeptide backbone structure of a zinc finger domain. A BLAST search shows that the designed sequence, full sequence design 1 (FSD-1), has very low identity to any known protein sequence. The solution structure of FSD-1 was solved by nuclear magnetic resonance spectroscopy and indicates that FSD-1 forms a compact well-ordered structure, which is in excellent agreement with the design target structure. This result demonstrates that computational methods can perform the immense combinatorial search required for protein design, and it suggests that an unbiased and quantitative algorithm can be used in various structural contexts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dahiyat, B I -- Mayo, S L -- GM08346/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Oct 3;278(5335):82-7.〈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/9311930" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): *Algorithms ; Amino Acid Sequence ; Computer Simulation ; Crystallography, X-Ray ; DNA-Binding Proteins/chemical synthesis/*chemistry ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Solutions ; Transcription Factors/chemical synthesis/*chemistry ; Zinc Fingers
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 5
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1997-06-20
    Beschreibung: Bactericidal/permeability-increasing protein (BPI), a potent antimicrobial protein of 456 residues, binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria. At a resolution of 2.4 angstroms, the crystal structure of human BPI shows a boomerang-shaped molecule formed by two similar domains. Two apolar pockets on the concave surface of the boomerang each bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide. As a model for the related plasma lipid transfer proteins, BPI illuminates a mechanism of lipid transfer for this protein family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beamer, L J -- Carroll, S F -- Eisenberg, D -- GM31299/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Jun 20;276(5320):1861-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, 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/9188532" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Antimicrobial Cationic Peptides ; Binding Sites ; Blood Bactericidal Activity ; Blood Proteins/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Humans ; Lipopolysaccharides/metabolism ; *Membrane Proteins ; Models, Molecular ; Molecular Sequence Data ; Phosphatidylcholines/chemistry/*metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 6
    Publikationsdatum: 1997-07-04
    Beschreibung: On the basis of x-ray diffraction data to a resolution of 2.9 angstroms, atomic models of most protein components of the bovine cytochrome bc1 complex were built, including core 1, core 2, cytochrome b, subunit 6, subunit 7, a carboxyl-terminal fragment of cytochrome c1, and an amino-terminal fragment of the iron-sulfur protein. The positions of the four iron centers within the bc1 complex and the binding sites of the two specific respiratory inhibitors antimycin A and myxothiazol were identified. The membrane-spanning region of each bc1 complex monomer consists of 13 transmembrane helices, eight of which belong to cytochrome b. Closely interacting monomers are arranged as symmetric dimers and form cavities through which the inhibitor binding pockets can be accessed. The proteins core 1 and core 2 are structurally similar to each other and consist of two domains of roughly equal size and identical folding topology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xia, D -- Yu, C A -- Kim, H -- Xia, J Z -- Kachurin, A M -- Zhang, L -- Yu, L -- Deisenhofer, J -- GM 30721/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Jul 4;277(5322):60-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9204897" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Antimycin A/metabolism/pharmacology ; Binding Sites ; Cattle ; Crystallography, X-Ray ; Cytochrome b Group/chemistry ; Cytochromes c1/chemistry ; Dimerization ; Electron Transport Complex III/*chemistry/metabolism ; Intracellular Membranes/enzymology ; Iron/metabolism ; Methacrylates ; Mitochondria, Heart/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thiazoles/metabolism/pharmacology
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 7
    Publikationsdatum: 1997-07-18
    Beschreibung: CD1 represents a third lineage of antigen-presenting molecules that are distantly related to major histocompatibility complex (MHC) molecules in the immune system. The crystal structure of mouse CD1d1, corresponding to human CD1d, at 2.8 resolution shows that CD1 adopts an MHC fold that is more closely related to that of MHC class I than to that of MHC class II. The binding groove, although significantly narrower, is substantially larger because of increased depth and it has only two major pockets that are almost completely hydrophobic. The extreme hydrophobicity and shape of the binding site are consistent with observations that human CD1b and CD1c can present mycobacterial cell wall antigens, such as mycolic acid and lipoarabinomannans. However, mouse CD1d1 can present very hydrophobic peptides, but must do so in a very different way from MHC class Ia and class II molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zeng, Z -- Castano, A R -- Segelke, B W -- Stura, E A -- Peterson, P A -- Wilson, I A -- CA-58896/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1997 Jul 18;277(5324):339-45.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute for Chemical Biology at the 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/9219685" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; *Antigen Presentation ; Antigens, CD1/*chemistry/immunology/metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Glycolipids/chemistry/immunology/metabolism ; Histocompatibility Antigens Class I/chemistry ; Histocompatibility Antigens Class II/chemistry ; Humans ; Hydrogen Bonding ; Ligands ; Lipid Metabolism ; Lipids/chemistry/immunology ; Mice ; Models, Molecular ; *Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; T-Lymphocyte Subsets/immunology
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 8
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1997-09-20
    Beschreibung: Structure determination at 2.4 angstrom resolution shows that lambda-exonuclease consists of three subunits that form a toroid. The central channel is funnel shaped, tapering from an inner diameter of about 30 angstroms at the wider end to 15 angstroms at the narrow end. This is adequate to accommodate the DNA substrate and thus provides a structural basis for the ability of the enzyme to sequentially hydrolyze thousands of nucleotides in a highly processive manner. The results also suggest the locations of the active sites and the constraints that limit cleavage to a single strand.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kovall, R -- Matthews, B W -- GM20066/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Sep 19;277(5333):1824-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, Howard Hughes Medical Institute, and Department of Physics, University of Oregon, Eugene, OR 97403, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9295273" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Bacteriophage lambda/enzymology ; Binding Sites ; Crystallography, X-Ray ; DNA/genetics/*metabolism ; DNA, Single-Stranded/genetics/*metabolism ; DNA, Viral/genetics/metabolism ; Evolution, Molecular ; Exodeoxyribonucleases/*chemistry/genetics/metabolism ; Hydrolysis ; Magnesium/metabolism ; Models, Molecular ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombination, Genetic ; Viral Proteins
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 9
    Publikationsdatum: 1997-03-21
    Beschreibung: Protein farnesyltransferase (FTase) catalyzes the carboxyl-terminal lipidation of Ras and several other cellular signal transduction proteins. The essential nature of this modification for proper function of these proteins has led to the emergence of FTase as a target for the development of new anticancer therapy. Inhibition of this enzyme suppresses the transformed phenotype in cultured cells and causes tumor regression in animal models. The crystal structure of heterodimeric mammalian FTase was determined at 2.25 angstrom resolution. The structure shows a combination of two unusual domains: a crescent-shaped seven-helical hairpin domain and an alpha-alpha barrel domain. The active site is formed by two clefts that intersect at a bound zinc ion. One cleft contains a nine-residue peptide that may mimic the binding of the Ras substrate; the other cleft is lined with highly conserved aromatic residues appropriate for binding the farnesyl isoprenoid with required specificity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, H W -- Boduluri, S R -- Moomaw, J F -- Casey, P J -- Beese, L S -- GM46372/GM/NIGMS NIH HHS/ -- GM52382/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Mar 21;275(5307):1800-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9065406" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): *Alkyl and Aryl Transferases ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Protein Conformation ; Protein Structure, Secondary ; Proteins/metabolism ; Sequence Alignment ; Transferases/*chemistry/genetics/metabolism ; Zinc/metabolism
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 10
    Publikationsdatum: 1997-07-18
    Beschreibung: The three-dimensional structure of the complex between human H-Ras bound to guanosine diphosphate and the guanosine triphosphatase (GTPase)-activating domain of the human GTPase-activating protein p120GAP (GAP-334) in the presence of aluminum fluoride was solved at a resolution of 2.5 angstroms. The structure shows the partly hydrophilic and partly hydrophobic nature of the communication between the two molecules, which explains the sensitivity of the interaction toward both salts and lipids. An arginine side chain (arginine-789) of GAP-334 is supplied into the active site of Ras to neutralize developing charges in the transition state. The switch II region of Ras is stabilized by GAP-334, thus allowing glutamine-61 of Ras, mutation of which activates the oncogenic potential, to participate in catalysis. The structural arrangement in the active site is consistent with a mostly associative mechanism of phosphoryl transfer and provides an explanation for the activation of Ras by glycine-12 and glutamine-61 mutations. Glycine-12 in the transition state mimic is within van der Waals distance of both arginine-789 of GAP-334 and glutamine-61 of Ras, and even its mutation to alanine would disturb the arrangements of residues in the transition state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scheffzek, K -- Ahmadian, M R -- Kabsch, W -- Wiesmuller, L -- Lautwein, A -- Schmitz, F -- Wittinghofer, A -- New York, N.Y. -- Science. 1997 Jul 18;277(5324):333-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur molekulare Physiologie, Abteilung Strukturelle Biologie, Rheinlanddamm 201, 44139 Dortmund, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9219684" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Aluminum Compounds/chemistry/metabolism ; Amino Acid Sequence ; Binding Sites ; Catalysis ; Cell Transformation, Neoplastic ; Crystallography, X-Ray ; Enzyme Activation ; Fluorides/chemistry/metabolism ; GTP Phosphohydrolases/chemistry/*metabolism ; GTP-Binding Proteins/chemistry/metabolism ; GTPase-Activating Proteins ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; Humans ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Protein Conformation ; Protein Structure, Secondary ; Proteins/*chemistry/*metabolism ; Signal Transduction ; ras GTPase-Activating Proteins ; ras Proteins/chemistry/genetics/*metabolism
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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