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  • 1
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    Biochemistry. Proteins in a small world (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yeates, Todd O -- Beeby, Morgan -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1882-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA90024-1569, USA. yeates@mbi.ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185587" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Metabolic Networks and Pathways ; Mutation ; Protein Binding ; *Protein Interaction Mapping ; Proteins/*chemistry/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism
    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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  • 2
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    Use of logic relationships to decipher protein network organization (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-25
    Description: A major focus of genome research is to decipher the networks of molecular interactions that underlie cellular function. We describe a computational approach for identifying detailed relationships between proteins on the basis of genomic data. Logic analysis of phylogenetic profiles identifies triplets of proteins whose presence or absence obey certain logic relationships. For example, protein C may be present in a genome only if proteins A and B are both present. The method reveals many previously unidentified higher order relationships. These relationships illustrate the complexities that arise in cellular networks because of branching and alternate pathways, and they also facilitate assignment of cellular functions to uncharacterized proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bowers, Peter M -- Cokus, Shawn J -- Eisenberg, David -- Yeates, Todd O -- New York, N.Y. -- Science. 2004 Dec 24;306(5705):2246-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15618515" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Physiological Phenomena ; Bacterial Proteins/*analysis/chemistry/*physiology ; *Computational Biology ; *Genome ; *Genome, Bacterial ; Logic ; Movement ; Phylogeny ; Protein Array Analysis ; *Protein Interaction Mapping ; Proteins/*analysis/genetics/*physiology ; Shikimic Acid/metabolism ; Virulence
    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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  • 3
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    Protein structures forming the shell of primitive bacterial organelles (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-08-06
    Description: Bacterial microcompartments are primitive organelles composed entirely of protein subunits. Genomic sequence databases reveal the widespread occurrence of microcompartments across diverse microbes. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. We report three-dimensional crystal structures of multiple carboxysome shell proteins, revealing a hexameric unit as the basic microcompartment building block and showing how these hexamers assemble to form flat facets of the polyhedral shell. The structures suggest how molecular transport across the shell may be controlled and how structural variations might govern the assembly and architecture of these subcellular compartments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kerfeld, Cheryl A -- Sawaya, Michael R -- Tanaka, Shiho -- Nguyen, Chau V -- Phillips, Martin -- Beeby, Morgan -- Yeates, Todd O -- New York, N.Y. -- Science. 2005 Aug 5;309(5736):936-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology Institute, University of California, Los Angeles (UCLA), Box 951570, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16081736" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Organelles/*chemistry ; Protein Conformation ; Protein Structure, Tertiary ; Sequence Alignment ; Synechocystis/*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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  • 4
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    Structure and mechanisms of a protein-based organelle in Escherichia coli (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-02
    Description: Many bacterial cells contain proteinaceous microcompartments that act as simple organelles by sequestering specific metabolic processes involving volatile or toxic metabolites. Here we report the three-dimensional (3D) crystal structures, with resolutions between 1.65 and 2.5 angstroms, of the four homologous proteins (EutS, EutL, EutK, and EutM) that are thought to be the major shell constituents of a functionally complex ethanolamine utilization (Eut) microcompartment. The Eut microcompartment is used to sequester the metabolism of ethanolamine in bacteria such as Escherichia coli and Salmonella enterica. The four Eut shell proteins share an overall similar 3D fold, but they have distinguishing structural features that help explain the specific roles they play in the microcompartment. For example, EutL undergoes a conformational change that is probably involved in gating molecular transport through shell protein pores, whereas structural evidence suggests that EutK might bind a nucleic acid component. Together these structures give mechanistic insight into bacterial microcompartments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tanaka, Shiho -- Sawaya, Michael R -- Yeates, Todd O -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jan 1;327(5961):81-4. doi: 10.1126/science.1179513.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20044574" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Cell Compartmentation ; Crystallography, X-Ray ; Escherichia coli K12/*chemistry/*metabolism/ultrastructure ; Escherichia coli Proteins/*chemistry/metabolism ; Ethanolamine/*metabolism ; Metabolic Networks and Pathways ; Models, Molecular ; Molecular Sequence Data ; Polyproteins/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism
    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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