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  • 1
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    Nuclear accumulation of NFAT4 opposed by the JNK signal transduction pathway (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-12-31
    Description: The nuclear factor of activated T cells (NFAT) group of transcription factors is retained in the cytoplasm of quiescent cells. NFAT activation is mediated in part by induced nuclear import. This process requires calcium-dependent dephosphorylation of NFAT caused by the phosphatase calcineurin. The c-Jun amino-terminal kinase (JNK) phosphorylates NFAT4 on two sites. Mutational removal of the JNK phosphorylation sites caused constitutive nuclear localization of NFAT4. In contrast, JNK activation in calcineurin-stimulated cells caused nuclear exclusion of NFAT4. These findings show that the nuclear accumulation of NFAT4 promoted by calcineurin is opposed by the JNK signal transduction pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chow, C W -- Rincon, M -- Cavanagh, J -- Dickens, M -- Davis, R J -- CA58396/CA/NCI NIH HHS/ -- CA65831/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1997 Nov 28;278(5343):1638-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Program in Molecular Medicine, Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9374467" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; COS Cells ; Calcineurin/metabolism ; Calcineurin Inhibitors ; Calcium-Calmodulin-Dependent Protein Kinases/*metabolism ; Cell Line ; Cell Nucleus/*metabolism ; Cyclosporine/pharmacology ; Cytoplasm/metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Humans ; JNK Mitogen-Activated Protein Kinases ; Jurkat Cells ; Mitogen-Activated Protein Kinase Kinases ; *Mitogen-Activated Protein Kinases ; Mutation ; NFATC Transcription Factors ; *Nuclear Proteins ; Phosphorylation ; Protein Kinases/metabolism ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction ; T-Lymphocytes/metabolism ; Transcription Factors/genetics/*metabolism ; Transcription, Genetic
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  • 2
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    Discrete determinants in transfer RNA for editing and aminoacylation (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-05-23
    Description: During translation errors of aminoacylation are corrected in editing reactions which ensure that an amino acid is stably attached to its corresponding transfer RNA (tRNA). Previous studies have not shown whether the tRNA nucleotides needed for effecting translational editing are the same as or distinct from those required for aminoacylation, but several considerations have suggested that they are the same. Here, designed tRNAs that are highly active for aminoacylation but are not active in translational editing are presented. The editing reaction can be controlled by manipulation of nucleotides at the corner of the L-shaped tRNA. In contrast, these manipulations do not affect aminoacylation. These results demonstrate the segregation of nucleotide determinants for the editing and aminoacylation functions of tRNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hale, S P -- Auld, D S -- Schmidt, E -- Schimmel, P -- GM15539/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 May 23;276(5316):1250-2.〈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/9157882" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Base Sequence ; Binding Sites ; Cloning, Molecular ; Escherichia coli ; Molecular Sequence Data ; Nucleic Acid Conformation ; *RNA Editing ; RNA, Transfer/*metabolism ; RNA, Transfer, Ile/chemistry/metabolism ; RNA, Transfer, Val/chemistry/metabolism
    Print ISSN: 0036-8075
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  • 3
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    Crystal structure of the nucleotide exchange factor GrpE bound to the ATPase domain of the molecular chaperone DnaK (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-04-18
    Description: 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〉
    Keywords: 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
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Amidation of bioactive peptides: the structure of peptidylglycine alpha-hydroxylating monooxygenase (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-11-21
    Description: 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〉
    Keywords: 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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  • 5
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    Precursor-directed biosynthesis of erythromycin analogs by an engineered polyketide synthase (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-07-18
    Description: A genetic block was introduced in the first condensation step of the polyketide biosynthetic pathway that leads to the formation of 6-deoxyerythronolide B (6-dEB), the macrocyclic precursor of erythromycin. Exogenous addition of designed synthetic molecules to small-scale cultures of this null mutant resulted in highly selective multimilligram production of unnatural polyketides, including aromatic and ring-expanded variants of 6-dEB. Unexpected incorporation patterns were observed, illustrating the catalytic versatility of modular polyketide synthases. Further processing of some of these scaffolds by postpolyketide enzymes of the erythromycin pathway resulted in the generation of novel antibacterials with in vitro potency comparable to that of their natural counterparts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacobsen, J R -- Hutchinson, C R -- Cane, D E -- Khosla, C -- CA66736/CA/NCI NIH HHS/ -- GM22172/GM/NIGMS NIH HHS/ -- GM31925/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1997 Jul 18;277(5324):367-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical Engineering, Stanford University, Stanford, CA 94305-5025, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9219693" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Bacillus cereus/drug effects/growth & development ; Binding Sites ; Catalysis ; Cyclization ; Erythromycin/*analogs & derivatives/biosynthesis/pharmacology ; Microbial Sensitivity Tests ; Multienzyme Complexes/*genetics/*metabolism ; *Mutagenesis, Site-Directed ; Saccharopolyspora/genetics/metabolism ; Streptomyces/enzymology/genetics/*metabolism ; Transformation, Genetic
    Print ISSN: 0036-8075
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  • 6
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    Formation of actin stress fibers and focal adhesions enhanced by Rho-kinase (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-02-28
    Description: The small guanosine triphosphatase (GTPase) Rho is implicated in the formation of stress fibers and focal adhesions in fibroblasts stimulated by extracellular signals such as lysophosphatidic acid (LPA). Rho-kinase is activated by Rho and may mediate some biological effects of Rho. Microinjection of the catalytic domain of Rho-kinase into serum-starved Swiss 3T3 cells induced the formation of stress fibers and focal adhesions, whereas microinjection of the inactive catalytic domain, the Rho-binding domain, or the pleckstrin-homology domain inhibited the LPA-induced formation of stress fibers and focal adhesions. Thus, Rho-kinase appears to mediate signals from Rho and to induce the formation of stress fibers and focal adhesions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Amano, M -- Chihara, K -- Kimura, K -- Fukata, Y -- Nakamura, N -- Matsuura, Y -- Kaibuchi, K -- New York, N.Y. -- Science. 1997 Feb 28;275(5304):1308-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Signal Transduction, Nara Institute of Science and Technology, Ikoma 630-01, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9036856" target="_blank"〉PubMed〈/a〉
    Keywords: 3T3 Cells ; Actins/*metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Binding Sites ; *Cell Adhesion ; Cell Line ; DNA, Complementary/genetics ; Enzyme Inhibitors/pharmacology ; GTP Phosphohydrolases/metabolism ; Intracellular Signaling Peptides and Proteins ; Lysophospholipids/pharmacology ; Mice ; Mutation ; Protein-Serine-Threonine Kinases/antagonists & inhibitors/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Staurosporine/pharmacology ; rho-Associated Kinases
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  • 7
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    New lesion found in diseased brains (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-07-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roush, W -- New York, N.Y. -- Science. 1997 Jul 4;277(5322):31-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9229767" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/metabolism/*pathology ; Amyloid beta-Peptides/immunology ; Antibodies/immunology ; Binding Sites ; Brain/*pathology ; Brain Chemistry ; Humans ; Phosphates/metabolism ; tau Proteins/immunology/metabolism
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  • 8
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    Structural insights into the evolution of an antibody combining site (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-06-13
    Description: 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〉
    Keywords: 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
    Print ISSN: 0036-8075
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  • 9
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    Membrane and morphological changes in apoptotic cells regulated by caspase-mediated activation of PAK2 (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-06-06
    Description: Apoptosis of Jurkat T cells induced the caspase-mediated proteolytic cleavage of p21-activated kinase 2 (PAK2). Cleavage occurred between the amino-terminal regulatory domain and the carboxyl-terminal catalytic domain, which generated a constitutively active PAK2 fragment. Stable Jurkat cell lines that expressed a dominant-negative PAK mutant were resistant to the Fas-induced formation of apoptotic bodies, but had an enhanced externalization of phosphatidylserine at the cell surface. Thus, proteolytic activation of PAK2 represents a guanosine triphosphatase-independent mechanism of PAK regulation that allows PAK2 to regulate morphological changes that are seen in apoptotic cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rudel, T -- Bokoch, G M -- GM39434/GM/NIGMS NIH HHS/ -- HL48008/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1997 Jun 6;276(5318):1571-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, 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/9171063" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Chloromethyl Ketones/pharmacology ; *Apoptosis ; Binding Sites ; Caspase 3 ; *Caspases ; Cell Membrane/*metabolism ; Cysteine Endopeptidases/*metabolism ; Cysteine Proteinase Inhibitors/pharmacology ; Enzyme Activation ; Fas Ligand Protein ; Humans ; Jurkat Cells ; Membrane Glycoproteins/metabolism ; Phosphatidylserines/metabolism ; Protein-Serine-Threonine Kinases/*metabolism ; Recombinant Proteins/metabolism ; T-Lymphocytes/*cytology/enzymology ; p21-Activated Kinases
    Print ISSN: 0036-8075
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  • 10
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    Telomerase catalytic subunit homologs from fission yeast and human (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-08-15
    Description: Catalytic protein subunits of telomerase from the ciliate Euplotes aediculatus and the yeast Saccharomyces cerevisiae contain reverse transcriptase motifs. Here the homologous genes from the fission yeast Schizosaccharomyces pombe and human are identified. Disruption of the S. pombe gene resulted in telomere shortening and senescence, and expression of mRNA from the human gene correlated with telomerase activity in cell lines. Sequence comparisons placed the telomerase proteins in the reverse transcriptase family but revealed hallmarks that distinguish them from retroviral and retrotransposon relatives. Thus, the proposed telomerase catalytic subunits are phylogenetically conserved and represent a deep branch in the evolution of reverse transcriptases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakamura, T M -- Morin, G B -- Chapman, K B -- Weinrich, S L -- Andrews, W H -- Lingner, J -- Harley, C B -- Cech, T R -- GM28039/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Aug 15;277(5328):955-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9252327" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Catalysis ; Cell Line ; DNA-Binding Proteins ; Evolution, Molecular ; Genes, Fungal ; Humans ; Introns ; Molecular Sequence Data ; Phylogeny ; Proteins/*chemistry/genetics/metabolism ; *Rna ; RNA, Messenger/genetics/metabolism ; RNA-Directed DNA Polymerase/chemistry ; Retroelements ; Schizosaccharomyces/*enzymology/genetics/growth & development ; Schizosaccharomyces pombe Proteins ; Sequence Alignment ; Telomerase/*chemistry/genetics/metabolism ; Telomere/metabolism
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  • 11
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    Cells count proteins to keep their telomeres in line (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barinaga, M -- New York, N.Y. -- Science. 1997 Feb 14;275(5302):928.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9053995" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chromosomes, Fungal/metabolism ; DNA, Fungal/metabolism ; DNA-Binding Proteins/metabolism ; Fungal Proteins/*metabolism ; GTP-Binding Proteins/*metabolism ; Repressor Proteins/metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; *Saccharomyces cerevisiae Proteins ; Telomerase/*metabolism ; Telomere/*metabolism ; *Telomere-Binding Proteins ; rap GTP-Binding Proteins
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  • 12
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    Crystal structure of human BPI and two bound phospholipids at 2.4 angstrom resolution (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-06-20
    Description: 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〉
    Keywords: 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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  • 13
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    Creating isoprenoid diversity (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-11-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sacchettini, J C -- Poulter, C D -- New York, N.Y. -- Science. 1997 Sep 19;277(5333):1788-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Texas A & M University, College Station, TX 77843-2128, USA. sacchett@seabass.tamu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9324768" target="_blank"〉PubMed〈/a〉
    Keywords: *Alkyl and Aryl Transferases ; Binding Sites ; Carotenoids/biosynthesis ; Catalysis ; Cyclization ; Geranyltranstransferase ; *Intramolecular Lyases ; *Intramolecular Transferases ; Isomerases/*chemistry/metabolism ; Protein Folding ; Sterols/biosynthesis ; Terpenes/*metabolism ; Transferases/chemistry/metabolism
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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 cytochrome bc1 complex from bovine heart mitochondria (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-07-04
    Description: 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〉
    Keywords: 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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  • 15
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    Receptor and betagamma binding sites in the alpha subunit of the retinal G protein transducin (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-01-17
    Description: Transmembrane receptors for hormones, neurotransmitters, light, and odorants mediate their cellular effects by activating heterotrimeric guanine nucleotide-binding proteins (G proteins). Crystal structures have revealed contact surfaces between G protein subunits, but not the surfaces or molecular mechanism through which Galphabetagamma responds to activation by transmembrane receptors. Such a surface was identified from the results of testing 100 mutant alpha subunits of the retinal G protein transducin for their ability to interact with rhodopsin. Sites at which alanine substitutions impaired this interaction mapped to two distinct Galpha surfaces: a betagamma-binding surface and a putative receptor-interacting surface. On the basis of these results a mechanism for receptor-catalyzed exchange of guanosine diphosphate for guanosine triphosphate is proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Onrust, R -- Herzmark, P -- Chi, P -- Garcia, P D -- Lichtarge, O -- Kingsley, C -- Bourne, H R -- CA-54427/CA/NCI NIH HHS/ -- GM-27800/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Jan 17;275(5298):381-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143-0450, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8994033" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum Compounds/pharmacology ; Animals ; Binding Sites ; COS Cells ; Fluorides/pharmacology ; Guanosine 5'-O-(3-Thiotriphosphate)/metabolism ; Guanosine Diphosphate/metabolism ; Models, Molecular ; Mutation ; Phenotype ; *Protein Conformation ; Retinaldehyde/pharmacology ; Rhodopsin/*metabolism/pharmacology ; Rod Cell Outer Segment/metabolism ; Transducin/*chemistry/metabolism
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  • 16
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    Crystal structure of mouse CD1: An MHC-like fold with a large hydrophobic binding groove (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-07-18
    Description: 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〉
    Keywords: 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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  • 17
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    Identification of a naturally occurring peroxidase-lipoxygenase fusion protein (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-09-26
    Description: A distant relative of catalase that is specialized for metabolism of a fatty acid hydroperoxide was identified. This heme peroxidase occurs in coral as part of a fusion protein, the other component of which is a lipoxygenase that forms the hydroperoxide substrate. The end product is an unstable epoxide (an allene oxide) that is a potential precursor of prostaglandin-like molecules. These results extend the known chemistry of catalase-like proteins and reveal a distinct type of enzymatic construct involved in the metabolism of polyunsaturated fatty acids.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koljak, R -- Boutaud, O -- Shieh, B H -- Samel, N -- Brash, A R -- GM49502/GM/NIGMS NIH HHS/ -- TW00404/TW/FIC NIH HHS/ -- New York, N.Y. -- Science. 1997 Sep 26;277(5334):1994-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232-6602, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9302294" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Arachidonic Acid/metabolism ; Binding Sites ; Catalase/chemistry ; Catalysis ; Cloning, Molecular ; Cnidaria/*enzymology/genetics ; Hydrogen Peroxide/metabolism ; *Intramolecular Oxidoreductases ; Isomerases/chemistry ; Lipoxygenase/*chemistry/genetics/isolation & purification/metabolism ; Molecular Sequence Data ; Peroxidase/*chemistry/genetics/isolation & purification/metabolism ; Peroxidases/*chemistry/isolation & purification/metabolism ; Recombinant Proteins/metabolism ; Sequence Homology, Amino Acid
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  • 18
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    Toroidal structure of lambda-exonuclease (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-09-20
    Description: 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〉
    Keywords: 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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  • 19
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    Crystal structure of protein farnesyltransferase at 2.25 angstrom resolution (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-03-21
    Description: 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〉
    Keywords: *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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  • 20
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    The telomerase picture fills in (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-04-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barinaga, M -- New York, N.Y. -- Science. 1997 Apr 25;276(5312):528-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9148410" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Catalysis ; DNA-Binding Proteins ; Euplotes/enzymology ; Fungal Proteins/*chemistry/genetics/isolation & purification/metabolism ; Genes, Fungal ; *Rna ; RNA-Directed DNA Polymerase/*chemistry/genetics/isolation & ; purification/metabolism ; Saccharomyces cerevisiae/enzymology/genetics ; Telomerase/*chemistry/genetics/isolation & purification/metabolism
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  • 21
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    The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-07-18
    Description: 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〉
    Keywords: 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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  • 22
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    How thiamine diphosphate is activated in enzymes (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-01-03
    Description: The controversial question of how thiamine diphosphate, the biologically active form of vitamin B1, is activated in different enzymes has been addressed. Activation of the coenzyme was studied by measuring thermodynamics and kinetics of deprotonation at the carbon in the 2-position (C2) of thiamine diphosphate in the enzymes pyruvate decarboxylase and transketolase by use of nuclear magnetic resonance spectroscopy, proton/deuterium exchange, coenzyme analogs, and site-specific mutant enzymes. Interaction of a glutamate with the nitrogen in the 1'-position in the pyrimidine ring activated the 4'-amino group to act as an efficient proton acceptor for the C2 proton. The protein component accelerated the deprotonation of the C2 atom by several orders of magnitude, beyond the rate of the overall enzyme reaction. Therefore, the earlier proposed concerted mechanism or stabilization of a C2 carbanion can be excluded.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kern, D -- Kern, G -- Neef, H -- Tittmann, K -- Killenberg-Jabs, M -- Wikner, C -- Schneider, G -- Hubner, G -- New York, N.Y. -- Science. 1997 Jan 3;275(5296):67-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Biochemie, Martin-Luther Universitat Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8974393" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Binding Sites ; Catalysis ; Deuterium/metabolism ; Enzyme Activation ; Glutamic Acid/metabolism ; Hydrogen-Ion Concentration ; Kinetics ; Magnetic Resonance Spectroscopy ; Mutagenesis, Site-Directed ; Protons ; Pyruvate Decarboxylase/chemistry/*metabolism ; Pyruvates/metabolism ; Thermodynamics ; Thiamine Pyrophosphate/chemistry/*metabolism ; Transketolase/chemistry/*metabolism
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  • 23
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    Direct measurement of a tethered ligand-receptor interaction potential (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-02-07
    Description: Many biological recognition interactions involve ligands and receptors that are tethered rather than rigidly bound on a cell surface. A surface forces apparatus was used to directly measure the force-distance interaction between a polymer-tethered ligand and its receptor. At separations near the fully extended tether length, the ligands rapidly lock onto their binding sites, pulling the ligand and receptor together. The measured interaction potential and its dynamics can be modeled with standard theories of polymer and colloidal interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wong, J Y -- Kuhl, T L -- Israelachvili, J N -- Mullah, N -- Zalipsky, S -- GM 47334/GM/NIGMS NIH HHS/ -- GM17876/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Feb 7;275(5301):820-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA. jywong@engineering.ucsb.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9012346" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/*metabolism ; Binding Sites ; Biotin/chemistry/*metabolism ; Chemistry, Physical ; Ligands ; Lipid Bilayers ; Mathematics ; Models, Chemical ; Molecular Conformation ; Physicochemical Phenomena ; Polyethylene Glycols/chemistry/*metabolism ; Streptavidin
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  • 24
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    Solution structure of 3-oxo-delta5-steroid isomerase (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-04-18
    Description: The three-dimensional structure of the enzyme 3-oxo-delta5-steroid isomerase (E.C. 5.3.3.1), a 28-kilodalton symmetrical dimer, was solved by multidimensional heteronuclear magnetic resonance spectroscopy. The two independently folded monomers pack together by means of extensive hydrophobic and electrostatic interactions. Each monomer comprises three alpha helices and a six-strand mixed beta-pleated sheet arranged to form a deep hydrophobic cavity. Catalytically important residues Tyr14 (general acid) and Asp38 (general base) are located near the bottom of the cavity and positioned as expected from mechanistic hypotheses. An unexpected acid group (Asp99) is also located in the active site adjacent to Tyr14, and kinetic and binding studies of the Asp99 to Ala mutant demonstrate that Asp99 contributes to catalysis by stabilizing the intermediate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Z R -- Ebrahimian, S -- Zawrotny, M E -- Thornburg, L D -- Perez-Alvarado, G C -- Brothers, P -- Pollack, R M -- Summers, M F -- GM38155/GM/NIGMS NIH HHS/ -- GM49082/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Apr 18;276(5311):415-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9103200" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Androstenedione/metabolism ; Binding Sites ; Dimerization ; Estradiol/metabolism ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; *Protein Conformation ; Protein Structure, Secondary ; Solutions ; Steroid Isomerases/*chemistry/genetics/metabolism
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  • 25
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    Src structure crystallizes 20 years of oncogene research (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-02-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Featherstone, C -- New York, N.Y. -- Science. 1997 Feb 21;275(5303):1066.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9054006" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Models, Molecular ; Phosphorylation ; *Protein Conformation ; Protein Structure, Secondary ; Protein-Tyrosine Kinases/chemistry ; Proto-Oncogene Proteins/chemistry ; Proto-Oncogene Proteins c-hck ; Proto-Oncogene Proteins pp60(c-src)/*chemistry/metabolism ; Tyrosine/chemistry/metabolism ; *src Homology Domains
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  • 26
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    Researchers seek new weapon against the flu (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-02-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 1997 Feb 7;275(5301):756-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9036534" target="_blank"〉PubMed〈/a〉
    Keywords: Administration, Oral ; Amines/chemistry/metabolism/*therapeutic use ; Animals ; Antiviral Agents/chemistry/metabolism/*therapeutic use ; Binding Sites ; Clinical Trials as Topic ; Drug Design ; Drug Evaluation, Preclinical ; Humans ; Influenza, Human/*drug therapy ; Membrane Proteins/*genetics/physiology ; Molecular Structure ; Neuraminidase/*antagonists & inhibitors/chemistry/metabolism ; Orthomyxoviridae/*drug effects/enzymology ; Oseltamivir ; *Plant Proteins ; Protein Conformation
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  • 27
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    An Fe2IVO2 diamond core structure for the key intermediate Q of methane monooxygenase (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-01-24
    Description: A new paradigm for oxygen activation is required for enzymes such as methane monooxygenase (MMO), for which catalysis depends on a nonheme diiron center instead of the more familiar Fe-porphyrin cofactor. On the basis of precedents from synthetic diiron complexes, a high-valent Fe2(micro-O)2 diamond core has been proposed as the key oxidizing species for MMO and other nonheme diiron enzymes such as ribonucleotide reductase and fatty acid desaturase. The presence of a single short Fe-O bond (1.77 angstroms) per Fe atom and an Fe-Fe distance of 2.46 angstroms in MMO reaction intermediate Q, obtained from extended x-ray absorption fine structure and Mossbauer analysis, provides spectroscopic evidence that the diiron center in Q has an Fe2IVO2 diamond core.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shu, L -- Nesheim, J C -- Kauffmann, K -- Munck, E -- Lipscomb, J D -- Que, L Jr -- GM-08277/GM/NIGMS NIH HHS/ -- GM-22701/GM/NIGMS NIH HHS/ -- GM-40466/GM/NIGMS NIH HHS/ -- R01 GM040466/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1997 Jan 24;275(5299):515-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8999792" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Crystallography, X-Ray ; Dimerization ; Gram-Negative Aerobic Bacteria/*enzymology ; Iron/*chemistry ; Molecular Structure ; Oxidation-Reduction ; Oxygen/*chemistry ; Oxygenases/*chemistry/metabolism ; Spectroscopy, Mossbauer ; Spectrum Analysis
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  • 28
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    Modulation of hepatic gene expression by hepatocyte nuclear factor 1 (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-07-04
    Description: Hepatocyte nuclear factors 1 and 4 (HNF-1 and HNF-4) are liver-enriched transcription factors that function in the regulation of several liver-specific genes. HNF-1 activates genes containing promoters with HNF-1 binding sites. However, this factor negatively regulates its own expression and that of other HNF-4-dependent genes that lack HNF-1 binding sites in their promoter region. This repression is exerted by a direct interaction of HNF-1 with AF2, the main activation domain of HNF-4. The dual functions of gene activation and repression suggest that HNF-1 is a global regulator of the transcriptional network involved in the maintenance of hepatocyte-specific phenotype.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ktistaki, E -- Talianidis, I -- New York, N.Y. -- Science. 1997 Jul 4;277(5322):109-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Post Office Box 1527, 711 10 Heraklion, Crete, Greece.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9204893" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; Binding Sites ; COS Cells ; *DNA-Binding Proteins ; *Gene Expression Regulation ; Hepatocyte Nuclear Factor 1 ; Hepatocyte Nuclear Factor 1-alpha ; Hepatocyte Nuclear Factor 1-beta ; Hepatocyte Nuclear Factor 4 ; Humans ; Liver/cytology/*metabolism ; Nuclear Proteins/genetics/metabolism ; Phosphoproteins/genetics/metabolism ; Promoter Regions, Genetic ; RNA, Messenger/genetics/metabolism ; Recombinant Fusion Proteins/metabolism ; Transcription Factors/*genetics/*metabolism ; Transcriptional Activation ; Tumor Cells, Cultured
    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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  • 29
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    A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-03-12
    Description: Disruption of the circadian clock exacerbates metabolic diseases, including obesity and diabetes. We show that histone deacetylase 3 (HDAC3) recruitment to the genome displays a circadian rhythm in mouse liver. Histone acetylation is inversely related to HDAC3 binding, and this rhythm is lost when HDAC3 is absent. Although amounts of HDAC3 are constant, its genomic recruitment in liver corresponds to the expression pattern of the circadian nuclear receptor Rev-erbalpha. Rev-erbalpha colocalizes with HDAC3 near genes regulating lipid metabolism, and deletion of HDAC3 or Rev-erbalpha in mouse liver causes hepatic steatosis. Thus, genomic recruitment of HDAC3 by Rev-erbalpha directs a circadian rhythm of histone acetylation and gene expression required for normal hepatic lipid homeostasis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389392/" 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/PMC3389392/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feng, Dan -- Liu, Tao -- Sun, Zheng -- Bugge, Anne -- Mullican, Shannon E -- Alenghat, Theresa -- Liu, X Shirley -- Lazar, Mitchell A -- DK19525/DK/NIDDK NIH HHS/ -- DK43806/DK/NIDDK NIH HHS/ -- DK45586/DK/NIDDK NIH HHS/ -- DK49210/DK/NIDDK NIH HHS/ -- HG4069/HG/NHGRI NIH HHS/ -- P30 DK019525/DK/NIDDK NIH HHS/ -- R01 DK045586/DK/NIDDK NIH HHS/ -- R37 DK043806/DK/NIDDK NIH HHS/ -- R37 DK043806-20/DK/NIDDK NIH HHS/ -- RC1 DK086239/DK/NIDDK NIH HHS/ -- RC1DK08623/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2011 Mar 11;331(6022):1315-9. doi: 10.1126/science.1198125.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, 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/21393543" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Chromatin Immunoprecipitation ; Chronobiology Disorders/genetics/metabolism ; *Circadian Clocks ; *Circadian Rhythm ; DNA/metabolism ; Epigenesis, Genetic ; Fatty Liver/*metabolism ; Gene Expression Regulation ; *Genome ; Histone Deacetylases/*metabolism ; Histones/metabolism ; Homeostasis ; *Lipid Metabolism ; Lipogenesis/genetics ; Liver/*metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Molecular Sequence Data ; Nuclear Receptor Co-Repressor 1/metabolism ; Nuclear Receptor Subfamily 1, Group D, Member 1/genetics/metabolism ; RNA Polymerase II/metabolism ; Up-Regulation
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    Computational design of proteins targeting the conserved stem region of influenza hemagglutinin (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-14
    Description: We describe a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions between disembodied amino acid residues and the target surface are identified and used to anchor de novo designed interfaces. The method was used to design proteins that bind a conserved surface patch on the stem of the influenza hemagglutinin (HA) from the 1918 H1N1 pandemic virus. After affinity maturation, two of the designed proteins, HB36 and HB80, bind H1 and H5 HAs with low nanomolar affinity. Further, HB80 inhibits the HA fusogenic conformational changes induced at low pH. The crystal structure of HB36 in complex with 1918/H1 HA revealed that the actual binding interface is nearly identical to that in the computational design model. Such designed binding proteins may be useful for both diagnostics and therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164876/" 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/PMC3164876/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fleishman, Sarel J -- Whitehead, Timothy A -- Ekiert, Damian C -- Dreyfus, Cyrille -- Corn, Jacob E -- Strauch, Eva-Maria -- Wilson, Ian A -- Baker, David -- AI057141/AI/NIAID NIH HHS/ -- AI058113/AI/NIAID NIH HHS/ -- GM080209/GM/NIGMS NIH HHS/ -- P01 AI058113/AI/NIAID NIH HHS/ -- P01 AI058113-07/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 May 13;332(6031):816-21. doi: 10.1126/science.1202617.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21566186" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Binding Sites ; Computational Biology ; *Computer Simulation ; Hemagglutinin Glycoproteins, Influenza Virus/chemistry/*metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; *Models, Molecular ; Molecular Sequence Data ; Mutation ; Peptide Library ; Protein Binding ; Protein Conformation ; *Protein Engineering ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Proteins/*chemistry/genetics/*metabolism ; Software
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    Crystal structure of the dynein motor domain (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-02-19
    Description: Dyneins are microtubule-based motor proteins that power ciliary beating, transport intracellular cargos, and help to construct the mitotic spindle. Evolved from ring-shaped hexameric AAA-family adenosine triphosphatases (ATPases), dynein's large size and complexity have posed challenges for understanding its structure and mechanism. Here, we present a 6 angstrom crystal structure of a functional dimer of two ~300-kilodalton motor domains of yeast cytoplasmic dynein. The structure reveals an unusual asymmetric arrangement of ATPase domains in the ring-shaped motor domain, the manner in which the mechanical element interacts with the ATPase ring, and an unexpected interaction between two coiled coils that create a base for the microtubule binding domain. The arrangement of these elements provides clues as to how adenosine triphosphate-driven conformational changes might be transmitted across the motor domain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169322/" 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/PMC3169322/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, Andrew P -- Cho, Carol -- Jin, Lan -- Vale, Ronald D -- MC_UP_A025_1011/Medical Research Council/United Kingdom -- R01 GM097312/GM/NIGMS NIH HHS/ -- R01 GM097312-01/GM/NIGMS NIH HHS/ -- R01 GM097312-02/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Mar 4;331(6021):1159-65. doi: 10.1126/science.1202393. Epub 2011 Feb 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California-San Francisco, 600 16th Street, San Francisco, CA 94158, USA. cartera@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21330489" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Allosteric Regulation ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Cytoplasmic Dyneins/*chemistry/*metabolism ; Methionine/chemistry ; Microtubules/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry ; Saccharomyces cerevisiae Proteins/*chemistry/*metabolism
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    A cell cycle phosphoproteome of the yeast centrosome (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-06-28
    Description: Centrosomes organize the bipolar mitotic spindle, and centrosomal defects cause chromosome instability. Protein phosphorylation modulates centrosome function, and we provide a comprehensive map of phosphorylation on intact yeast centrosomes (18 proteins). Mass spectrometry was used to identify 297 phosphorylation sites on centrosomes from different cell cycle stages. We observed different modes of phosphoregulation via specific protein kinases, phosphorylation site clustering, and conserved phosphorylated residues. Mutating all eight cyclin-dependent kinase (Cdk)-directed sites within the core component, Spc42, resulted in lethality and reduced centrosomal assembly. Alternatively, mutation of one conserved Cdk site within gamma-tubulin (Tub4-S360D) caused mitotic delay and aberrant anaphase spindle elongation. Our work establishes the extent and complexity of this prominent posttranslational modification in centrosome biology and provides specific examples of phosphorylation control in centrosome function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825980/" 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/PMC3825980/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keck, Jamie M -- Jones, Michele H -- Wong, Catherine C L -- Binkley, Jonathan -- Chen, Daici -- Jaspersen, Sue L -- Holinger, Eric P -- Xu, Tao -- Niepel, Mario -- Rout, Michael P -- Vogel, Jackie -- Sidow, Arend -- Yates, John R 3rd -- Winey, Mark -- F32 GM086038/GM/NIGMS NIH HHS/ -- GM51312/GM/NIGMS NIH HHS/ -- MOP-64404/Canadian Institutes of Health Research/Canada -- P41 RR011823/RR/NCRR NIH HHS/ -- R01 GM051312/GM/NIGMS NIH HHS/ -- R01 GM051312-16/GM/NIGMS NIH HHS/ -- R01 GM051312-16S1/GM/NIGMS NIH HHS/ -- R01 GM062427/GM/NIGMS NIH HHS/ -- R01 HG003039/HG/NHGRI NIH HHS/ -- T32 GM008759/GM/NIGMS NIH HHS/ -- U54 RR022220/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2011 Jun 24;332(6037):1557-61. doi: 10.1126/science.1205193.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21700874" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; CDC2 Protein Kinase/metabolism ; *Cell Cycle ; Centrosome/*metabolism/ultrastructure ; Cytoskeletal Proteins/genetics/metabolism ; Fungal Proteins/chemistry/metabolism ; Fungi/metabolism ; G1 Phase ; Mitosis ; Mutation ; Phosphoproteins/genetics/metabolism ; Phosphorylation ; Protein Processing, Post-Translational ; Proteome/*metabolism ; Saccharomyces cerevisiae/cytology/genetics/growth & development/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Spindle Apparatus/metabolism/ultrastructure ; Tubulin/chemistry/metabolism
    Print ISSN: 0036-8075
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    Cardiac myosin activation: a potential therapeutic approach for systolic heart failure (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-03-19
    Description: Decreased cardiac contractility is a central feature of systolic heart failure. Existing drugs increase cardiac contractility indirectly through signaling cascades but are limited by their mechanism-related adverse effects. To avoid these limitations, we previously developed omecamtiv mecarbil, a small-molecule, direct activator of cardiac myosin. Here, we show that it binds to the myosin catalytic domain and operates by an allosteric mechanism to increase the transition rate of myosin into the strongly actin-bound force-generating state. Paradoxically, it inhibits adenosine 5'-triphosphate turnover in the absence of actin, which suggests that it stabilizes an actin-bound conformation of myosin. In animal models, omecamtiv mecarbil increases cardiac function by increasing the duration of ejection without changing the rates of contraction. Cardiac myosin activation may provide a new therapeutic approach for systolic heart failure.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090309/" 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/PMC4090309/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Malik, Fady I -- Hartman, James J -- Elias, Kathleen A -- Morgan, Bradley P -- Rodriguez, Hector -- Brejc, Katjusa -- Anderson, Robert L -- Sueoka, Sandra H -- Lee, Kenneth H -- Finer, Jeffrey T -- Sakowicz, Roman -- Baliga, Ramesh -- Cox, David R -- Garard, Marc -- Godinez, Guillermo -- Kawas, Raja -- Kraynack, Erica -- Lenzi, David -- Lu, Pu Ping -- Muci, Alexander -- Niu, Congrong -- Qian, Xiangping -- Pierce, Daniel W -- Pokrovskii, Maria -- Suehiro, Ion -- Sylvester, Sheila -- Tochimoto, Todd -- Valdez, Corey -- Wang, Wenyue -- Katori, Tatsuo -- Kass, David A -- Shen, You-Tang -- Vatner, Stephen F -- Morgans, David J -- 1-R43-HL-66647-1/HL/NHLBI NIH HHS/ -- R01 HL106511/HL/NHLBI NIH HHS/ -- R43 HL066647/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2011 Mar 18;331(6023):1439-43. doi: 10.1126/science.1200113.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Preclinical Research and Development, Cytokinetics, Inc., South San Francisco, CA 94080, USA. fmalik@cytokinetics.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21415352" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/metabolism ; Actins/metabolism ; Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Adrenergic beta-Agonists/pharmacology ; Allosteric Regulation ; Animals ; Binding Sites ; Calcium/metabolism ; Cardiac Myosins/chemistry/*metabolism ; Cardiac Output/drug effects ; Dogs ; Female ; Heart Failure, Systolic/*drug therapy/physiopathology ; Isoproterenol/pharmacology ; Male ; Myocardial Contraction/*drug effects ; Myocytes, Cardiac/*drug effects/physiology ; Phosphates/metabolism ; Protein Binding ; Protein Conformation ; Protein Isoforms/chemistry/metabolism ; Rats ; Rats, Sprague-Dawley ; Urea/*analogs & derivatives/chemistry/metabolism/pharmacology ; Ventricular Function, Left/drug effects
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    Proteoglycan-specific molecular switch for RPTPsigma clustering and neuronal extension (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-04-02
    Description: Heparan and chondroitin sulfate proteoglycans (HSPGs and CSPGs, respectively) regulate numerous cell surface signaling events, with typically opposite effects on cell function. CSPGs inhibit nerve regeneration through receptor protein tyrosine phosphatase sigma (RPTPsigma). Here we report that RPTPsigma acts bimodally in sensory neuron extension, mediating CSPG inhibition and HSPG growth promotion. Crystallographic analyses of a shared HSPG-CSPG binding site reveal a conformational plasticity that can accommodate diverse glycosaminoglycans with comparable affinities. Heparan sulfate and analogs induced RPTPsigma ectodomain oligomerization in solution, which was inhibited by chondroitin sulfate. RPTPsigma and HSPGs colocalize in puncta on sensory neurons in culture, whereas CSPGs occupy the extracellular matrix. These results lead to a model where proteoglycans can exert opposing effects on neuronal extension by competing to control the oligomerization of a common receptor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154093/" 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/PMC3154093/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coles, Charlotte H -- Shen, Yingjie -- Tenney, Alan P -- Siebold, Christian -- Sutton, Geoffrey C -- Lu, Weixian -- Gallagher, John T -- Jones, E Yvonne -- Flanagan, John G -- Aricescu, A Radu -- 090532/Wellcome Trust/United Kingdom -- 10976/Cancer Research UK/United Kingdom -- EY11559/EY/NEI NIH HHS/ -- G0700232/Medical Research Council/United Kingdom -- G0900084/Medical Research Council/United Kingdom -- HD29417/HD/NICHD NIH HHS/ -- R01 EY011559/EY/NEI NIH HHS/ -- R01 EY011559-19/EY/NEI NIH HHS/ -- R37 HD029417/HD/NICHD NIH HHS/ -- R37 HD029417-20/HD/NICHD NIH HHS/ -- Cancer Research UK/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2011 Apr 22;332(6028):484-8. doi: 10.1126/science.1200840. Epub 2011 Mar 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21454754" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Axons/*physiology ; Binding Sites ; Cell Membrane/metabolism ; Cells, Cultured ; Chondroitin Sulfate Proteoglycans/chemistry/*metabolism ; Chondroitin Sulfates/chemistry/metabolism ; Crystallography, X-Ray ; Extracellular Matrix ; Ganglia, Spinal ; Glypicans/metabolism ; Growth Cones/metabolism ; Heparan Sulfate Proteoglycans/chemistry/*metabolism ; Heparitin Sulfate/analogs & derivatives/chemistry/metabolism ; Humans ; Mice ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Neurites/physiology ; Neurocan/metabolism ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; Receptor-Like Protein Tyrosine Phosphatases, Class 2/*chemistry/*metabolism ; Sensory Receptor Cells/*physiology
    Print ISSN: 0036-8075
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    The structure of the kinesin-1 motor-tail complex reveals the mechanism of autoinhibition (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-13
    Description: When not transporting cargo, kinesin-1 is autoinhibited by binding of a tail region to the motor domains, but the mechanism of inhibition is unclear. We report the crystal structure of a motor domain dimer in complex with its tail domain at 2.2 angstroms and compare it with a structure of the motor domain alone at 2.7 angstroms. These structures indicate that neither an induced conformational change nor steric blocking is the cause of inhibition. Instead, the tail cross-links the motor domains at a second position, in addition to the coiled coil. This "double lockdown," by cross-linking at two positions, prevents the movement of the motor domains that is needed to undock the neck linker and release adenosine diphosphate. This autoinhibition mechanism could extend to some other kinesins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339660/" 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/PMC3339660/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaan, Hung Yi Kristal -- Hackney, David D -- Kozielski, Frank -- NS058848/NS/NINDS NIH HHS/ -- R01 NS058848/NS/NINDS NIH HHS/ -- R01 NS058848-01A2/NS/NINDS NIH HHS/ -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2011 Aug 12;333(6044):883-5. doi: 10.1126/science.1204824.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21836017" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Drosophila Proteins/*antagonists & inhibitors/*chemistry/metabolism ; Hydrogen Bonding ; Kinesin/*antagonists & inhibitors/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary
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    Cartilage acidic protein-1B (LOTUS), an endogenous Nogo receptor antagonist for axon tract formation (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-06
    Description: Neural circuitry formation depends on the molecular control of axonal projection during development. By screening with fluorophore-assisted light inactivation in the developing mouse brain, we identified cartilage acidic protein-1B as a key molecule for lateral olfactory tract (LOT) formation and named it LOT usher substance (LOTUS). We further identified Nogo receptor-1 (NgR1) as a LOTUS-binding protein. NgR1 is a receptor of myelin-derived axon growth inhibitors, such as Nogo, which prevent neural regeneration in the adult. LOTUS suppressed Nogo-NgR1 binding and Nogo-induced growth cone collapse. A defasciculated LOT was present in lotus-deficient mice but not in mice lacking both lotus- and ngr1. These findings suggest that endogenous antagonism of NgR1 by LOTUS is crucial for normal LOT formation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244695/" 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/PMC3244695/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sato, Yasufumi -- Iketani, Masumi -- Kurihara, Yuji -- Yamaguchi, Megumi -- Yamashita, Naoya -- Nakamura, Fumio -- Arie, Yuko -- Kawasaki, Takahiko -- Hirata, Tatsumi -- Abe, Takaya -- Kiyonari, Hiroshi -- Strittmatter, Stephen M -- Goshima, Yoshio -- Takei, Kohtaro -- R37 NS033020/NS/NINDS NIH HHS/ -- R37 NS033020-19/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2011 Aug 5;333(6043):769-73. doi: 10.1126/science.1204144.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Pharmacology and Neurobiology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21817055" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axons/*physiology ; Binding Sites ; Calcium-Binding Proteins/chemistry/genetics/*metabolism ; Cell Line ; Cells, Cultured ; GPI-Linked Proteins/genetics/metabolism ; Growth Cones/metabolism ; Humans ; Immunohistochemistry ; Ligands ; Mice ; Mice, Inbred ICR ; Myelin Proteins/genetics/*metabolism ; Olfactory Pathways/*cytology/*growth & development/metabolism ; Prosencephalon/embryology/metabolism ; Protein Binding ; Receptors, Cell Surface/genetics/*metabolism ; Signal Transduction
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    Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 A resolution (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-11-19
    Description: Gene silencing is essential for regulating cell fate in eukaryotes. Altered chromatin architectures contribute to maintaining the silenced state in a variety of species. The silent information regulator (Sir) proteins regulate mating type in Saccharomyces cerevisiae. One of these proteins, Sir3, interacts directly with the nucleosome to help generate silenced domains. We determined the crystal structure of a complex of the yeast Sir3 BAH (bromo-associated homology) domain and the nucleosome core particle at 3.0 angstrom resolution. We see multiple molecular interactions between the protein surfaces of the nucleosome and the BAH domain that explain numerous genetic mutations. These interactions are accompanied by structural rearrangements in both the nucleosome and the BAH domain. The structure explains how covalent modifications on H4K16 and H3K79 regulate formation of a silencing complex that contains the nucleosome as a central component.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098850/" 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/PMC4098850/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armache, Karim-Jean -- Garlick, Joseph D -- Canzio, Daniele -- Narlikar, Geeta J -- Kingston, Robert E -- GM043901/GM/NIGMS NIH HHS/ -- P41 RR012408/RR/NCRR NIH HHS/ -- R01 GM043901/GM/NIGMS NIH HHS/ -- R37 GM048405/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Nov 18;334(6058):977-82. doi: 10.1126/science.1210915.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22096199" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; *Gene Silencing ; Histones/*chemistry/metabolism ; Hydrogen Bonding ; Methylation ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Mutant Proteins/chemistry/metabolism ; Nucleosomes/*chemistry/metabolism/ultrastructure ; Physicochemical Processes ; Protein Folding ; *Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/chemistry/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; Silent Information Regulator Proteins, Saccharomyces ; cerevisiae/*chemistry/genetics/metabolism ; Static Electricity
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    Unfolded proteins are Ire1-activating ligands that directly induce the unfolded protein response (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-20
    Description: The unfolded protein response (UPR) detects the accumulation of unfolded proteins in the endoplasmic reticulum (ER) and adjusts the protein-folding capacity to the needs of the cell. Under conditions of ER stress, the transmembrane protein Ire1 oligomerizes to activate its cytoplasmic kinase and ribonuclease domains. It is unclear what feature of ER stress Ire1 detects. We found that the core ER-lumenal domain (cLD) of yeast Ire1 binds to unfolded proteins in yeast cells and to peptides primarily composed of basic and hydrophobic residues in vitro. Mutation of amino acid side chains exposed in a putative peptide-binding groove of Ire1 cLD impaired peptide binding. Peptide binding caused Ire1 cLD oligomerization in vitro, suggesting that direct binding to unfolded proteins activates the UPR.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202989/" 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/PMC3202989/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gardner, Brooke M -- Walter, Peter -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 30;333(6051):1891-4. doi: 10.1126/science.1209126. Epub 2011 Aug 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21852455" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cathepsin A/chemistry/metabolism ; Endoplasmic Reticulum/*metabolism ; Fluorescence Polarization ; Fungal Proteins/chemistry/metabolism ; Glutathione Transferase/metabolism ; HSP70 Heat-Shock Proteins/chemistry/metabolism ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Membrane Glycoproteins/*chemistry/*metabolism ; Mutant Proteins/chemistry/metabolism ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein-Serine-Threonine Kinases/*chemistry/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Stress, Physiological ; *Unfolded Protein Response
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    NMR detection of structures in the HIV-1 5'-leader RNA that regulate genome packaging (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-10-15
    Description: The 5'-leader of the HIV-1 genome regulates multiple functions during viral replication via mechanisms that have yet to be established. We developed a nuclear magnetic resonance approach that enabled direct detection of structural elements within the intact leader (712-nucleotide dimer) that are critical for genome packaging. Residues spanning the gag start codon (AUG) form a hairpin in the monomeric leader and base pair with residues of the unique-5' region (U5) in the dimer. U5:AUG formation promotes dimerization by displacing and exposing a dimer-promoting hairpin and enhances binding by the nucleocapsid (NC) protein, which is the cognate domain of the viral Gag polyprotein that directs packaging. Our findings support a packaging mechanism in which translation, dimerization, NC binding, and packaging are regulated by a common RNA structural switch.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3335204/" 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/PMC3335204/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Kun -- Heng, Xiao -- Garyu, Lianko -- Monti, Sarah -- Garcia, Eric L -- Kharytonchyk, Siarhei -- Dorjsuren, Bilguujin -- Kulandaivel, Gowry -- Jones, Simonne -- Hiremath, Atheeth -- Divakaruni, Sai Sachin -- LaCotti, Courtney -- Barton, Shawn -- Tummillo, Daniel -- Hosic, Azra -- Edme, Kedy -- Albrecht, Sara -- Telesnitsky, Alice -- Summers, Michael F -- 2T34 GM008663/GM/NIGMS NIH HHS/ -- R01 GM042561/GM/NIGMS NIH HHS/ -- R01 GM042561-21/GM/NIGMS NIH HHS/ -- R01 GM042561-22/GM/NIGMS NIH HHS/ -- R01 GM042561-23/GM/NIGMS NIH HHS/ -- R01 GM042561-24/GM/NIGMS NIH HHS/ -- R01 GM42561/GM/NIGMS NIH HHS/ -- R25 GM055036/GM/NIGMS NIH HHS/ -- R25 GM055036-14/GM/NIGMS NIH HHS/ -- R25 GM055036-15/GM/NIGMS NIH HHS/ -- R25 GM055036-16/GM/NIGMS NIH HHS/ -- R25 GM55036/GM/NIGMS NIH HHS/ -- T34 GM008663/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Oct 14;334(6053):242-5. doi: 10.1126/science.1210460.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21998393" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions ; Base Pairing ; Binding Sites ; Codon, Initiator ; Dimerization ; Genes, gag ; *Genome, Viral ; HIV-1/*genetics/*physiology ; Human Immunodeficiency Virus Proteins/metabolism ; Mutagenesis, Site-Directed ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Conformation ; Nucleocapsid Proteins/metabolism ; Protein Binding ; Protein Biosynthesis ; RNA, Viral/*chemistry/*genetics ; *Virus Assembly ; gag Gene Products, Human Immunodeficiency Virus/metabolism
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    AMPK is a direct adenylate charge-regulated protein kinase (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-06-18
    Description: The adenosine monophosphate (AMP)-activated protein kinase (AMPK) regulates whole-body and cellular energy balance in response to energy demand and supply. AMPK is an alphabetagamma heterotrimer activated by decreasing concentrations of adenosine triphosphate (ATP) and increasing AMP concentrations. AMPK activation depends on phosphorylation of the alpha catalytic subunit on threonine-172 (Thr(172)) by kinases LKB1 or CaMKKbeta, and this is promoted by AMP binding to the gamma subunit. AMP sustains activity by inhibiting dephosphorylation of alpha-Thr(172), whereas ATP promotes dephosphorylation. Adenosine diphosphate (ADP), like AMP, bound to gamma sites 1 and 3 and stimulated alpha-Thr(172) phosphorylation. However, in contrast to AMP, ADP did not directly activate phosphorylated AMPK. In this way, both ADP/ATP and AMP/ATP ratios contribute to AMPK regulation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oakhill, Jonathan S -- Steel, Rohan -- Chen, Zhi-Ping -- Scott, John W -- Ling, Naomi -- Tam, Shanna -- Kemp, Bruce E -- New York, N.Y. -- Science. 2011 Jun 17;332(6036):1433-5. doi: 10.1126/science.1200094.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Protein Chemistry and Metabolism, St. Vincent's Institute of Medical Research, University of Melbourne, 41 Victoria Parade, Fitzroy 3065, Victoria, Australia. joakhill@svi.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21680840" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases/chemistry/*metabolism ; Adenosine Diphosphate/*metabolism ; Adenosine Monophosphate/*metabolism ; Adenosine Triphosphate/*metabolism ; Animals ; Binding Sites ; COS Cells ; Calcium-Calmodulin-Dependent Protein Kinase Kinase/metabolism ; Cercopithecus aethiops ; Enzyme Activation ; Myristic Acid/metabolism ; Phosphorylation ; Protein Subunits/chemistry/metabolism ; Protein-Serine-Threonine Kinases/metabolism ; Recombinant Fusion Proteins/metabolism ; Threonine/metabolism
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    Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-07-19
    Description: Passive transfer of broadly neutralizing HIV antibodies can prevent infection, which suggests that vaccines that elicit such antibodies would be protective. Thus far, however, few broadly neutralizing HIV antibodies that occur naturally have been characterized. To determine whether these antibodies are part of a larger group of related molecules, we cloned 576 new HIV antibodies from four unrelated individuals. All four individuals produced expanded clones of potent broadly neutralizing CD4-binding-site antibodies that mimic binding to CD4. Despite extensive hypermutation, the new antibodies shared a consensus sequence of 68 immunoglobulin H (IgH) chain amino acids and arise independently from two related IgH genes. Comparison of the crystal structure of one of the antibodies to the broadly neutralizing antibody VRC01 revealed conservation of the contacts to the HIV spike.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351836/" 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/PMC3351836/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scheid, Johannes F -- Mouquet, Hugo -- Ueberheide, Beatrix -- Diskin, Ron -- Klein, Florian -- Oliveira, Thiago Y K -- Pietzsch, John -- Fenyo, David -- Abadir, Alexander -- Velinzon, Klara -- Hurley, Arlene -- Myung, Sunnie -- Boulad, Farid -- Poignard, Pascal -- Burton, Dennis R -- Pereyra, Florencia -- Ho, David D -- Walker, Bruce D -- Seaman, Michael S -- Bjorkman, Pamela J -- Chait, Brian T -- Nussenzweig, Michel C -- P01 AI081677/AI/NIAID NIH HHS/ -- P30 AI060354/AI/NIAID NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- RR00862/RR/NCRR NIH HHS/ -- RR022220/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1633-7. doi: 10.1126/science.1207227. Epub 2011 Jul 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764753" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Neutralizing/*chemistry/*immunology/metabolism ; Antibody Affinity ; Antibody Specificity ; Antigens, CD4/immunology/*metabolism ; Binding Sites ; Binding Sites, Antibody ; Cloning, Molecular ; Consensus Sequence ; Crystallography, X-Ray ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/*chemistry/*immunology/metabolism ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; Humans ; Immunoglobulin Fab Fragments/chemistry ; Immunoglobulin Heavy Chains/chemistry ; Immunoglobulin Light Chains/chemistry ; Molecular Mimicry ; Molecular Sequence Data ; Mutation ; Protein Conformation
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    The crystal structure of the signal recognition particle in complex with its receptor (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-02-19
    Description: Cotranslational targeting of membrane and secretory proteins is mediated by the universally conserved signal recognition particle (SRP). Together with its receptor (SR), SRP mediates the guanine triphosphate (GTP)-dependent delivery of translating ribosomes bearing signal sequences to translocons on the target membrane. Here, we present the crystal structure of the SRP:SR complex at 3.9 angstrom resolution and biochemical data revealing that the activated SRP:SR guanine triphosphatase (GTPase) complex binds the distal end of the SRP hairpin RNA where GTP hydrolysis is stimulated. Combined with previous findings, these results suggest that the SRP:SR GTPase complex initially assembles at the tetraloop end of the SRP RNA and then relocalizes to the opposite end of the RNA. This rearrangement provides a mechanism for coupling GTP hydrolysis to the handover of cargo to the translocon.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758919/" 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/PMC3758919/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ataide, Sandro F -- Schmitz, Nikolaus -- Shen, Kuang -- Ke, Ailong -- Shan, Shu-ou -- Doudna, Jennifer A -- Ban, Nenad -- GM078024/GM/NIGMS NIH HHS/ -- R01 GM078024/GM/NIGMS NIH HHS/ -- R01 GM086766/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Feb 18;331(6019):881-6. doi: 10.1126/science.1196473.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, Eidgenossische Technische Hochschule Zurich (ETH Zurich), Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21330537" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Base Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Enzyme Activation ; Escherichia coli/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; GTP Phosphohydrolases/chemistry/metabolism ; Guanosine Triphosphate/analogs & derivatives/chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Biological ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; Protein Transport ; RNA, Bacterial/*chemistry/metabolism ; Receptors, Cytoplasmic and Nuclear/*chemistry/metabolism ; Ribosomal Proteins/chemistry/metabolism ; Ribosomes/metabolism ; Signal Recognition Particle/*chemistry/metabolism
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    A crystal structure of the complex between human complement receptor 2 and its ligand C3d (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-04-30
    Description: The interaction of complement receptor 2 (CR2)--which is present on B cells and follicular dendritic cells--with its antigen-bound ligand C3d results in an enhanced antibody response, thus providing an important link between the innate and adaptive immune systems. Although a cocrystal structure of a complex between C3d and the ligand-binding domains of CR2 has been published, several aspects of this structure, including the position in C3d of the binding interface, remained controversial because of disagreement with biochemical data. We now report a cocrystal structure of a CR2(SCR1-2):C3d complex at 3.2 angstrom resolution in which the interaction interfaces differ markedly from the previously published structure and are consistent with the biochemical data. It is likely that, in the previous structure, the interaction was influenced by the presence of zinc acetate additive in the crystallization buffer, leading to a nonphysiological complex. Detailed knowledge of the binding interface now at hand gives the potential to exploit the interaction in vaccine design or in therapeutics directed against autoreactive B cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van den Elsen, Jean M H -- Isenman, David E -- New York, N.Y. -- Science. 2011 Apr 29;332(6029):608-11. doi: 10.1126/science.1201954.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK. bssjmhve@bath.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21527715" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Complement C3d/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Mutagenesis, Site-Directed ; Protein Binding ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Receptors, Complement 3d/*chemistry/genetics/metabolism ; Zinc Acetate
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 44
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    Crystal structure of the maltose transporter in a pretranslocation intermediate state (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-14
    Description: Adenosine triphosphate (ATP)-binding cassette (ABC) transporters convert chemical energy from ATP hydrolysis to mechanical work for substrate translocation. They function by alternating between two states, exposing the substrate-binding site to either side of the membrane. A key question that remains to be addressed is how substrates initiate the transport cycle. Using x-ray crystallography, we have captured the maltose transporter in an intermediate step between the inward- and outward-facing states. We show that interactions with substrate-loaded maltose-binding protein in the periplasm induce a partial closure of the MalK dimer in the cytoplasm. ATP binding to this conformation then promotes progression to the outward-facing state. These results, interpreted in light of biochemical and functional studies, provide a structural basis to understand allosteric communication in ABC transporters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oldham, Michael L -- Chen, Jue -- GM070515/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Jun 3;332(6034):1202-5. doi: 10.1126/science.1200767. Epub 2011 May 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, Howard Hughes Medical Institute, West Lafayette, IN 47907, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21566157" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Binding Sites ; Biological Transport, Active ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; Hydrogen Bonding ; Maltose/metabolism ; Maltose-Binding Proteins/chemistry/metabolism ; Models, Biological ; Models, Molecular ; Monosaccharide Transport Proteins/*chemistry/metabolism ; Periplasm/metabolism ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 45
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    A diiron protein autogenerates a valine-phenylalanine cross-link (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-21
    Description: All known internal covalent cross-links in proteins involve functionalized groups having oxygen, nitrogen, or sulfur atoms present to facilitate their formation. Here, we report a carbon-carbon cross-link between two unfunctionalized side chains. This valine-phenyalanine cross-link, produced in an oxygen-dependent reaction, is generated by its own carboxylate-bridged diiron center and serves to stabilize the metallocenter. This finding opens the door to new types of posttranslational modifications, and it demonstrates new catalytic potential of diiron centers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736988/" 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/PMC3736988/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cooley, Richard B -- Rhoads, Timothy W -- Arp, Daniel J -- Karplus, P Andrew -- ES00210/ES/NIEHS NIH HHS/ -- GM R01-083136/GM/NIGMS NIH HHS/ -- R01 GM083136/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 May 20;332(6032):929. doi: 10.1126/science.1205687.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, 2011 Agriculture and Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21596985" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Cyanophora/*chemistry/metabolism ; Iron/*chemistry ; Metalloproteins/*chemistry/metabolism ; Oxygen/chemistry ; Phenylalanine/*chemistry ; Plant Proteins/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Valine/*chemistry
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  • 46
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    How a DNA polymerase clamp loader opens a sliding clamp (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-12-24
    Description: Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of adenosine triphosphatases (ATPases). We present structures for the ATP-bound state of the clamp loader complex from bacteriophage T4, bound to an open clamp and primer-template DNA. The clamp loader traps a spiral conformation of the open clamp so that both the loader and the clamp match the helical symmetry of DNA. One structure reveals that ATP has been hydrolyzed in one subunit and suggests that clamp closure and ejection of the loader involves disruption of the ATP-dependent match in symmetry. The structures explain how synergy among the loader, the clamp, and DNA can trigger ATP hydrolysis and release of the closed clamp on DNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281585/" 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/PMC3281585/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelch, Brian A -- Makino, Debora L -- O'Donnell, Mike -- Kuriyan, John -- F32 GM087888/GM/NIGMS NIH HHS/ -- F32 GM087888-02/GM/NIGMS NIH HHS/ -- F32-087888/PHS HHS/ -- R01 GM038839/GM/NIGMS NIH HHS/ -- R01 GM038839-26/GM/NIGMS NIH HHS/ -- R01 GM045547/GM/NIGMS NIH HHS/ -- R01 GM045547-20/GM/NIGMS NIH HHS/ -- R01-GM308839/GM/NIGMS NIH HHS/ -- R01-GM45547/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Dec 23;334(6063):1675-80. doi: 10.1126/science.1211884.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22194570" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Bacteriophage T4 ; Binding Sites ; Crystallography, X-Ray ; DNA, A-Form/*chemistry/metabolism ; DNA, Viral/*chemistry/metabolism ; DNA-Directed DNA Polymerase/chemistry/*metabolism ; Hydrolysis ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Static Electricity ; Templates, Genetic ; Trans-Activators/*chemistry/metabolism ; Viral Proteins/*chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 47
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    Chromosome organization by a nucleoid-associated protein in live bacteria (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-10
    Description: Bacterial chromosomes are confined in submicrometer-sized nucleoids. Chromosome organization is facilitated by nucleoid-associated proteins (NAPs), but the mechanisms of action remain elusive. In this work, we used super-resolution fluorescence microscopy, in combination with a chromosome-conformation capture assay, to study the distributions of major NAPs in live Escherichia coli cells. Four NAPs--HU, Fis, IHF, and StpA--were largely scattered throughout the nucleoid. In contrast, H-NS, a global transcriptional silencer, formed two compact clusters per chromosome, driven by oligomerization of DNA-bound H-NS through interactions mediated by the amino-terminal domain of the protein. H-NS sequestered the regulated operons into these clusters and juxtaposed numerous DNA segments broadly distributed throughout the chromosome. Deleting H-NS led to substantial chromosome reorganization. These observations demonstrate that H-NS plays a key role in global chromosome organization in bacteria.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329943/" 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/PMC3329943/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Wenqin -- Li, Gene-Wei -- Chen, Chongyi -- Xie, X Sunney -- Zhuang, Xiaowei -- GM 096450/GM/NIGMS NIH HHS/ -- R01 GM096450/GM/NIGMS NIH HHS/ -- R01 GM096450-03/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 9;333(6048):1445-9. doi: 10.1126/science.1204697.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21903814" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Division ; Chromosomes, Bacterial/*metabolism/*ultrastructure ; DNA, Bacterial/chemistry/*metabolism ; DNA-Binding Proteins/metabolism ; Escherichia coli K12/genetics/metabolism/*ultrastructure ; Escherichia coli Proteins/chemistry/genetics/*metabolism ; Factor For Inversion Stimulation Protein/metabolism ; Fimbriae Proteins/chemistry/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Genetic Loci ; Genome, Bacterial ; Integration Host Factors/metabolism ; Molecular Chaperones/metabolism ; Nucleic Acid Conformation ; Operon ; Protein Multimerization ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/chemistry/genetics/*metabolism
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  • 48
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    Biochemistry. KSR plays CRAF-ty (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shi, Fumin -- Lemmon, Mark A -- New York, N.Y. -- Science. 2011 May 27;332(6033):1043-4. doi: 10.1126/science.1208063.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, and Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, 422 Curie Boulevard, Philadelphia, PA 19104-6059, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21617065" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Animals ; Binding Sites ; Catalytic Domain ; Cell Membrane/enzymology ; Enzyme Activation ; Extracellular Signal-Regulated MAP Kinases/*metabolism ; Humans ; *MAP Kinase Signaling System ; Mitogen-Activated Protein Kinase Kinases/*metabolism ; Mutation ; Phosphorylation ; Protein Conformation ; Protein Kinases/chemistry/genetics/*metabolism ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proto-Oncogene Proteins B-raf/antagonists & inhibitors/*metabolism ; Proto-Oncogene Proteins c-raf/*metabolism
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  • 49
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    Increasing the potency and breadth of an HIV antibody by using structure-based rational design (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-10-29
    Description: Antibodies against the CD4 binding site (CD4bs) on the HIV-1 spike protein gp120 can show exceptional potency and breadth. We determined structures of NIH45-46, a more potent clonal variant of VRC01, alone and bound to gp120. Comparisons with VRC01-gp120 revealed that a four-residue insertion in heavy chain complementarity-determining region 3 (CDRH3) contributed to increased interaction between NIH45-46 and the gp120 inner domain, which correlated with enhanced neutralization. We used structure-based design to create NIH45-46(G54W), a single substitution in CDRH2 that increases contact with the gp120 bridging sheet and improves breadth and potency, critical properties for potential clinical use, by an order of magnitude. Together with the NIH45-46-gp120 structure, these results indicate that gp120 inner domain and bridging sheet residues should be included in immunogens to elicit CD4bs antibodies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232316/" 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/PMC3232316/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Diskin, Ron -- Scheid, Johannes F -- Marcovecchio, Paola M -- West, Anthony P Jr -- Klein, Florian -- Gao, Han -- Gnanapragasam, Priyanthi N P -- Abadir, Alexander -- Seaman, Michael S -- Nussenzweig, Michel C -- Bjorkman, Pamela J -- P01 AI081677-01/AI/NIAID NIH HHS/ -- RR00862/RR/NCRR NIH HHS/ -- RR022220/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Dec 2;334(6060):1289-93. doi: 10.1126/science.1213782. Epub 2011 Oct 27.〈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/22033520" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Amino Acid Sequence ; Antibodies, Neutralizing/chemistry/*immunology/metabolism ; Antibody Affinity ; Antigens, CD4/chemistry/metabolism ; Binding Sites ; Complementarity Determining Regions ; Crystallography, X-Ray ; HIV Antibodies/chemistry/*immunology/metabolism ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV-1/*immunology ; Humans ; Hydrophobic and Hydrophilic Interactions ; Immunoglobulin Fab Fragments/chemistry/immunology/metabolism ; Immunoglobulin Heavy Chains/chemistry/immunology/metabolism ; Molecular Mimicry ; Molecular Sequence Data ; Mutant Proteins/chemistry/immunology/metabolism ; Protein Conformation ; *Protein Engineering ; Protein Structure, Tertiary
    Print ISSN: 0036-8075
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  • 50
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    Structural basis for tail-anchored membrane protein biogenesis by the Get3-receptor complex (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-07-02
    Description: Tail-anchored (TA) proteins are involved in cellular processes including trafficking, degradation, and apoptosis. They contain a C-terminal membrane anchor and are posttranslationally delivered to the endoplasmic reticulum (ER) membrane by the Get3 adenosine triphosphatase interacting with the hetero-oligomeric Get1/2 receptor. We have determined crystal structures of Get3 in complex with the cytosolic domains of Get1 and Get2 in different functional states at 3.0, 3.2, and 4.6 angstrom resolution. The structural data, together with biochemical experiments, show that Get1 and Get2 use adjacent, partially overlapping binding sites and that both can bind simultaneously to Get3. Docking to the Get1/2 complex allows for conformational changes in Get3 that are required for TA protein insertion. These data suggest a molecular mechanism for nucleotide-regulated delivery of TA proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601824/" 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/PMC3601824/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stefer, Susanne -- Reitz, Simon -- Wang, Fei -- Wild, Klemens -- Pang, Yin-Yuin -- Schwarz, Daniel -- Bomke, Jorg -- Hein, Christopher -- Lohr, Frank -- Bernhard, Frank -- Denic, Vladimir -- Dotsch, Volker -- Sinning, Irmgard -- R01 GM099943/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Aug 5;333(6043):758-62. doi: 10.1126/science.1207125. Epub 2011 Jun 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, Goethe University, D-60325 Frankfurt am Main, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21719644" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Vesicular Transport/*chemistry/*metabolism ; Adenosine Triphosphatases/*chemistry/*metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Cytosol/chemistry ; Endoplasmic Reticulum/metabolism ; Guanine Nucleotide Exchange Factors/*chemistry/*metabolism ; Membrane Proteins/*chemistry/*metabolism ; Microsomes/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Saccharomyces cerevisiae/*chemistry/metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/*metabolism
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    AIDS/HIV. Converging on an HIV vaccine (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korber, Bette -- Gnanakaran, S -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1589-90. doi: 10.1126/science.1211919.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Theoretical Biology and Biophysics, T6, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. btk@lanl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21921189" target="_blank"〉PubMed〈/a〉
    Keywords: *AIDS Vaccines ; Antibodies, Neutralizing/chemistry/*immunology/metabolism ; Antibody Affinity ; Antigens, CD4/chemistry/immunology/metabolism ; Binding Sites ; Binding Sites, Antibody ; Complementarity Determining Regions/genetics ; Crystallography, X-Ray ; Epitopes ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/chemistry/*immunology/metabolism ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; Humans ; Models, Molecular ; Molecular Mimicry ; Protein Conformation
    Print ISSN: 0036-8075
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    Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-13
    Description: Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516815/" 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/PMC3516815/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Xueling -- Zhou, Tongqing -- Zhu, Jiang -- Zhang, Baoshan -- Georgiev, Ivelin -- Wang, Charlene -- Chen, Xuejun -- Longo, Nancy S -- Louder, Mark -- McKee, Krisha -- O'Dell, Sijy -- Perfetto, Stephen -- Schmidt, Stephen D -- Shi, Wei -- Wu, Lan -- Yang, Yongping -- Yang, Zhi-Yong -- Yang, Zhongjia -- Zhang, Zhenhai -- Bonsignori, Mattia -- Crump, John A -- Kapiga, Saidi H -- Sam, Noel E -- Haynes, Barton F -- Simek, Melissa -- Burton, Dennis R -- Koff, Wayne C -- Doria-Rose, Nicole A -- Connors, Mark -- NISC Comparative Sequencing Program -- Mullikin, James C -- Nabel, Gary J -- Roederer, Mario -- Shapiro, Lawrence -- Kwong, Peter D -- Mascola, John R -- 5U19 AI 067854-06/AI/NIAID NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- U19 AI067854/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1593-602. doi: 10.1126/science.1207532. Epub 2011 Aug 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21835983" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Amino Acid Sequence ; Antibodies, Neutralizing/*chemistry/genetics/*immunology/isolation & purification ; Antibody Affinity ; Antibody Specificity ; Antigens, CD4/metabolism ; Base Sequence ; Binding Sites ; Binding Sites, Antibody ; Complementarity Determining Regions/genetics ; Crystallography, X-Ray ; Epitopes ; *Evolution, Molecular ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/*chemistry/genetics/*immunology/isolation & purification ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; HIV-1/chemistry/*immunology ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoglobulin Fab Fragments/chemistry/immunology ; Immunoglobulin Heavy Chains/chemistry/immunology ; Immunoglobulin J-Chains/genetics ; Immunoglobulin Light Chains/chemistry/immunology ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Sequence Analysis, DNA
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    Conversion of channelrhodopsin into a light-gated chloride channel (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-03-29
    Description: The field of optogenetics uses channelrhodopsins (ChRs) for light-induced neuronal activation. However, optimized tools for cellular inhibition at moderate light levels are lacking. We found that replacement of E90 in the central gate of ChR with positively charged residues produces chloride-conducting ChRs (ChloCs) with only negligible cation conductance. Molecular dynamics modeling unveiled that a high-affinity Cl(-)-binding site had been generated near the gate. Stabilizing the open state dramatically increased the operational light sensitivity of expressing cells (slow ChloC). In CA1 pyramidal cells, ChloCs completely inhibited action potentials triggered by depolarizing current injections or synaptic stimulation. Thus, by inverting the charge of the selectivity filter, we have created a class of directly light-gated anion channels that can be used to block neuronal output in a fully reversible fashion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wietek, Jonas -- Wiegert, J Simon -- Adeishvili, Nona -- Schneider, Franziska -- Watanabe, Hiroshi -- Tsunoda, Satoshi P -- Vogt, Arend -- Elstner, Marcus -- Oertner, Thomas G -- Hegemann, Peter -- New York, N.Y. -- Science. 2014 Apr 25;344(6182):409-12. doi: 10.1126/science.1249375. Epub 2014 Mar 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Biology, Experimental Biophysics, Humboldt Universitat zu Berlin, D-10115 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24674867" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Animals ; Binding Sites ; CA1 Region, Hippocampal/cytology ; Chloride Channels/*chemistry/*metabolism ; Chlorides/*metabolism ; HEK293 Cells ; Humans ; Hydrogen Bonding ; Ion Channel Gating ; Light ; Models, Molecular ; Molecular Dynamics Simulation ; Mutation ; Patch-Clamp Techniques ; Protein Conformation ; Protein Engineering ; Pyramidal Cells/metabolism ; Rats ; Recombinant Fusion Proteins/chemistry ; Rhodopsin/*chemistry/genetics/*metabolism ; Transfection
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    Structure of a class C GPCR metabotropic glutamate receptor 1 bound to an allosteric modulator (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-03-08
    Description: The excitatory neurotransmitter glutamate induces modulatory actions via the metabotropic glutamate receptors (mGlus), which are class C G protein-coupled receptors (GPCRs). We determined the structure of the human mGlu1 receptor seven-transmembrane (7TM) domain bound to a negative allosteric modulator, FITM, at a resolution of 2.8 angstroms. The modulator binding site partially overlaps with the orthosteric binding sites of class A GPCRs but is more restricted than most other GPCRs. We observed a parallel 7TM dimer mediated by cholesterols, which suggests that signaling initiated by glutamate's interaction with the extracellular domain might be mediated via 7TM interactions within the full-length receptor dimer. A combination of crystallography, structure-activity relationships, mutagenesis, and full-length dimer modeling provides insights about the allosteric modulation and activation mechanism of class C GPCRs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991565/" 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/PMC3991565/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Huixian -- Wang, Chong -- Gregory, Karen J -- Han, Gye Won -- Cho, Hyekyung P -- Xia, Yan -- Niswender, Colleen M -- Katritch, Vsevolod -- Meiler, Jens -- Cherezov, Vadim -- Conn, P Jeffrey -- Stevens, Raymond C -- P50 GM073197/GM/NIGMS NIH HHS/ -- R01 DK097376/DK/NIDDK NIH HHS/ -- R01 GM080403/GM/NIGMS NIH HHS/ -- R01 GM099842/GM/NIGMS NIH HHS/ -- R01 MH062646/MH/NIMH NIH HHS/ -- R01 MH090192/MH/NIMH NIH HHS/ -- R01 NS031373/NS/NINDS NIH HHS/ -- R21 NS078262/NS/NINDS NIH HHS/ -- R37 NS031373/NS/NINDS NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Apr 4;344(6179):58-64. doi: 10.1126/science.1249489. Epub 2014 Mar 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational 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/24603153" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Allosteric Site ; Amino Acid Sequence ; Benzamides/*chemistry/*metabolism ; Binding Sites ; Cholesterol ; Crystallography, X-Ray ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Metabotropic Glutamate/*chemistry/*metabolism ; Structure-Activity Relationship ; Thiazoles/*chemistry/*metabolism
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    Regulation of protein phosphatase 2A by direct interaction with casein kinase 2alpha (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-05-09
    Description: Timely deactivation of kinase cascades is crucial to the normal control of cell signaling and is partly accomplished by protein phosphatase 2A (PP2A). The catalytic (alpha) subunit of the serine-threonine kinase casein kinase 2 (CK2) bound to PP2A in vitro and in mitogen-starved cells; binding required the integrity of a sequence motif common to CK2alpha and SV40 small t antigen. Overexpression of CK2alpha resulted in deactivation of mitogen-activated protein kinase kinase (MEK) and suppression of cell growth. Moreover, CK2alpha inhibited the transforming activity of oncogenic Ras, but not that of constitutively activated MEK. Thus, CK2alpha may regulate the deactivation of the mitogen-activated protein kinase pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heriche, J K -- Lebrin, F -- Rabilloud, T -- Leroy, D -- Chambaz, E M -- Goldberg, Y -- New York, N.Y. -- Science. 1997 May 9;276(5314):952-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commissariat a l'Energie Atomique, Departement de Biologie Moleculaire et Structurale, Laboratoire de Biochimie des Regulations Cellulaires Endocrines, Unite 244, F-38054 Grenoble Cedex 9, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9139659" target="_blank"〉PubMed〈/a〉
    Keywords: 3T3 Cells ; Amino Acid Sequence ; Animals ; Antigens, Polyomavirus Transforming ; Binding Sites ; Casein Kinase II ; Cell Division ; Cell Transformation, Neoplastic ; MAP Kinase Kinase 1 ; Mice ; *Mitogen-Activated Protein Kinase Kinases ; Mutation ; Okadaic Acid/pharmacology ; Phosphoprotein Phosphatases/*metabolism ; Phosphorylation ; Platelet-Derived Growth Factor/pharmacology ; Protein Phosphatase 2 ; Protein-Serine-Threonine Kinases/*metabolism/pharmacology ; Protein-Tyrosine Kinases/metabolism/pharmacology ; Recombinant Fusion Proteins/metabolism ; Transfection ; ras Proteins/pharmacology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    The cis-trans paradox of integrase (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-04-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jayaram, M -- New York, N.Y. -- Science. 1997 Apr 4;276(5309):49-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, University of Texas at Austin, Austin, TX 78712, USA. jayaram@almach.cc.utexas.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9122709" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/*enzymology ; Binding Sites ; Crystallography, X-Ray ; DNA/*metabolism ; DNA Nucleotidyltransferases/chemistry/metabolism ; DNA, Circular/metabolism ; Integrases/*chemistry/metabolism ; Models, Molecular ; *Protein Conformation ; Recombinases ; *Recombination, Genetic ; Tyrosine/metabolism ; Virus Integration
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  • 57
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    Bimolecular exon ligation by the human spliceosome (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-06-13
    Description: Intron excision is an essential step in eukaryotic gene expression, but the molecular mechanisms by which the spliceosome accurately identifies splice sites in nuclear precursors to messenger RNAs (pre-mRNAs) are not well understood. A bimolecular assay for the second step of splicing has now revealed that exon ligation by the human spliceosome does not require covalent attachment of a 3' splice site to the branch site. Furthermore, accurate definition of the 3' splice site in this system is independent of either a covalently attached polypyrimidine tract or specific 3' exon sequences. Rather, in this system 3' splice site selection apparently occurs with a 5' --〉 3' directionality.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anderson, K -- Moore, M J -- GM53007/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Jun 13;276(5319):1712-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉W. M. Keck Institute for Cellular Visualization, Department of Biochemistry, Brandeis University, Waltham, MA 02254, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9180084" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviridae/genetics ; Base Sequence ; Binding Sites ; *Exons ; Humans ; Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA Precursors/genetics/*metabolism ; *RNA Splicing ; Spliceosomes/*metabolism
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    Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-12-31
    Description: Methyl-coenzyme M reductase (MCR), the enzyme responsible for the microbial formation of methane, is a 300-kilodalton protein organized as a hexamer in an alpha2beta2gamma2 arrangement. The crystal structure of the enzyme from Methanobacterium thermoautotrophicum, determined at 1.45 angstrom resolution for the inactive enzyme state MCRox1-silent, reveals that two molecules of the nickel porphinoid coenzyme F430 are embedded between the subunits alpha, alpha', beta, and gamma and alpha', alpha, beta', and gamma', forming two identical active sites. Each site is accessible for the substrate methyl-coenzyme M through a narrow channel locked after binding of the second substrate coenzyme B. Together with a second structurally characterized enzyme state (MCRsilent) containing the heterodisulfide of coenzymes M and B, a reaction mechanism is proposed that uses a radical intermediate and a nickel organic compound.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ermler, U -- Grabarse, W -- Shima, S -- Goubeaud, M -- Thauer, R K -- New York, N.Y. -- Science. 1997 Nov 21;278(5342):1457-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Biophysik, Heinrich-Hoffmann-Strabetae 7, 60528 Frankfurt, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9367957" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Coenzymes/chemistry/metabolism ; Crystallography, X-Ray ; Disulfides/chemistry/metabolism ; Hydrogen/metabolism ; Hydrogen Bonding ; Ligands ; Mesna/analogs & derivatives/chemistry/metabolism ; Metalloporphyrins/chemistry/metabolism ; Methane/*metabolism ; Methanobacterium/*enzymology ; Models, Molecular ; Nickel/chemistry/metabolism ; Oxidation-Reduction ; Oxidoreductases/*chemistry/*metabolism ; Phosphothreonine/analogs & derivatives/chemistry/metabolism ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary
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  • 59
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    Synaptic vesicle endocytosis impaired by disruption of dynamin-SH3 domain interactions (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-04-11
    Description: The proline-rich COOH-terminal region of dynamin binds various Src homology 3 (SH3) domain-containing proteins, but the physiological role of these interactions is unknown. In living nerve terminals, the function of the interaction with SH3 domains was examined. Amphiphysin contains an SH3 domain and is a major dynamin binding partner at the synapse. Microinjection of amphiphysin's SH3 domain or of a dynamin peptide containing the SH3 binding site inhibited synaptic vesicle endocytosis at the stage of invaginated clathrin-coated pits, which resulted in an activity-dependent distortion of the synaptic architecture and a depression of transmitter release. These findings demonstrate that SH3-mediated interactions are required for dynamin function and support an essential role of clathrin-mediated endocytosis in synaptic vesicle recycling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shupliakov, O -- Low, P -- Grabs, D -- Gad, H -- Chen, H -- David, C -- Takei, K -- De Camilli, P -- Brodin, L -- CA46128/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1997 Apr 11;276(5310):259-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Nobel Institute for Neurophysiology, Department of Neuroscience, Karolinska Institutet, S-171 77 Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9092476" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Cell Membrane/ultrastructure ; Coated Pits, Cell-Membrane/ultrastructure ; Dynamins ; *Endocytosis ; GTP Phosphohydrolases/*metabolism ; Humans ; Lampreys ; Microscopy, Electron ; Molecular Sequence Data ; Nerve Tissue Proteins/chemistry/*metabolism ; Proline/chemistry ; Recombinant Fusion Proteins/metabolism ; Synapses/metabolism/ultrastructure ; Synaptic Transmission ; Synaptic Vesicles/*metabolism/ultrastructure ; *src Homology Domains
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    Structure of the carboxyl-terminal dimerization domain of the HIV-1 capsid protein (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-11-05
    Description: The carboxyl-terminal domain, residues 146 to 231, of the human immunodeficiency virus-1 (HIV-1) capsid protein [CA(146-231)] is required for capsid dimerization and viral assembly. This domain contains a stretch of 20 residues, called the major homology region (MHR), which is conserved across retroviruses and is essential for viral assembly, maturation, and infectivity. The crystal structures of CA(146-231) and CA(151-231) reveal that the globular domain is composed of four helices and an extended amino-terminal strand. CA(146-231) dimerizes through parallel packing of helix 2 across a dyad. The MHR is distinct from the dimer interface and instead forms an intricate hydrogen-bonding network that interconnects strand 1 and helices 1 and 2. Alignment of the CA(146-231) dimer with the crystal structure of the capsid amino-terminal domain provides a model for the intact protein and extends models for assembly of the central conical core of HIV-1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gamble, T R -- Yoo, S -- Vajdos, F F -- von Schwedler, U K -- Worthylake, D K -- Wang, H -- McCutcheon, J P -- Sundquist, W I -- Hill, C P -- R01 AI40333/AI/NIAID NIH HHS/ -- R01 AI43036/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1997 Oct 31;278(5339):849-53.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Utah, Salt Lake City, UT 84132, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9346481" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Capsid/*chemistry/genetics ; Cell Line ; Cloning, Molecular ; Cloning, Organism ; Crystallography, X-Ray ; Dimerization ; HIV-1/*chemistry/genetics/physiology ; Humans ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Peptidylprolyl Isomerase/chemistry ; *Protein Conformation ; Virus Replication
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    The complete genome sequence of Escherichia coli K-12 (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-09-05
    Description: The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blattner, F R -- Plunkett, G 3rd -- Bloch, C A -- Perna, N T -- Burland, V -- Riley, M -- Collado-Vides, J -- Glasner, J D -- Rode, C K -- Mayhew, G F -- Gregor, J -- Davis, N W -- Kirkpatrick, H A -- Goeden, M A -- Rose, D J -- Mau, B -- Shao, Y -- P01 HG01428/HG/NHGRI NIH HHS/ -- S10 RR10379/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1997 Sep 5;277(5331):1453-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Genetics, University of Wisconsin-Madison, 445 Henry Mall, Madison, WI 53706, USA. ecoli@genetics.wisc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9278503" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/genetics/metabolism ; Bacteriophage lambda/genetics ; Base Composition ; Binding Sites ; Chromosome Mapping ; DNA Replication ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Escherichia coli/*genetics ; Genes, Bacterial ; *Genome, Bacterial ; Molecular Sequence Data ; Mutation ; Operon ; RNA, Bacterial/genetics ; RNA, Transfer/genetics ; Recombination, Genetic ; Regulatory Sequences, Nucleic Acid ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Sequence Homology, Amino Acid
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    Structure of a protein photocycle intermediate by millisecond time-resolved crystallography (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-03-07
    Description: The blue-light photoreceptor photoactive yellow protein (PYP) undergoes a self-contained light cycle. The atomic structure of the bleached signaling intermediate in the light cycle of PYP was determined by millisecond time-resolved, multiwavelength Laue crystallography and simultaneous optical spectroscopy. Light-induced trans-to-cis isomerization of the 4-hydroxycinnamyl chromophore and coupled protein rearrangements produce a new set of active-site hydrogen bonds. An arginine gateway opens, allowing solvent exposure and protonation of the chromophore's phenolic oxygen. Resulting changes in shape, hydrogen bonding, and electrostatic potential at the protein surface form a likely basis for signal transduction. The structural results suggest a general framework for the interpretation of protein photocycles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Genick, U K -- Borgstahl, G E -- Ng, K -- Ren, Z -- Pradervand, C -- Burke, P M -- Srajer, V -- Teng, T Y -- Schildkamp, W -- McRee, D E -- Moffat, K -- Getzoff, E D -- GM36452/GM/NIGMS NIH HHS/ -- GM37684/GM/NIGMS NIH HHS/ -- RR07707/RR/NCRR NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1997 Mar 7;275(5305):1471-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, 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/9045611" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/physiology ; Binding Sites ; Chromatiaceae ; Crystallography, X-Ray ; Electrochemistry ; Hydrogen Bonding ; Isomerism ; Light ; Models, Molecular ; *Photoreceptors, Microbial ; *Protein Conformation ; Signal Transduction ; Spectrum Analysis
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    Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-02-28
    Description: Formate dehydrogenase H from Escherichia coli contains selenocysteine (SeCys), molybdenum, two molybdopterin guanine dinucleotide (MGD) cofactors, and an Fe4S4 cluster at the active site and catalyzes the two-electron oxidation of formate to carbon dioxide. The crystal structures of the oxidized [Mo(VI), Fe4S4(ox)] form of formate dehydrogenase H (with and without bound inhibitor) and the reduced [Mo(IV), Fe4S4(red)] form have been determined, revealing a four-domain alphabeta structure with the molybdenum directly coordinated to selenium and both MGD cofactors. These structures suggest a reaction mechanism that directly involves SeCys140 and His141 in proton abstraction and the molybdenum, molybdopterin, Lys44, and the Fe4S4 cluster in electron transfer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boyington, J C -- Gladyshev, V N -- Khangulov, S V -- Stadtman, T C -- Sun, P D -- New York, N.Y. -- Science. 1997 Feb 28;275(5304):1305-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Structure, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Rockville, MD 20852, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9036855" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbon Dioxide/metabolism ; Catalysis ; Crystallography, X-Ray ; Electron Transport ; Escherichia coli/enzymology ; Ferrous Compounds/*chemistry ; Formate Dehydrogenases/*chemistry/metabolism ; Formates/*metabolism ; Guanine Nucleotides/chemistry/metabolism ; Hydrogen Bonding ; Hydrogenase/*chemistry/metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Molybdenum/chemistry/metabolism ; Multienzyme Complexes/*chemistry/metabolism ; Nitrites/chemistry ; Oxidation-Reduction ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protons ; Pterins/chemistry/metabolism ; Selenocysteine/chemistry/metabolism
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    Structural basis for ligand-regulated oligomerization of AraC (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-04-18
    Description: The crystal structure of the arabinose-binding and dimerization domain of the Escherchia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The 1.5 angstrom structure of the arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the 2.8 angstrom structure of the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface. The ligand-gated oligomerization as seen in AraC provides the basis of a plausible mechanism for modulating the protein's DNA-looping properties.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Soisson, S M -- MacDougall-Shackleton, B -- Schleif, R -- Wolberger, C -- GM18277/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Apr 18;276(5311):421-5.〈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/9103202" target="_blank"〉PubMed〈/a〉
    Keywords: AraC Transcription Factor ; Arabinose/metabolism ; *Bacterial Proteins ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/*metabolism ; Dimerization ; Hydrogen Bonding ; Ligands ; Models, Molecular ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Repressor Proteins/*chemistry/metabolism ; *Transcription Factors
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    Nucleosome mobility and the maintenance of nucleosome positioning (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-05-02
    Description: To study nucleosome mobility and positioning, the R3 lac repressor was used with an adenosine triphosphate (ATP)-dependent chromatin assembly system to establish the positioning of five nucleosomes, with one nucleosome located between two R3 lac operators. When R3 protein was dissociated from DNA with isopropyl beta-D-thiogalactopyranoside, the R3-induced nucleosome positions remained unchanged for at least 60 minutes in the absence of ATP but rearranged within 15 minutes in the presence of ATP. These results suggest that nucleosomes are dynamic and mobile rather than static and that a DNA binding factor is continuously required for the maintenance of nucleosome positioning.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pazin, M J -- Bhargava, P -- Geiduschek, E P -- Kadonaga, J T -- New York, N.Y. -- Science. 1997 May 2;276(5313):809-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9115208" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Apyrase/metabolism ; Binding Sites ; Chromatin/*metabolism ; DNA/*metabolism ; DNA-Binding Proteins/*metabolism ; Isopropyl Thiogalactoside/pharmacology ; Nucleosomes/*physiology ; Operator Regions, Genetic ; Repressor Proteins/*metabolism
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    Flexibility in DNA recombination: structure of the lambda integrase catalytic core (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-04-04
    Description: Lambda integrase is archetypic of site-specific recombinases that catalyze intermolecular DNA rearrangements without energetic input. DNA cleavage, strand exchange, and religation steps are linked by a covalent phosphotyrosine intermediate in which Tyr342 is attached to the 3'-phosphate of the DNA cut site. The 1.9 angstrom crystal structure of the integrase catalytic domain reveals a protein fold that is conserved in organisms ranging from archaebacteria to yeast and that suggests a model for interaction with target DNA. The attacking Tyr342 nucleophile is located on a flexible loop about 20 angstroms from a basic groove that contains all the other catalytically essential residues. This bipartite active site can account for several apparently paradoxical features of integrase family recombinases, including the capacity for both cis and trans cleavage of DNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839824/" 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/PMC1839824/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kwon, H J -- Tirumalai, R -- Landy, A -- Ellenberger, T -- AI13544/AI/NIAID NIH HHS/ -- GM33928/GM/NIGMS NIH HHS/ -- R01 GM033928/GM/NIGMS NIH HHS/ -- R01 GM062723/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Apr 4;276(5309):126-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9082984" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Attachment Sites, Microbiological ; Bacteriophage lambda/*enzymology ; Binding Sites ; Cloning, Molecular ; Conserved Sequence ; Crystallography, X-Ray ; DNA/*metabolism ; DNA Nucleotidyltransferases/chemistry/metabolism ; Hydrogen Bonding ; Integrases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinases ; *Recombination, Genetic ; Tyrosine/chemistry/metabolism ; Virus Integration
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    Recognition of unique carboxyl-terminal motifs by distinct PDZ domains (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-01-03
    Description: The oriented peptide library technique was used to investigate the peptide-binding specificities of nine PDZ domains. Each PDZ domain selected peptides with hydrophobic residues at the carboxyl terminus. Individual PDZ domains selected unique optimal motifs defined primarily by the carboxyl terminal three to seven residues of the peptides. One family of PDZ domains, including those of the Discs Large protein, selected peptides with the consensus motif Glu-(Ser/Thr)-Xxx-(Val/Ile) (where Xxx represents any amino acid) at the carboxyl terminus. In contrast, another family of PDZ domains, including those of LIN-2, p55, and Tiam-1, selected peptides with hydrophobic or aromatic side chains at the carboxyl terminal three residues. On the basis of crystal structures of the PSD-95-3 PDZ domain, the specificities observed with the peptide library can be rationalized.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Songyang, Z -- Fanning, A S -- Fu, C -- Xu, J -- Marfatia, S M -- Chishti, A H -- Crompton, A -- Chan, A C -- Anderson, J M -- Cantley, L C -- CA66263/CA/NCI NIH HHS/ -- DK34989/DK/NIDDK NIH HHS/ -- R01 GM056203/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Jan 3;275(5296):73-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Signal Transduction, Beth Israel Hospital, and Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8974395" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Guanine Nucleotide Exchange Factors ; Guanylate Kinase ; Helminth Proteins/chemistry/metabolism ; Humans ; Kinesin/chemistry/metabolism ; Membrane Proteins/chemistry/metabolism ; Models, Molecular ; Myosins/chemistry/metabolism ; Nerve Tissue Proteins/chemistry/metabolism ; Nucleoside-Phosphate Kinase/chemistry/metabolism ; Peptide Library ; Peptides/chemistry/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Tyrosine Phosphatases/chemistry/metabolism ; Proteins/chemistry/*metabolism ; Sequence Homology, Amino Acid
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    GAP into the breach (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-07-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sprang, S R -- New York, N.Y. -- Science. 1997 Jul 18;277(5324):329-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical School, Dallas, TX 75235, USA. sprang@howie.swmed.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9518363" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum Compounds/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Fluorides/metabolism ; GTP Phosphohydrolases/*metabolism ; GTP-Binding Proteins/chemistry/*metabolism ; GTPase-Activating Proteins ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/*metabolism ; Hydrolysis ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Proteins/*chemistry/metabolism ; *RGS Proteins ; ras GTPase-Activating Proteins ; ras Proteins/chemistry/*metabolism
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    Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-09-20
    Description: Terpene cyclases catalyze the synthesis of cyclic terpenes with 10-, 15-, and 20-carbon acyclic isoprenoid diphosphates as substrates. Plants have been a source of these natural products by providing a homologous set of terpene synthases. The crystal structures of 5-epi-aristolochene synthase, a sesquiterpene cyclase from tobacco, alone and complexed separately with two farnesyl diphosphate analogs were analyzed. These structures reveal an unexpected enzymatic mechanism for the synthesis of the bicyclic product, 5-epi-aristolochene, and provide a basis for understanding the stereochemical selectivity displayed by other cyclases in the biosynthesis of pharmacologically important cyclic terpenes. As such, these structures provide templates for the engineering of novel terpene cyclases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Starks, C M -- Back, K -- Chappell, J -- Noel, J P -- GM07240/GM/NIGMS NIH HHS/ -- GM54029/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Sep 19;277(5333):1815-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Laboratory, The Salk Institute for Biological Studies, 10010 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/9295271" target="_blank"〉PubMed〈/a〉
    Keywords: *Alkyl and Aryl Transferases ; Binding Sites ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Cyclization ; Magnesium/metabolism ; Models, Molecular ; Physicochemical Phenomena ; *Plants, Toxic ; Polyisoprenyl Phosphates/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protons ; Sesquiterpenes/*chemical synthesis ; Tobacco/*enzymology ; Transferases/*chemistry/metabolism
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    A proficient enzyme revisited: the predicted mechanism for orotidine monophosphate decarboxylase (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-05-09
    Description: A mechanism is proposed to explain the activity of orotidine 5'-monophosphate decarboxylase (ODCase). This enzyme is the one of the most proficient known, with a catalytic proficiency (kcat/Km)/knon = 10(23) M-1. Quantum mechanical calculations predict a mechanism involving a stabilized carbene intermediate, which represents a previously unrecognized mode of enzymatic activity for ODCase. The proposed mechanism involves proton transfer from a weak acid (pKa = 7, where Ka is the acid constant) concerted with decarboxylation, in a nonpolar enzyme environment. Such a mechanism makes possible different approaches to the design of ODCase inhibitors. Furthermore, the prediction that general acid catalysis may only be effective in low dielectric media is of general significance for understanding the activity of many enzymes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, J K -- Houk, K N -- New York, N.Y. -- Science. 1997 May 9;276(5314):942-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉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/9139656" target="_blank"〉PubMed〈/a〉
    Keywords: Barbiturates/pharmacology ; Binding Sites ; Catalysis ; Decarboxylation ; Enzyme Inhibitors/pharmacology ; Hydrogen-Ion Concentration ; Kinetics ; Orotidine-5'-Phosphate Decarboxylase/antagonists & inhibitors/*metabolism ; Protons ; Thermodynamics ; Uridine Monophosphate/*analogs & derivatives/metabolism
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    Crystal structure of pentalenene synthase: mechanistic insights on terpenoid cyclization reactions in biology (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-09-20
    Description: The crystal structure of pentalenene synthase at 2.6 angstrom resolution reveals critical active site features responsible for the cyclization of farnesyl diphosphate into the tricyclic hydrocarbon pentalenene. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. The core active site structure of the enzyme may be preserved among the greater family of terpenoid synthases, possibly implying divergence from a common ancestral synthase to satisfy biological requirements for increasingly diverse natural products.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lesburg, C A -- Zhai, G -- Cane, D E -- Christianson, D W -- New York, N.Y. -- Science. 1997 Sep 19;277(5333):1820-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9295272" target="_blank"〉PubMed〈/a〉
    Keywords: *Alkyl and Aryl Transferases ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Cyclization ; Cyclopentanes/chemical synthesis/chemistry ; Geranyltranstransferase ; *Intramolecular Lyases ; Isomerases/*chemistry/metabolism ; Models, Molecular ; Polyisoprenyl Phosphates/chemistry/metabolism ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/metabolism ; Sesquiterpenes ; Streptomyces/*enzymology ; Transferases/chemistry/metabolism
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    A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-01-31
    Description: A method is described for selecting DNA-binding proteins that recognize desired sequences. The protocol involves gradually extending a new zinc finger protein across the desired 9- or 10-base pair target site, adding and optimizing one finger at a time. This procedure was tested with a TATA box, a p53 binding site, and a nuclear receptor element, and proteins were obtained that bind with nanomolar dissociation constants and discriminate effectively (greater than 20,000-fold) against nonspecific DNA. This strategy may provide important information about protein-DNA recognition as well as powerful tools for biomedical research.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Greisman, H A -- Pabo, C O -- New York, N.Y. -- Science. 1997 Jan 31;275(5300):657-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and 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/9005850" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Composition ; Base Sequence ; Binding Sites ; DNA/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Genes, p53 ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptide Library ; Protein Conformation ; *Protein Engineering ; Protein Structure, Secondary ; Receptors, Cytoplasmic and Nuclear/genetics ; TATA Box ; Transcription Factors/chemistry/metabolism ; *Zinc Fingers
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    Light-induced structural changes in photosynthetic reaction center: implications for mechanism of electron-proton transfer (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-05-02
    Description: High resolution x-ray diffraction data from crystals of the Rhodobacter sphaeroides photosynthetic reaction center (RC) have been collected at cryogenic temperature in the dark and under illumination, and the structures were refined at 2.2 and 2.6 angstrom resolution, respectively. In the charge-separated D+QAQB- state (where D is the primary electron donor (a bacteriochlorophyll dimer), and QA and QB are the primary and secondary quinone acceptors, respectively), QB- is located approximately 5 angstroms from the QB position in the charge-neutral (DQAQB) state, and has undergone a 180 degrees propeller twist around the isoprene chain. A model based on the difference between the two structures is proposed to explain the observed kinetics of electron transfer from QA-QB to QAQB- and the relative binding affinities of the different ubiquinone species in the QB pocket. In addition, several water channels (putative proton pathways) leading from the QB pocket to the surface of the RC were delineated, one of which leads directly to the membrane surface.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stowell, M H -- McPhillips, T M -- Rees, D C -- Soltis, S M -- Abresch, E -- Feher, G -- GM13191/GM/NIGMS NIH HHS/ -- GM45162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 May 2;276(5313):812-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, 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/9115209" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Darkness ; Electron Transport ; Freezing ; Hydrogen Bonding ; *Light ; Light-Harvesting Protein Complexes ; Models, Molecular ; Photosynthetic Reaction Center Complex Proteins/*chemistry/metabolism ; *Protein Conformation ; *Protons ; Rhodobacter sphaeroides/*chemistry ; Temperature ; Ubiquinone/chemistry/metabolism
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    Structure-based analysis of catalysis and substrate definition in the HIT protein family (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-10-10
    Description: The histidine triad (HIT) protein family is among the most ubiquitous and highly conserved in nature, but a biological activity has not yet been identified for any member of the HIT family. Fragile histidine triad protein (FHIT) and protein kinase C interacting protein (PKCI) were used in a structure-based approach to elucidate characteristics of in vivo ligands and reactions. Crystallographic structures of apo, substrate analog, pentacovalent transition-state analog, and product states of both enzymes reveal a catalytic mechanism and define substrate characteristics required for catalysis, thus unifying the HIT family as nucleotidyl hydrolases, transferases, or both. The approach described here may be useful in identifying structure-function relations between protein families identified through genomics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lima, C D -- Klein, M G -- Hendrickson, W A -- T32CA09503/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1997 Oct 10;278(5336):286-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9323207" target="_blank"〉PubMed〈/a〉
    Keywords: *Acid Anhydride Hydrolases ; Adenosine/metabolism ; Adenosine Diphosphate/analogs & derivatives/metabolism ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Dimerization ; Dinucleoside Phosphates/metabolism ; Hydrogen Bonding ; *Neoplasm Proteins ; Nerve Tissue Proteins/chemistry/*metabolism ; Protein Structure, Secondary ; Proteins/chemistry/*metabolism ; Structure-Activity Relationship ; Substrate Specificity ; Tungsten Compounds/metabolism
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    Structural convergence in the active sites of a family of catalytic antibodies (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-02-21
    Description: The x-ray structures of three esterase-like catalytic antibodies identified by screening for catalytic activity the entire hybridoma repertoire, elicited in response to a phosphonate transition state analog (TSA) hapten, were analyzed. The high resolution structures account for catalysis by transition state stabilization, and in all three antibodies a tyrosine residue participates in the oxyanion hole. Despite significant conformational differences in their combining sites, the three antibodies, which are the most efficient among those elicited, achieve catalysis in essentially the same mode, suggesting that evolution for binding to a single TSA followed by screening for catalysis lead to antibodies with structural convergence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Charbonnier, J B -- Golinelli-Pimpaneau, B -- Gigant, B -- Tawfik, D S -- Chap, R -- Schindler, D G -- Kim, S H -- Green, B S -- Eshhar, Z -- Knossow, M -- New York, N.Y. -- Science. 1997 Feb 21;275(5303):1140-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire d'Enzymologie et de Biochimie Structurales, CNRS, 91198 Gif sur Yvette Cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9027317" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Catalytic/*chemistry/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Enzyme-Linked Immunosorbent Assay ; *Evolution, Molecular ; Haptens/chemistry/metabolism ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/chemistry/metabolism ; Mice ; Mice, Inbred BALB C ; Models, Molecular ; Organophosphonates/chemistry/metabolism ; *Protein Conformation ; Tyrosine/chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    A functional model related to cytochrome c oxidase and its electrocatalytic four-electron reduction of O2 (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-02-14
    Description: A cytochrome c oxidase model that consists of a cobalt(II) porphyrin with a copper(I) triazacyclononane macrocycle fastened on the distal face and an imidazole covalently attached to the proximal face has been synthesized and characterized. Redox titrations with molecular oxygen (O2) and cobaltocene were carried out, and O2 was found to bind irreversibly in a 1:1 ratio to the model compound. This O2 adduct (a bridged peroxide) can be fully reduced to the deoxygenated form with four equivalents of cobaltocene. The model compound was adsorbed on an edge-plane graphite electrode, and rotating ring-disk voltammetry was used to monitor the electrocatalytic reduction of O2. Four-electron reduction of O2 was observed at physiological pH.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Collman, J P -- Fu, L -- Herrmann, P C -- Zhang, X -- 5R37 GM-17880-26/GM/NIGMS NIH HHS/ -- CHE9123187-A2/PHS HHS/ -- RR 04122/RR/NCRR NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1997 Feb 14;275(5302):949-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9020071" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Bridged Compounds/chemical synthesis/*chemistry ; Catalysis ; Cobalt/chemistry ; Copper/chemistry ; Electron Transport Complex IV/chemistry/*metabolism ; Electrons ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Oxygen/chemistry/*metabolism ; Porphyrins/chemical synthesis/*chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    The structure of nitric oxide synthase oxygenase domain and inhibitor complexes (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-10-23
    Description: The nitric oxide synthase oxygenase domain (NOSox) oxidizes arginine to synthesize the cellular signal and defensive cytotoxin nitric oxide (NO). Crystal structures determined for cytokine-inducible NOSox reveal an unusual fold and heme environment for stabilization of activated oxygen intermediates key for catalysis. A winged beta sheet engenders a curved alpha-beta domain resembling a baseball catcher's mitt with heme clasped in the palm. The location of exposed hydrophobic residues and the results of mutational analysis place the dimer interface adjacent to the heme-binding pocket. Juxtaposed hydrophobic O2- and polar L-arginine-binding sites occupied by imidazole and aminoguanidine, respectively, provide a template for designing dual-function inhibitors and imply substrate-assisted catalysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crane, B R -- Arvai, A S -- Gachhui, R -- Wu, C -- Ghosh, D K -- Getzoff, E D -- Stuehr, D J -- Tainer, J A -- CA53914/CA/NCI NIH HHS/ -- HL58883/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1997 Oct 17;278(5337):425-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute for Chemical Biology, 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/9334294" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/chemistry/metabolism ; Binding Sites ; Biopterin/analogs & derivatives/metabolism ; *Caenorhabditis elegans Proteins ; Catalysis ; Crystallography, X-Ray ; Dimerization ; Enzyme Induction ; Enzyme Inhibitors/metabolism ; Guanidines/metabolism ; Heme/chemistry ; Homeodomain Proteins/chemistry/*genetics/physiology ; Hydrogen Bonding ; Imidazoles/metabolism ; Isoenzymes/antagonists & inhibitors/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nitric Oxide Synthase/antagonists & inhibitors/*chemistry/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Oxygenases/chemistry/metabolism ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary
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    Ste5 RING-H2 domain: role in Ste4-promoted oligomerization for yeast pheromone signaling (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-10-06
    Description: Ste5 is a scaffold for the mitogen-activated protein kinase (MAPK) cascade components in a yeast pheromone response pathway. Ste5 also associates with Ste4, the beta subunit of a heterotrimeric guanine nucleotide-binding protein, potentially linking receptor activation to stimulation of the MAPK cascade. A RING-H2 motif at the Ste5 amino terminus is apparently essential for function because Ste5(C177S) and Ste5(C177A C180A) mutants did not rescue the mating defect of a ste5Delta cell. In vitro Ste5(C177A C180A) bound each component of the MAPK cascade, but not Ste4. Unlike wild-type Ste5, the mutant did not appear to oligomerize; however, when fused to a heterologous dimerization domain (glutathione S-transferase), the chimeric protein restored mating in an ste5Delta cell and an ste4Delta ste5Delta double mutant. Thus, the RING-H2 domain mediates Ste4-Ste5 interaction, which is a prerequisite for Ste5-Ste5 self-association and signaling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Inouye, C -- Dhillon, N -- Thorner, J -- CA09041/CA/NCI NIH HHS/ -- GM21841/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Oct 3;278(5335):103-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, CA 94720-3202, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9311911" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptor Proteins, Signal Transducing ; Amino Acid Sequence ; Binding Sites ; Calcium-Calmodulin-Dependent Protein Kinases/metabolism ; *Carrier Proteins ; Dimerization ; Fungal Proteins/*chemistry/genetics/*metabolism ; *GTP-Binding Protein beta Subunits ; GTP-Binding Proteins/*metabolism ; Genetic Complementation Test ; Glutathione Transferase/chemistry ; *Heterotrimeric GTP-Binding Proteins ; Molecular Sequence Data ; Peptides/*physiology ; Pheromones/physiology ; Point Mutation ; Polymers ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/chemistry/genetics/*metabolism ; *Saccharomyces cerevisiae Proteins ; *Signal Transduction ; Transformation, Genetic
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    ARF1, a transcription factor that binds to auxin response elements (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-06-20
    Description: The plant hormone auxin regulates plant physiology by modulating the interaction of transcription factors with auxin response elements (AuxREs) of the affected genes. A transcription factor, Auxin Response Factor 1 (ARF1), that binds to the sequence TGTCTC in AuxREs was cloned from Arabidopsis by using a yeast one-hybrid system. ARF1 has an amino-terminal DNA-binding domain related to the carboxyl terminus of the maize transactivator Viviparous-1. Sequence requirements for ARF1 binding in vitro are identical to those that confer auxin responsiveness in vivo. The carboxyl terminus of ARF1 contains two motifs found in the Aux/IAA class of proteins and appears to mediate protein-protein interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ulmasov, T -- Hagen, G -- Guilfoyle, T J -- New York, N.Y. -- Science. 1997 Jun 20;276(5320):1865-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9188533" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/genetics ; Arabidopsis Proteins ; Base Sequence ; Binding Sites ; Cloning, Molecular ; DNA, Plant/genetics/*metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Genes, Plant ; Indoleacetic Acids/*pharmacology ; Molecular Sequence Data ; Mutation ; Plant Proteins ; *Promoter Regions, Genetic ; *Repetitive Sequences, Nucleic Acid ; Transcription Factors/chemistry/genetics/*metabolism
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  • 80
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    A protein-counting mechanism for telomere length regulation in yeast (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-02-14
    Description: In the yeast Saccharomyces cerevisiae, telomere elongation is negatively regulated by the telomere repeat-binding protein Rap1p, such that a narrow length distribution of telomere repeat tracts is observed. This length regulation was shown to function independently of the orientation of the telomere repeats. The number of repeats at an individual telomere was reduced when hybrid proteins containing the Rap1p carboxyl terminus were targeted there by a heterologous DNA-binding domain. The extent of this telomere tract shortening was proportional to the number of targeted molecules, consistent with a feedback mechanism of telomere length regulation that can discriminate the precise number of Rap1p molecules bound to the chromosome end.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marcand, S -- Gilson, E -- Shore, D -- GM40094/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Feb 14;275(5302):986-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9020083" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chromosomes, Fungal/metabolism ; Fungal Proteins/*metabolism ; GTP-Binding Proteins/*metabolism ; Gene Expression Regulation, Fungal ; Genetic Markers ; Mutation ; Saccharomyces cerevisiae/genetics/*metabolism ; Telomerase/metabolism ; Telomere/*metabolism ; Transformation, Genetic ; rap GTP-Binding Proteins
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    Structure and function of a squalene cyclase (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-09-20
    Description: The crystal structure of squalene-hopene cyclase from Alicyclobacillus acidocaldarius was determined at 2.9 angstrom resolution. The mechanism and sequence of this cyclase are closely related to those of 2,3-oxidosqualene cyclases that catalyze the cyclization step in cholesterol biosynthesis. The structure reveals a membrane protein with membrane-binding characteristics similar to those of prostaglandin-H2 synthase, the only other reported protein of this type. The active site of the enzyme is located in a large central cavity that is of suitable size to bind squalene in its required conformation and that is lined by aromatic residues. The structure supports a mechanism in which the acid starting the reaction by protonating a carbon-carbon double bond is an aspartate that is coupled to a histidine. Numerous surface alpha helices are connected by characteristic QW-motifs (Q is glutamine and W is tryptophan) that tighten the protein structure, possibly for absorbing the reaction energy without structural damage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wendt, K U -- Poralla, K -- Schulz, G E -- New York, N.Y. -- Science. 1997 Sep 19;277(5333):1811-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albertstrasse 21, D-79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9295270" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacillaceae/*enzymology ; Binding Sites ; Cell Membrane/enzymology ; Crystallization ; Crystallography, X-Ray ; Cyclization ; Dimerization ; Humans ; Hydrogen Bonding ; *Intramolecular Transferases ; Isomerases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/metabolism ; Sequence Alignment ; Squalene/metabolism ; Thermodynamics
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    A low-barrier hydrogen bond in the catalytic triad of serine proteases? Theory versus experiment (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-11-14
    Description: Cleland and Kreevoy recently advanced the idea that a special type of hydrogen bond (H-bond), termed a low-barrier hydrogen bond (LBHB), may account for the "missing" transition state stabilization underlying the catalytic power of many enzymes, and Frey et al. have proposed that the H-bond between aspartic acid 102 and histidine 57 in the catalytic triad of serine proteases is an example of a catalytically important LBHB. Experimental facts are here considered regarding the aspartic acid-histidine and cis-urocanic H-bonds that are inconsistent with fundamental tenets of the LBHB hypothesis. The inconsistencies between theory and experiment in these paradigm systems cast doubt on the existence of LBHBs, as currently defined, within enzyme active sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ash, E L -- Sudmeier, J L -- De Fabo, E C -- Bachovchin, W W -- GM27927/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Nov 7;278(5340):1128-32.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Tufts University School of Medicine, Boston, MA 02111, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9353195" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid/chemistry ; Binding Sites ; Boronic Acids/metabolism ; Catalysis ; Histidine/chemistry ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Magnetic Resonance Spectroscopy ; Oligopeptides/metabolism ; Protons ; Serine Endopeptidases/*chemistry/metabolism ; Serine Proteinase Inhibitors/metabolism ; Subtilisins/chemistry ; Temperature ; Urocanic Acid/chemistry
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  • 83
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    Repression of c-myc transcription by Blimp-1, an inducer of terminal B cell differentiation (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-04-25
    Description: Transcription of c-myc in plasma cells, which are terminally differentiated B cells, is repressed by plasmacytoma repressor factor. This factor was identified as Blimp-1, known for its ability to induce B cell differentiation. Blimp-1 repressed c-myc promoter activity in a binding site-dependent manner. Treatment of BCL1 lymphoma cells with interleukin-2 (IL-2) plus IL-5 induced Blimp-1 and caused a subsequent decline in c-Myc protein. Ectopic expression of Blimp-1 in Abelson-transformed precursor B cells repressed endogenous c-Myc and caused apoptosis; Blimp-1-induced death was partially overcome by ectopic expression of c-Myc. Thus, repression of c-myc is a component of the Blimp-1 program of terminal B cell differentiation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, Y -- Wong, K -- Calame, K -- New York, N.Y. -- Science. 1997 Apr 25;276(5312):596-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, 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/9110979" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis ; B-Lymphocytes/*cytology/metabolism ; Binding Sites ; Cell Differentiation ; Cell Line ; Gene Expression Regulation ; *Genes, myc ; Interleukin-2/pharmacology ; Interleukin-5/pharmacology ; Mice ; Mutagenesis, Site-Directed ; Plasmacytoma ; Promoter Regions, Genetic ; *Repressor Proteins ; Transcription Factors/genetics/*metabolism ; *Transcription, Genetic ; Transfection ; Tumor Cells, Cultured ; Zinc Fingers
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    A light-actuated nanovalve derived from a channel protein (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-07-30
    Description: Toward the realization of nanoscale device control, we report a molecular valve embedded in a membrane that can be opened by illumination with long-wavelength ultraviolet (366 nanometers) light and then resealed by visible irradiation. The valve consists of a channel protein, the mechanosensitive channel of large conductance (MscL) from Escherichia coli, modified by attachment of synthetic compounds that undergo light-induced charge separation to reversibly open and close a 3-nanometer pore. The system is compatible with a classical encapsulation system, the liposome, and external photochemical control over transport through the channel is achieved.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kocer, Armagan -- Walko, Martin -- Meijberg, Wim -- Feringa, Ben L -- New York, N.Y. -- Science. 2005 Jul 29;309(5735):755-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BiOMaDe Technology Foundation, Nijenborgh 4, 9747 AG Groningen, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16051792" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Cysteine/chemistry ; Escherichia coli Proteins/*chemistry ; Fluoresceins/chemistry ; Hydrophobic and Hydrophilic Interactions ; Ion Channel Gating ; Ion Channels/*chemistry ; *Light ; Lipid Bilayers ; Liposomes ; *Nanostructures ; Nanotechnology ; Osmolar Concentration ; Patch-Clamp Techniques ; Photolysis ; Protein Structure, Secondary ; *Ultraviolet Rays
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    Functional genomic analysis of the Wnt-wingless signaling pathway (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-04-09
    Description: The Wnt-Wingless (Wg) pathway is one of a core set of evolutionarily conserved signaling pathways that regulates many aspects of metazoan development. Aberrant Wnt signaling has been linked to human disease. In the present study, we used a genomewide RNA interference (RNAi) screen in Drosophila cells to screen for regulators of the Wnt pathway. We identified 238 potential regulators, which include known pathway components, genes with functions not previously linked to this pathway, and genes with no previously assigned functions. Reciprocal-Best-Blast analyses reveal that 50% of the genes identified in the screen have human orthologs, of which approximately 18% are associated with human disease. Functional assays of selected genes from the cell-based screen in Drosophila, mammalian cells, and zebrafish embryos demonstrated that these genes have evolutionarily conserved functions in Wnt signaling. High-throughput RNAi screens in cultured cells, followed by functional analyses in model organisms, prove to be a rapid means of identifying regulators of signaling pathways implicated in development and disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DasGupta, Ramanuj -- Kaykas, Ajamete -- Moon, Randall T -- Perrimon, Norbert -- New York, N.Y. -- Science. 2005 May 6;308(5723):826-33. Epub 2005 Apr 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Howard Hughes Medical Institute (HHMI), Harvard Medical School, New Research Building, No. 339, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. rdasgupt@genetics.med.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15817814" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Line ; Cloning, Molecular ; Computational Biology ; Cytoskeletal Proteins/metabolism ; Drosophila Proteins/chemistry/genetics/*metabolism ; Drosophila melanogaster/*genetics/metabolism ; Embryo, Nonmammalian/metabolism ; Embryonic Development ; Epistasis, Genetic ; *Gene Expression Regulation ; Genes, Insect ; Genes, Reporter ; *Genomics ; Mutation ; Phenotype ; Phosphorylation ; Protein Kinases/metabolism ; Proteins/metabolism ; Proto-Oncogene Proteins/genetics/*metabolism ; *RNA Interference ; *Signal Transduction ; Trans-Activators/metabolism ; Transcription Factors/chemistry/genetics/metabolism ; Transfection ; Wnt Proteins ; Wnt1 Protein ; Wnt3 Protein ; Zebrafish ; Zebrafish Proteins ; beta Catenin ; rab5 GTP-Binding Proteins/genetics/metabolism
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  • 86
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    Crystal structure of the malaria vaccine candidate apical membrane antigen 1 (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-02-26
    Description: Apical membrane antigen 1 from Plasmodium is a leading malaria vaccine candidate. The protein is essential for host-cell invasion, but its molecular function is unknown. The crystal structure of the three domains comprising the ectoplasmic region of the antigen from P. vivax, solved at 1.8 angstrom resolution, shows that domains I and II belong to the PAN motif, which defines a superfamily of protein folds implicated in receptor binding. We also mapped the epitope of an invasion-inhibitory monoclonal antibody specific for the P. falciparum ortholog and modeled this to the structure. The location of the epitope and current knowledge on structure-function correlations for PAN domains together suggest a receptor-binding role during invasion in which domain II plays a critical part. These results are likely to aid vaccine and drug design.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pizarro, Juan Carlos -- Vulliez-Le Normand, Brigitte -- Chesne-Seck, Marie-Laure -- Collins, Christine R -- Withers-Martinez, Chrislaine -- Hackett, Fiona -- Blackman, Michael J -- Faber, Bart W -- Remarque, Edmond J -- Kocken, Clemens H M -- Thomas, Alan W -- Bentley, Graham A -- MC_U117532063/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2005 Apr 15;308(5720):408-11. Epub 2005 Feb 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Unite d'Immunologie Structurale, Centre National de la Recherche Scientifique, URA 2185, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15731407" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Antibodies, Monoclonal/immunology ; Antigens, Protozoan/*chemistry/immunology ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Epitope Mapping ; Epitopes ; Heparin/metabolism ; Malaria Vaccines ; Membrane Proteins/*chemistry/immunology ; Models, Molecular ; Molecular Sequence Data ; Plasmodium falciparum/chemistry/immunology ; Plasmodium vivax/chemistry/*immunology ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protozoan Proteins/*chemistry/immunology ; Recombinant Proteins/chemistry ; Sequence Alignment
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    Complement factor H variant increases the risk of age-related macular degeneration (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-03-12
    Description: Age-related macular degeneration (AMD) is a leading cause of visual impairment and blindness in the elderly whose etiology remains largely unknown. Previous studies identified chromosome 1q32 as harboring a susceptibility locus for AMD. We used single-nucleotide polymorphisms to interrogate this region and identified a strongly associated haplotype in two independent data sets. DNA resequencing of the complement factor H gene within this haplotype revealed a common coding variant, Y402H, that significantly increases the risk for AMD with odds ratios between 2.45 and 5.57. This common variant likely explains approximately 43% of AMD in older adults.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haines, Jonathan L -- Hauser, Michael A -- Schmidt, Silke -- Scott, William K -- Olson, Lana M -- Gallins, Paul -- Spencer, Kylee L -- Kwan, Shu Ying -- Noureddine, Maher -- Gilbert, John R -- Schnetz-Boutaud, Nathalie -- Agarwal, Anita -- Postel, Eric A -- Pericak-Vance, Margaret A -- AG11268/AG/NIA NIH HHS/ -- EY015216/EY/NEI NIH HHS/ -- EY12118/EY/NEI NIH HHS/ -- M01 RR-00095/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2005 Apr 15;308(5720):419-21. Epub 2005 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15761120" target="_blank"〉PubMed〈/a〉
    Keywords: Aged ; Alleles ; Binding Sites ; C-Reactive Protein/metabolism ; Case-Control Studies ; Chromosomes, Human, Pair 1/genetics ; Complement Activation ; Complement Factor H/analysis/*genetics/physiology ; Gene Frequency ; Genetic Predisposition to Disease ; *Genetic Variation ; Genotype ; Haplotypes ; Heparin/metabolism ; Humans ; Linkage Disequilibrium ; Macular Degeneration/*genetics ; Odds Ratio ; *Polymorphism, Single Nucleotide ; Risk Factors ; Sequence Analysis, DNA ; Smoking
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    Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-10-01
    Description: Chlorinated natural products include vancomycin and cryptophycin A. Their biosynthesis involves regioselective chlorination by flavin-dependent halogenases. We report the structural characterization of tryptophan 7-halogenase (PrnA), which regioselectively chlorinates tryptophan. Tryptophan and flavin adenine dinucleotide (FAD) are separated by a 10 angstrom-long tunnel and bound by distinct enzyme modules. The FAD module is conserved in halogenases and is related to flavin-dependent monooxygenases. On the basis of biochemical studies, crystal structures, and by analogy with monooxygenases, we predict that FADH2 reacts with O2 to make peroxyflavin, which is decomposed by Cl-. The resulting HOCl is guided through the tunnel to tryptophan, where it is activated to participate in electrophilic aromatic substitution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315827/" 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/PMC3315827/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dong, Changjiang -- Flecks, Silvana -- Unversucht, Susanne -- Haupt, Caroline -- van Pee, Karl-Heinz -- Naismith, James H -- BB/C000080/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/14426/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2005 Sep 30;309(5744):2216-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Biomolecular Sciences, EaStchem, University of St. Andrews, St. Andrews KY16 9ST, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16195462" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chlorides/*metabolism ; Crystallography, X-Ray ; Dimerization ; Flavin-Adenine Dinucleotide/analogs & derivatives/metabolism ; Hydrogen Bonding ; Hypochlorous Acid/metabolism ; Indoles/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/*chemistry/isolation & purification/metabolism ; Oxygen/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pseudomonas fluorescens/*enzymology ; Tryptophan/analogs & derivatives/metabolism
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  • 89
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    Structural roles for human translation factor eIF3 in initiation of protein synthesis (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-03
    Description: Protein synthesis in mammalian cells requires initiation factor eIF3, a approximately 750-kilodalton complex that controls assembly of 40S ribosomal subunits on messenger RNAs (mRNAs) bearing either a 5'-cap or an internal ribosome entry site (IRES). Cryo-electron microscopy reconstructions show that eIF3, a five-lobed particle, interacts with the hepatitis C virus (HCV) IRES RNA and the 5'-cap binding complex eIF4F via the same domain. Detailed modeling of eIF3 and eIF4F onto the 40S ribosomal subunit reveals that eIF3 uses eIF4F or the HCV IRES in structurally similar ways to position the mRNA strand near the exit site of 40S, promoting initiation complex assembly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siridechadilok, Bunpote -- Fraser, Christopher S -- Hall, Richard J -- Doudna, Jennifer A -- Nogales, Eva -- New York, N.Y. -- Science. 2005 Dec 2;310(5753):1513-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16322461" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Eukaryotic Initiation Factor-3/chemistry/*physiology/ultrastructure ; Eukaryotic Initiation Factor-4F/metabolism ; HeLa Cells ; Hepacivirus/genetics ; Humans ; Models, Molecular ; Protein Binding ; Protein Biosynthesis/*physiology ; Protein Conformation ; RNA, Messenger/metabolism ; RNA, Viral/metabolism ; Ribosomes/metabolism ; Structure-Activity Relationship
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  • 90
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    Immunology. Insects diversify one molecule to serve two systems (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Du Pasquier, Louis -- New York, N.Y. -- Science. 2005 Sep 16;309(5742):1826-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Zoology and Evolutionary Biology, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland. dupasquier@dial.eunet.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16166509" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Animals ; Axons/physiology ; Binding Sites ; Biological Evolution ; Cell Adhesion Molecules ; Drosophila Proteins/chemistry/*genetics/*immunology/metabolism ; Drosophila melanogaster/*genetics/*immunology ; Genetic Variation ; Hemocytes/immunology/*metabolism ; Humans ; Immunity, Innate ; Immunoglobulins/chemistry ; Membrane Proteins ; Neurons/metabolism ; Protein Isoforms/chemistry/genetics/metabolism ; Proteins/genetics/physiology ; Receptors, Antigen/immunology/metabolism ; Vertebrates/physiology
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    Structure of SARS coronavirus spike receptor-binding domain complexed with receptor (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-17
    Description: The spike protein (S) of SARS coronavirus (SARS-CoV) attaches the virus to its cellular receptor, angiotensin-converting enzyme 2 (ACE2). A defined receptor-binding domain (RBD) on S mediates this interaction. The crystal structure at 2.9 angstrom resolution of the RBD bound with the peptidase domain of human ACE2 shows that the RBD presents a gently concave surface, which cradles the N-terminal lobe of the peptidase. The atomic details at the interface between the two proteins clarify the importance of residue changes that facilitate efficient cross-species infection and human-to-human transmission. The structure of the RBD suggests ways to make truncated disulfide-stabilized RBD variants for use in the design of coronavirus vaccines.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Fang -- Li, Wenhui -- Farzan, Michael -- Harrison, Stephen C -- AI061601/AI/NIAID NIH HHS/ -- CA13202/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2005 Sep 16;309(5742):1864-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and 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/16166518" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Antibodies, Viral/immunology ; Binding Sites ; Carboxypeptidases/*chemistry/metabolism ; Cell Line ; Crystallography, X-Ray ; Disease Outbreaks ; Epitopes ; Glycosylation ; Humans ; Hydrophobic and Hydrophilic Interactions ; Membrane Glycoproteins/*chemistry/genetics/immunology/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Peptidyl-Dipeptidase A ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Virus/*chemistry/metabolism ; SARS Virus/*chemistry/genetics/physiology ; Severe Acute Respiratory Syndrome/transmission/*virology ; Species Specificity ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins/*chemistry/genetics/immunology/*metabolism ; Viral Vaccines ; Viverridae/virology
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    Structural insights into the activity of enhancer-binding proteins (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-03-26
    Description: Activators of bacterial sigma54-RNA polymerase holoenzyme are mechanochemical proteins that use adenosine triphosphate (ATP) hydrolysis to activate transcription. We have determined by cryogenic electron microscopy (cryo-EM) a 20 angstrom resolution structure of an activator, phage shock protein F [PspF(1-275)], which is bound to an ATP transition state analog in complex with its basal factor, sigma54. By fitting the crystal structure of PspF(1-275) at 1.75 angstroms into the EM map, we identified two loops involved in binding sigma54. Comparing enhancer-binding structures in different nucleotide states and mutational analysis led us to propose nucleotide-dependent conformational changes that free the loops for association with sigma54.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756573/" 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/PMC2756573/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rappas, Mathieu -- Schumacher, Jorg -- Beuron, Fabienne -- Niwa, Hajime -- Bordes, Patricia -- Wigneshweraraj, Sivaramesh -- Keetch, Catherine A -- Robinson, Carol V -- Buck, Martin -- Zhang, Xiaodong -- B17129/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2005 Mar 25;307(5717):1972-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Imperial College London, London, SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15790859" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/chemistry/metabolism ; Binding Sites ; Cryoelectron Microscopy ; Crystallography, X-Ray ; DNA-Binding Proteins/chemistry/metabolism ; DNA-Directed RNA Polymerases/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; PII Nitrogen Regulatory Proteins ; *Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Polymerase Sigma 54 ; Sigma Factor/chemistry/metabolism ; Trans-Activators/*chemistry/*metabolism ; Transcription Factors/chemistry/metabolism
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    Disulfide isomerization after membrane release of its SAR domain activates P1 lysozyme (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-01-08
    Description: The P1 lysozyme Lyz is secreted to the periplasm of Escherichia coli and accumulates in an inactive membrane-tethered form. Genetic and biochemical experiments show that, when released from the bilayer, Lyz is activated by an intramolecular thiol-disulfide isomerization, which requires a cysteine in its N-terminal SAR (signal-arrest-release) domain. Crystal structures confirm the alternative disulfide linkages in the two forms of Lyz and reveal dramatic conformational differences in the catalytic domain. Thus, the exported P1 endolysin is kept inactive by three levels of control-topological, conformational, and covalent-until its release from the membrane is triggered by the P1 holin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Min -- Arulandu, Arockiasamy -- Struck, Douglas K -- Swanson, Stephanie -- Sacchettini, James C -- Young, Ry -- GM27099/GM/NIGMS NIH HHS/ -- GM62410/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Jan 7;307(5706):113-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15637279" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteriophage P1/*enzymology ; Binding Sites ; Catalytic Domain ; Cell Membrane/enzymology ; Chemistry, Physical ; Crystallography, X-Ray ; Cysteine/chemistry ; Enzyme Activation ; Escherichia coli/enzymology/virology ; Isomerism ; Lipid Bilayers ; Models, Molecular ; Molecular Sequence Data ; Muramidase/*chemistry/genetics/*metabolism ; Mutation ; Physicochemical Phenomena ; Protein Conformation ; Protein Sorting Signals ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism
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    Ribo-gnome: the big world of small RNAs (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-09-06
    Description: Small RNA guides--microRNAs, small interfering RNAs, and repeat-associated small interfering RNAs, 21 to 30 nucleotides in length--shape diverse cellular pathways, from chromosome architecture to stem cell maintenance. Fifteen years after the discovery of RNA silencing, we are only just beginning to understand the depth and complexity of how these RNAs regulate gene expression and to consider their role in shaping the evolutionary history of higher eukaryotes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zamore, Phillip D -- Haley, Benjamin -- GM62862-01/GM/NIGMS NIH HHS/ -- GM65236-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Sep 2;309(5740):1519-24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA. phillip.zamore@umassmed.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16141061" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Nucleus/genetics ; History, 20th Century ; Humans ; MicroRNAs/chemistry/history/*physiology ; Models, Genetic ; Molecular Biology/history ; *RNA Interference ; RNA, Messenger/chemistry/metabolism ; RNA, Small Interfering/chemistry/history/*physiology ; Stem Cells/cytology
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  • 95
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    Crystal structure of human toll-like receptor 3 (TLR3) ectodomain (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-06-18
    Description: Toll-like receptors (TLRs) play key roles in activating immune responses during infection. The human TLR3 ectodomain structure at 2.1 angstroms reveals a large horseshoe-shaped solenoid assembled from 23 leucine-rich repeats (LRRs). Asparagines conserved in the 24-residue LRR motif contribute extensive hydrogen-bonding networks for solenoid stabilization. TLR3 is largely masked by carbohydrate, but one face is glycosylation-free, which suggests its potential role in ligand binding and oligomerization. Highly conserved surface residues and a TLR3-specific LRR insertion form a homodimer interface in the crystal, whereas two patches of positively charged residues and a second insertion would provide an appropriate binding site for double-stranded RNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choe, Jungwoo -- Kelker, Matthew S -- Wilson, Ian A -- AI-42266/AI/NIAID NIH HHS/ -- CA-58896/CA/NCI NIH HHS/ -- T32 AI077606/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2005 Jul 22;309(5734):581-5. Epub 2005 Jun 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, 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/15961631" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Glycosylation ; Humans ; Hydrogen Bonding ; Leucine/chemistry ; Ligands ; Membrane Glycoproteins/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Double-Stranded/metabolism ; Receptors, Cell Surface/*chemistry/metabolism ; Repetitive Sequences, Amino Acid ; Signal Transduction ; Static Electricity ; Surface Properties ; Toll-Like Receptor 3 ; Toll-Like Receptors
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    The floral regulator LEAFY evolves by substitutions in the DNA binding domain (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-04-12
    Description: The plant-specific transcription factor LEAFY controls general aspects of the life cycle in a basal plant, the moss Physcomitrella patens. In contrast, LEAFY has more specialized functions in angiosperms, where it specifically induces floral fate during the reproductive phase. This raises the question of a concomitant change in the biochemical function of LEAFY during the evolution of land plants. We report that the DNA binding domain of LEAFY, although largely conserved, has diverged in activity. On the contrary, other, more rapidly evolving portions of the protein have few effects on LEAFY activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maizel, Alexis -- Busch, Maximilian A -- Tanahashi, Takako -- Perkovic, Josip -- Kato, Masahiro -- Hasebe, Mitsuyasu -- Weigel, Detlef -- New York, N.Y. -- Science. 2005 Apr 8;308(5719):260-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tubingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15821093" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; DNA, Plant/metabolism ; *Evolution, Molecular ; Flowers/*growth & development ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Plants/genetics ; Transcription Factors/*genetics/metabolism
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    Human Mpp11 J protein: ribosome-tethered molecular chaperones are ubiquitous (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-04-02
    Description: The existence of specialized molecular chaperones that interact directly with ribosomes is well established in microorganisms. Such proteins bind polypeptides exiting the ribosomal tunnel and provide a physical link between translation and protein folding. We report that ribosome-associated molecular chaperones have been maintained throughout eukaryotic evolution, as illustrated by Mpp11, the human ortholog of the yeast ribosome-associated J protein Zuo. When expressed in yeast, Mpp11 partially substituted for Zuo by partnering with the multipurpose Hsp70 Ssa, the homolog of mammalian Hsc70. We propose that in metazoans, ribosome-associated Mpp11 recruits the multifunctional soluble Hsc70 to nascent polypeptide chains as they exit the ribosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hundley, Heather A -- Walter, William -- Bairstow, Shawn -- Craig, Elizabeth A -- R01GM031107/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 May 13;308(5724):1032-4. Epub 2005 Mar 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, 433 Babcock Drive, University of Wisconsin-Madison, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15802566" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Amino Acid Substitution ; Binding Sites ; Cell Line ; DNA-Binding Proteins/chemistry/*metabolism ; HSC70 Heat-Shock Proteins ; HSP70 Heat-Shock Proteins/metabolism ; Humans ; Molecular Chaperones/chemistry/*metabolism ; Oncogene Proteins/chemistry/*metabolism ; Potassium Chloride/pharmacology ; Protein Structure, Tertiary ; Ribosomes/*metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism
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    A homolog of Drosophila grainy head is essential for epidermal integrity in mice (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-04-16
    Description: The Drosophila cuticle is essential for maintaining the surface barrier defenses of the fly. Integral to cuticle resilience is the transcription factor grainy head, which regulates production of the enzyme required for covalent cross-linking of the cuticular structural components. We report that formation and maintenance of the epidermal barrier in mice are dependent on a mammalian homolog of grainy head, Grainy head-like 3. Mice lacking this factor display defective skin barrier function and deficient wound repair, accompanied by reduced expression of transglutaminase 1, the key enzyme involved in cross-linking the structural components of the superficial epidermis. These findings suggest that the functional mechanisms involving protein cross-linking that maintain the epidermal barrier and induce tissue repair are conserved across 700 million years of evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ting, Stephen B -- Caddy, Jacinta -- Hislop, Nikki -- Wilanowski, Tomasz -- Auden, Alana -- Zhao, Lin-Lin -- Ellis, Sarah -- Kaur, Pritinder -- Uchida, Yoshikazu -- Holleran, Walter M -- Elias, Peter M -- Cunningham, John M -- Jane, Stephen M -- P01 HL53749-03/HL/NHLBI NIH HHS/ -- P01-AR39448/AR/NIAMS NIH HHS/ -- P30 CA 21765/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2005 Apr 15;308(5720):411-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rotary Bone Marrow Research Laboratories, c/o Royal Melbourne Hospital Post Office, Grattan Street, Parkville, Victoria, Australia 3050.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15831758" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Biological Evolution ; DNA-Binding Proteins/*genetics/metabolism/*physiology ; Embryo, Mammalian/physiology ; Embryonic Development ; Epidermis/*embryology/*physiology ; Epithelium/physiology ; Gene Expression ; Kruppel-Like Transcription Factors ; Mice ; Mutation ; Permeability ; Transcription Factors/*genetics/metabolism/*physiology ; Transglutaminases/genetics/metabolism ; Wound Healing/*physiology
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  • 99
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    Structures of the bacterial ribosome at 3.5 A resolution (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-11-08
    Description: We describe two structures of the intact bacterial ribosome from Escherichia coli determined to a resolution of 3.5 angstroms by x-ray crystallography. These structures provide a detailed view of the interface between the small and large ribosomal subunits and the conformation of the peptidyl transferase center in the context of the intact ribosome. Differences between the two ribosomes reveal a high degree of flexibility between the head and the rest of the small subunit. Swiveling of the head of the small subunit observed in the present structures, coupled to the ratchet-like motion of the two subunits observed previously, suggests a mechanism for the final movements of messenger RNA (mRNA) and transfer RNAs (tRNAs) during translocation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schuwirth, Barbara S -- Borovinskaya, Maria A -- Hau, Cathy W -- Zhang, Wen -- Vila-Sanjurjo, Anton -- Holton, James M -- Cate, Jamie H Doudna -- CA92584/CA/NCI NIH HHS/ -- GM65050/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Nov 4;310(5749):827-34.〈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/16272117" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/*ultrastructure ; Escherichia coli Proteins/biosynthesis/chemistry ; Hydrogen Bonding ; Magnesium/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Peptidyl Transferases/chemistry ; Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Ribosomal/*chemistry ; RNA, Transfer/chemistry/metabolism ; Ribosomal Proteins/*chemistry ; Ribosomes/*chemistry/*ultrastructure
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Computational thermostabilization of an enzyme (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-05-10
    Description: Thermostabilizing an enzyme while maintaining its activity for industrial or biomedical applications can be difficult with traditional selection methods. We describe a rapid computational approach that identified three mutations within a model enzyme that produced a 10 degrees C increase in apparent melting temperature T(m) and a 30-fold increase in half-life at 50 degrees C, with no reduction in catalytic efficiency. The effects of the mutations were synergistic, giving an increase in excess of the sum of their individual effects. The redesigned enzyme induced an increased, temperature-dependent bacterial growth rate under conditions that required its activity, thereby coupling molecular and metabolic engineering.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412875/" 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/PMC3412875/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korkegian, Aaron -- Black, Margaret E -- Baker, David -- Stoddard, Barry L -- CA85939/CA/NCI NIH HHS/ -- CA97328/CA/NCI NIH HHS/ -- GM49857/GM/NIGMS NIH HHS/ -- GM59224/GM/NIGMS NIH HHS/ -- R01 CA097328/CA/NCI NIH HHS/ -- R01 GM049857/GM/NIGMS NIH HHS/ -- T32-GM08268/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 May 6;308(5723):857-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Basic Sciences, Fred Hutchinson Cancer Research Center (FHCRC), 1100 Fairview Avenue North, Seattle, WA 98109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15879217" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Catalysis ; Circular Dichroism ; *Computer Simulation ; Crystallography, X-Ray ; Cytosine Deaminase/*chemistry/*metabolism ; Enzyme Stability ; Escherichia coli/genetics/metabolism ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Monte Carlo Method ; Mutagenesis, Site-Directed ; Point Mutation ; Protein Conformation ; Protein Denaturation ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; Software ; Temperature ; Thermodynamics ; Transformation, Genetic ; Yeasts/enzymology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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