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  • Amino Acid Sequence  (89)
  • American Association for the Advancement of Science (AAAS)  (89)
  • 2005-2009  (80)
  • 1980-1984  (9)
  • 1940-1944
  • 2007  (80)
  • 1981  (9)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (89)
Years
  • 2005-2009  (80)
  • 1980-1984  (9)
  • 1940-1944
Year
  • 1
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    Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4 (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-29
    Description: The CCR5 co-receptor binds to the HIV-1 gp120 envelope glycoprotein and facilitates HIV-1 entry into cells. Its N terminus is tyrosine-sulfated, as are many antibodies that react with the co-receptor binding site on gp120. We applied nuclear magnetic resonance and crystallographic techniques to analyze the structure of the CCR5 N terminus and that of the tyrosine-sulfated antibody 412d in complex with gp120 and CD4. The conformations of tyrosine-sulfated regions of CCR5 (alpha-helix) and 412d (extended loop) are surprisingly different. Nonetheless, a critical sulfotyrosine on CCR5 and on 412d induces similar structural rearrangements in gp120. These results now provide a framework for understanding HIV-1 interactions with the CCR5 N terminus during viral entry and define a conserved site on gp120, whose recognition of sulfotyrosine engenders posttranslational mimicry by the immune system.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278242/" 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/PMC2278242/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Chih-Chin -- Lam, Son N -- Acharya, Priyamvada -- Tang, Min -- Xiang, Shi-Hua -- Hussan, Syed Shahzad-Ul -- Stanfield, Robyn L -- Robinson, James -- Sodroski, Joseph -- Wilson, Ian A -- Wyatt, Richard -- Bewley, Carole A -- Kwong, Peter D -- P30 AI060354/AI/NIAID NIH HHS/ -- U19 AI067854/AI/NIAID NIH HHS/ -- U19 AI067854-03/AI/NIAID NIH HHS/ -- Z99 AI999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 28;317(5846):1930-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, 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/17901336" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antigens, CD4/*chemistry/immunology ; Crystallography, X-Ray ; HIV Antibodies/*chemistry/immunology ; HIV Envelope Protein gp120/*chemistry/immunology/metabolism ; HIV-1/metabolism ; Humans ; Models, Molecular ; Molecular Mimicry ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Peptide Fragments/chemistry/metabolism ; Receptors, CCR5/*chemistry/metabolism ; Sulfates/metabolism ; Tyrosine/metabolism ; Virus Internalization
    Print ISSN: 0036-8075
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  • 2
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    Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-04
    Description: BtuCD is an adenosine triphosphate-binding cassette (ABC) transporter that translocates vitamin B12 from the periplasmic binding protein BtuF into the cytoplasm of Escherichia coli. The 2.6 angstrom crystal structure of a complex BtuCD-F reveals substantial conformational changes as compared with the previously reported structures of BtuCD and BtuF. The lobes of BtuF are spread apart, and B12 is displaced from the binding pocket. The transmembrane BtuC subunits reveal two distinct conformations, and the translocation pathway is closed to both sides of the membrane. Electron paramagnetic resonance spectra of spin-labeled cysteine mutants reconstituted in proteoliposomes are consistent with the conformation of BtuCD-F that was observed in the crystal structure. A comparison with BtuCD and the homologous HI1470/71 protein suggests that the structure of BtuCD-F may reflect a posttranslocation intermediate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hvorup, Rikki N -- Goetz, Birke A -- Niederer, Martina -- Hollenstein, Kaspar -- Perozo, Eduardo -- Locher, Kaspar P -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1387-90. Epub 2007 Aug 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, HPK D14.3, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17673622" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry ; Amino Acid Sequence ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Escherichia coli ; Escherichia coli Proteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Periplasmic Binding Proteins/*chemistry ; Protein Binding ; Protein Conformation ; Recombinant Fusion Proteins/chemistry
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  • 3
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    Changes in regulation of a transcription factor lead to autogamy in cultivated tomatoes (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-27
    Description: We report the cloning of Style2.1, the major quantitative trait locus responsible for a key floral attribute (style length) associated with the evolution of self-pollination in cultivated tomatoes. The gene encodes a putative transcription factor that regulates cell elongation in developing styles. The transition from cross-pollination to self-pollination was accompanied, not by a change in the STYLE2.1 protein, but rather by a mutation in the Style2.1 promoter that results in a down-regulation of Style2.1 expression during flower development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Kai-Yi -- Cong, Bin -- Wing, Rod -- Vrebalov, Julia -- Tanksley, Steven D -- New York, N.Y. -- Science. 2007 Oct 26;318(5850):643-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17962563" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Chromosome Mapping ; Cloning, Molecular ; Crosses, Genetic ; Down-Regulation ; Flowers/*anatomy & histology/genetics/growth & development ; Genes, Plant ; Genotype ; Helix-Loop-Helix Motifs ; Lycopersicon esculentum/anatomy & histology/*genetics/*physiology ; Molecular Sequence Data ; Plant Proteins/chemistry/*genetics/metabolism ; Pollen/physiology ; Promoter Regions, Genetic ; Quantitative Trait Loci ; Reproduction ; Sequence Deletion ; Transcription Factors/chemistry/*genetics/metabolism ; Transformation, Genetic
    Print ISSN: 0036-8075
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  • 4
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    Structure of Nup58/45 suggests flexible nuclear pore diameter by intermolecular sliding (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-24
    Description: The nucleoporins Nup58 and Nup45 are part of the central transport channel of the nuclear pore complex, which is thought to have a flexible diameter. In the crystal structure of an alpha-helical region of mammalian Nup58/45, we identified distinct tetramers, each consisting of two antiparallel hairpin dimers. The intradimeric interface is hydrophobic, whereas dimer-dimer association occurs through large hydrophilic residues. These residues are laterally displaced in various tetramer conformations, which suggests an intermolecular sliding by 11 angstroms. We propose that circumferential sliding plays a role in adjusting the diameter of the central transport channel.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Melcak, Ivo -- Hoelz, Andre -- Blobel, Gunter -- R01 GM111461/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Mar 23;315(5819):1729-32.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Cell Biology, 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/17379812" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Membrane Glycoproteins/chemistry ; Molecular Sequence Data ; Nuclear Pore Complex Proteins/*chemistry ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Rats ; Static Electricity
    Print ISSN: 0036-8075
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  • 5
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    Structure of fungal fatty acid synthase and implications for iterative substrate shuttling (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-14
    Description: We report crystal structures of the 2.6-megadalton alpha6beta6 heterododecameric fatty acid synthase from Thermomyces lanuginosus at 3.1 angstrom resolution. The alpha and beta polypeptide chains form the six catalytic domains required for fatty acid synthesis and numerous expansion segments responsible for extensive intersubunit connections. Detailed views of all active sites provide insights into substrate specificities and catalytic mechanisms and reveal their unique characteristics, which are due to the integration into the multienzyme. The mode of acyl carrier protein attachment in the reaction chamber, together with the spatial distribution of active sites, suggests that iterative substrate shuttling is achieved by a relatively restricted circular motion of the carrier domain in the multifunctional enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jenni, Simon -- Leibundgut, Marc -- Boehringer, Daniel -- Frick, Christian -- Mikolasek, Bohdan -- Ban, Nenad -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):254-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, 8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431175" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase/metabolism ; Acetyltransferases/metabolism ; Acyl Carrier Protein/chemistry/metabolism/ultrastructure ; Acyltransferases/metabolism ; Amino Acid Sequence ; Ascomycota/*enzymology ; Catalytic Domain ; Crystallography, X-Ray ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/metabolism ; Fatty Acid Synthases/*chemistry/metabolism ; Fungal Proteins/*chemistry/metabolism ; Hydro-Lyases/metabolism ; Models, Molecular ; Molecular Sequence Data ; NADP/chemistry ; Protein Conformation ; Protein Subunits/chemistry ; Substrate Specificity
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  • 6
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    Signals from chloroplasts converge to regulate nuclear gene expression (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-31
    Description: Plastid-to-nucleus retrograde signaling coordinates nuclear gene expression with chloroplast function and is essential for the photoautotrophic life-style of plants. Three retrograde signals have been described, but little is known of their signaling pathways. We show here that GUN1, a chloroplast-localized pentatricopeptide-repeat protein, and ABI4, an Apetala 2 (AP2)-type transcription factor, are common to all three pathways. ABI4 binds the promoter of a retrograde-regulated gene through a conserved motif found in close proximity to a light-regulatory element. We propose a model in which multiple indicators of aberrant plastid function in Arabidopsis are integrated upstream of GUN1 within plastids, which leads to ABI4-mediated repression of nuclear-encoded genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koussevitzky, Shai -- Nott, Ajit -- Mockler, Todd C -- Hong, Fangxin -- Sachetto-Martins, Gilberto -- Surpin, Marci -- Lim, Jason -- Mittler, Ron -- Chory, Joanne -- DRG-1865-05/PHS HHS/ -- F32 GM 18172/GM/NIGMS NIH HHS/ -- F32 GM 69090/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 May 4;316(5825):715-9. Epub 2007 Mar 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, 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/17395793" target="_blank"〉PubMed〈/a〉
    Keywords: Abscisic Acid ; Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Cell Nucleus/*metabolism/*microbiology ; Chloroplasts/*metabolism ; DNA, Plant/metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Electron Transport ; *Gene Expression Regulation, Plant ; Light-Harvesting Protein Complexes/genetics ; Lincomycin/pharmacology ; Models, Biological ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Plants, Genetically Modified ; Promoter Regions, Genetic ; Protoporphyrins/metabolism ; Pyridazines/pharmacology ; Signal Transduction ; Transcription Factors/*metabolism
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  • 7
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    Structure of the membrane protein FhaC: a member of the Omp85-TpsB transporter superfamily (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-19
    Description: In Gram-negative bacteria and eukaryotic organelles, beta-barrel proteins of the outer membrane protein 85-two-partner secretion B (Omp85-TpsB) superfamily are essential components of protein transport machineries. The TpsB transporter FhaC mediates the secretion of Bordetella pertussis filamentous hemagglutinin (FHA). We report the 3.15 A crystal structure of FhaC. The transporter comprises a 16-stranded beta barrel that is occluded by an N-terminal alpha helix and an extracellular loop and a periplasmic module composed of two aligned polypeptide-transport-associated (POTRA) domains. Functional data reveal that FHA binds to the POTRA 1 domain via its N-terminal domain and likely translocates the adhesin-repeated motifs in an extended hairpin conformation, with folding occurring at the cell surface. General features of the mechanism obtained here are likely to apply throughout the superfamily.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clantin, Bernard -- Delattre, Anne-Sophie -- Rucktooa, Prakash -- Saint, Nathalie -- Meli, Albano C -- Locht, Camille -- Jacob-Dubuisson, Francoise -- Villeret, Vincent -- New York, N.Y. -- Science. 2007 Aug 17;317(5840):957-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UMR8161 CNRS, Institut de Biologie de Lille, Universite de Lille 1, Universite de Lille 2, 1 rue du Prof. Calmette, F-59021 Lille cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702945" target="_blank"〉PubMed〈/a〉
    Keywords: Adhesins, Bacterial/chemistry/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/genetics/*metabolism ; Bordetella pertussis/*chemistry/metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers/chemistry/metabolism ; Membrane Transport Proteins/chemistry/metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport ; Virulence Factors, Bordetella/chemistry/*metabolism
    Print ISSN: 0036-8075
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  • 8
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    A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-15
    Description: The assimilation of carbon dioxide (CO2) into organic material is quantitatively the most important biosynthetic process. We discovered that an autotrophic member of the archaeal order Sulfolobales, Metallosphaera sedula, fixed CO2 with acetyl-coenzyme A (acetyl-CoA)/propionyl-CoA carboxylase as the key carboxylating enzyme. In this system, one acetyl-CoA and two bicarbonate molecules were reductively converted via 3-hydroxypropionate to succinyl-CoA. This intermediate was reduced to 4-hydroxybutyrate and converted into two acetyl-CoA molecules via 4-hydroxybutyryl-CoA dehydratase. The key genes of this pathway were found not only in Metallosphaera but also in Sulfolobus, Archaeoglobus, and Cenarchaeum species. Moreover, the Global Ocean Sampling database contains half as many 4-hydroxybutyryl-CoA dehydratase sequences as compared with those found for another key photosynthetic CO2-fixing enzyme, ribulose-1,5-bisphosphate carboxylase-oxygenase. This indicates the importance of this enzyme in global carbon cycling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berg, Ivan A -- Kockelkorn, Daniel -- Buckel, Wolfgang -- Fuchs, Georg -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1782-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Mikrobiologie, Fakultat Biologie, Universitat Freiburg, Schanzlestrasse 1, D-79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079405" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl Coenzyme A/metabolism ; Acetyl-CoA Carboxylase/metabolism ; Acyl Coenzyme A/metabolism ; Amino Acid Sequence ; Anaerobiosis ; Archaea/genetics/metabolism ; Autotrophic Processes ; Bicarbonates/metabolism ; Carbon Dioxide/*metabolism ; Genes, Archaeal ; Hydro-Lyases/genetics/metabolism ; Hydroxybutyrates/*metabolism ; Kinetics ; Lactic Acid/*analogs & derivatives/metabolism ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Oxidation-Reduction ; Photosynthesis ; Phylogeny ; Sulfolobaceae/genetics/*metabolism
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  • 9
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    Comment on "A G protein coupled receptor is a plasma membrane receptor for the plant hormone abscisic acid" (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-10
    Description: Liu et al. (Reports, 23 March 2007, p. 1712) reported that the Arabidopsis thaliana gene GCR2 encodes a seven-transmembrane, G protein-coupled receptor for abscisic acid. We argue that GCR2 is not likely to be a transmembrane protein nor a G protein-coupled receptor. Instead, GCR2 is most likely a plant homolog of bacterial lanthionine synthetases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnston, Christopher A -- Temple, Brenda R -- Chen, Jin-Gui -- Gao, Yajun -- Moriyama, Etsuko N -- Jones, Alan M -- Siderovski, David P -- Willard, Francis S -- New York, N.Y. -- Science. 2007 Nov 9;318(5852):914; author reply 914.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991845" target="_blank"〉PubMed〈/a〉
    Keywords: Abscisic Acid/*metabolism ; Algorithms ; Amino Acid Sequence ; Arabidopsis/chemistry/*metabolism ; Arabidopsis Proteins/*chemistry/isolation & purification/*metabolism ; GTP-Binding Protein alpha Subunits/metabolism ; Hydro-Lyases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/metabolism ; Plant Growth Regulators/*metabolism ; Protein Binding ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, G-Protein-Coupled/*chemistry/isolation & purification/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Sequence Alignment
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  • 10
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    The slit receptor EVA-1 coactivates a SAX-3/Robo mediated guidance signal in C. elegans (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-29
    Description: The SAX-3/roundabout (Robo) receptor has SLT-1/Slit-dependent and -independent functions in guiding cell and axon migrations. We identified enhancer of ventral-axon guidance defects of unc-40 mutants (EVA-1) as a Caenorhabditis elegans transmembrane receptor for SLT-1. EVA-1 has two predicted galactose-binding ectodomains, acts cell-autonomously for SLT-1/Slit-dependent axon migration functions of SAX-3/Robo, binds to SLT-1 and SAX-3, colocalizes with SAX-3 on cells, and provides cell specificity to the activation of SAX-3 signaling by SLT-1. Double mutants of eva-1 or slt-1 with sax-3 mutations suggest that SAX-3 can (when slt-1 or eva-1 function is reduced) inhibit a parallel-acting guidance mechanism, which involves UNC-40/deleted in colorectal cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fujisawa, Kazuko -- Wrana, Jeffrey L -- Culotti, Joseph G -- NS41397/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 28;317(5846):1934-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Samuel Lunenfeld Research Institute of Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17901337" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Axons/*physiology ; Caenorhabditis elegans/cytology/genetics/growth & development/*physiology ; Caenorhabditis elegans Proteins/*chemistry/genetics/*metabolism ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Line ; Cell Movement ; Cloning, Molecular ; Humans ; Molecular Sequence Data ; Mutation ; Nerve Tissue Proteins/*metabolism ; Nervous System/growth & development/metabolism ; Neurons/physiology ; Protein Structure, Tertiary ; Receptors, Immunologic/*metabolism ; Recombinant Fusion Proteins/metabolism ; Signal Transduction
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  • 11
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    RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-26
    Description: Mutations affecting the BRCT domains of the breast cancer-associated tumor suppressor BRCA1 disrupt the recruitment of this protein to DNA double-strand breaks (DSBs). The molecular structures at DSBs recognized by BRCA1 are presently unknown. We report the interaction of the BRCA1 BRCT domain with RAP80, a ubiquitin-binding protein. RAP80 targets a complex containing the BRCA1-BARD1 (BRCA1-associated ring domain protein 1) E3 ligase and the deubiquitinating enzyme (DUB) BRCC36 to MDC1-gammaH2AX-dependent lysine(6)- and lysine(63)-linked ubiquitin polymers at DSBs. These events are required for cell cycle checkpoint and repair responses to ionizing radiation, implicating ubiquitin chain recognition and turnover in the BRCA1-mediated repair of DSBs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2706583/" 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/PMC2706583/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sobhian, Bijan -- Shao, Genze -- Lilli, Dana R -- Culhane, Aedin C -- Moreau, Lisa A -- Xia, Bing -- Livingston, David M -- Greenberg, Roger A -- K08 CA106597/CA/NCI NIH HHS/ -- K08 CA106597-01A2/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2007 May 25;316(5828):1198-202.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dana-Farber Cancer Institute and Department of Genetics and Department of Medicine, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17525341" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; BRCA1 Protein/*metabolism ; Binding Sites ; Carrier Proteins/*metabolism ; Cell Line ; DNA/*metabolism ; *DNA Breaks, Double-Stranded ; DNA Repair/physiology ; HeLa Cells ; Humans ; Mice ; Molecular Sequence Data ; Nuclear Proteins/*metabolism ; Nucleic Acid Conformation ; Protein Structure, Tertiary ; Tumor Suppressor Proteins/metabolism ; Ubiquitin/*metabolism ; Ubiquitin-Protein Ligases/metabolism
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  • 12
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    Functional divergence of former alleles in an ancient asexual invertebrate (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-10-13
    Description: Theory suggests it should be difficult for asexual organisms to adapt to a changing environment because genetic diversity can only arise from mutations accumulating within direct antecedents and not through sexual exchange. In an asexual microinvertebrate, the bdelloid rotifer, we have observed a mechanism by which such organisms could acquire the diversity needed for adaptation. Gene copies most likely representing former alleles have diverged in function so that the proteins they encode play complementary roles in survival of dry conditions. One protein prevents desiccation-sensitive enzymes from aggregating during drying, whereas its counterpart does not have this activity, but is able to associate with phospholipid bilayers and is potentially involved in maintenance of membrane integrity. The functional divergence of former alleles observed here suggests that adoption of asexual reproduction could itself be an evolutionary mechanism for the generation of diversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pouchkina-Stantcheva, Natalia N -- McGee, Brian M -- Boschetti, Chiara -- Tolleter, Dimitri -- Chakrabortee, Sohini -- Popova, Antoaneta V -- Meersman, Filip -- Macherel, David -- Hincha, Dirk K -- Tunnacliffe, Alan -- New York, N.Y. -- Science. 2007 Oct 12;318(5848):268-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17932297" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; *Alleles ; Amino Acid Sequence ; Animals ; Biological Evolution ; Chromosomes/genetics ; DNA, Complementary ; Dehydration ; Gene Dosage ; *Genes, Helminth ; *Genetic Variation ; Helminth Proteins/chemistry/genetics/*physiology ; Lipid Bilayers ; Molecular Sequence Data ; Protein Structure, Secondary ; *Reproduction, Asexual ; Rotifera/*genetics/*physiology
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  • 13
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    Genome transplantation in bacteria: changing one species to another (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-06-30
    Description: As a step toward propagation of synthetic genomes, we completely replaced the genome of a bacterial cell with one from another species by transplanting a whole genome as naked DNA. Intact genomic DNA from Mycoplasma mycoides large colony (LC), virtually free of protein, was transplanted into Mycoplasma capricolum cells by polyethylene glycol-mediated transformation. Cells selected for tetracycline resistance, carried by the M. mycoides LC chromosome, contain the complete donor genome and are free of detectable recipient genomic sequences. These cells that result from genome transplantation are phenotypically identical to the M. mycoides LC donor strain as judged by several criteria.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lartigue, Carole -- Glass, John I -- Alperovich, Nina -- Pieper, Rembert -- Parmar, Prashanth P -- Hutchison, Clyde A 3rd -- Smith, Hamilton O -- Venter, J Craig -- New York, N.Y. -- Science. 2007 Aug 3;317(5838):632-8. Epub 2007 Jun 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉J. Craig Venter Institute, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17600181" target="_blank"〉PubMed〈/a〉
    Keywords: Acetate Kinase/chemistry/genetics ; Amino Acid Sequence ; DNA, Bacterial/*genetics/isolation & purification ; *Genome, Bacterial ; Genotype ; Molecular Sequence Data ; Mycoplasma/chemistry/*genetics ; Mycoplasma mycoides/chemistry/*genetics ; Phenotype ; Polyethylene Glycols ; Proteome/analysis ; Recombination, Genetic ; Sequence Analysis, DNA ; *Transformation, Bacterial
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  • 14
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    Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-07-14
    Description: Many human cancers involve up-regulation of the phosphoinositide 3-kinase PI3Kalpha, with oncogenic mutations identified in both the p110alpha catalytic and the p85alpha regulatory subunits. We used crystallographic and biochemical approaches to gain insight into activating mutations in two noncatalytic p110alpha domains-the adaptor-binding and the helical domains. A structure of the adaptor-binding domain of p110alpha in a complex with the p85alpha inter-Src homology 2 (inter-SH2) domain shows that oncogenic mutations in the adaptor-binding domain are not at the inter-SH2 interface but in a polar surface patch that is a plausible docking site for other domains in the holo p110/p85 complex. We also examined helical domain mutations and found that the Glu545 to Lys545 (E545K) oncogenic mutant disrupts an inhibitory charge-charge interaction with the p85 N-terminal SH2 domain. These studies extend our understanding of the architecture of PI3Ks and provide insight into how two classes of mutations that cause a gain in function can lead to cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miled, Nabil -- Yan, Ying -- Hon, Wai-Ching -- Perisic, Olga -- Zvelebil, Marketa -- Inbar, Yuval -- Schneidman-Duhovny, Dina -- Wolfson, Haim J -- Backer, Jonathan M -- Williams, Roger L -- GM55692/GM/NIGMS NIH HHS/ -- MC_U105184308/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 Jul 13;317(5835):239-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17626883" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; *Catalytic Domain ; Cattle ; Cell Line ; Cell Transformation, Neoplastic ; Crystallography, X-Ray ; Dimerization ; Humans ; Models, Molecular ; Molecular Sequence Data ; *Mutation ; Neoplasms/*genetics ; Phosphatidylinositol 3-Kinases/antagonists & ; inhibitors/chemistry/*genetics/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; src Homology Domains
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  • 15
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    Protein composition of catalytically active human telomerase from immortal cells (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-03-31
    Description: Telomerase is a ribonucleoprotein enzyme complex that adds 5'-TTAGGG-3' repeats onto the ends of human chromosomes, providing a telomere maintenance mechanism for approximately 90% of human cancers. We have purified human telomerase approximately 10(8)-fold, with the final elution dependent on the enzyme's ability to catalyze nucleotide addition onto a DNA oligonucleotide of telomeric sequence, thereby providing specificity for catalytically active telomerase. Mass spectrometric sequencing of the protein components and molecular size determination indicated an enzyme composition of two molecules each of telomerase reverse transcriptase, telomerase RNA, and dyskerin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, Scott B -- Graham, Mark E -- Lovrecz, George O -- Bache, Nicolai -- Robinson, Phillip J -- Reddel, Roger R -- New York, N.Y. -- Science. 2007 Mar 30;315(5820):1850-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research Unit, Children's Medical Research Institute, 214 Hawkesbury Road, Westmead NSW 2145, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17395830" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Cycle Proteins/*chemistry/isolation & purification ; Cell Line ; Cell Line, Tumor ; Centrifugation, Density Gradient ; Humans ; Molecular Sequence Data ; Molecular Weight ; Multienzyme Complexes/chemistry ; Nuclear Proteins/*chemistry/isolation & purification ; RNA/*chemistry/isolation & purification ; Tandem Mass Spectrometry ; Telomerase/*chemistry/isolation & purification/metabolism
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  • 16
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    PDZ domain binding selectivity is optimized across the mouse proteome (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-07-21
    Description: PDZ domains have long been thought to cluster into discrete functional classes defined by their peptide-binding preferences. We used protein microarrays and quantitative fluorescence polarization to characterize the binding selectivity of 157 mouse PDZ domains with respect to 217 genome-encoded peptides. We then trained a multidomain selectivity model to predict PDZ domain-peptide interactions across the mouse proteome with an accuracy that exceeds many large-scale, experimental investigations of protein-protein interactions. Contrary to the current paradigm, PDZ domains do not fall into discrete classes; instead, they are evenly distributed throughout selectivity space, which suggests that they have been optimized across the proteome to minimize cross-reactivity. We predict that focusing on families of interaction domains, which facilitates the integration of experimentation and modeling, will play an increasingly important role in future investigations of protein function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674608/" 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/PMC2674608/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stiffler, Michael A -- Chen, Jiunn R -- Grantcharova, Viara P -- Lei, Ying -- Fuchs, Daniel -- Allen, John E -- Zaslavskaia, Lioudmila A -- MacBeath, Gavin -- 1 RO1 GM072872-01/GM/NIGMS NIH HHS/ -- 5 T32 GM07598-25/GM/NIGMS NIH HHS/ -- R01 GM072872/GM/NIGMS NIH HHS/ -- R01 GM072872-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Jul 20;317(5836):364-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17641200" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Animals ; Computational Biology ; Computer Simulation ; Fluorescence Polarization ; Mice ; Peptides/*metabolism ; Protein Array Analysis ; Protein Binding ; *Protein Structure, Tertiary ; Proteome/chemistry/*metabolism
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  • 17
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    LeuT-desipramine structure reveals how antidepressants block neurotransmitter reuptake (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-11
    Description: Tricyclic antidepressants exert their pharmacological effect-inhibiting the reuptake of serotonin, norepinephrine, and dopamine-by directly blocking neurotransmitter transporters (SERT, NET, and DAT, respectively) in the presynaptic membrane. The drug-binding site and the mechanism of this inhibition are poorly understood. We determined the crystal structure at 2.9 angstroms of the bacterial leucine transporter (LeuT), a homolog of SERT, NET, and DAT, in complex with leucine and the antidepressant desipramine. Desipramine binds at the inner end of the extracellular cavity of the transporter and is held in place by a hairpin loop and by a salt bridge. This binding site is separated from the leucine-binding site by the extracellular gate of the transporter. By directly locking the gate, desipramine prevents conformational changes and blocks substrate transport. Mutagenesis experiments on human SERT and DAT indicate that both the desipramine-binding site and its inhibition mechanism are probably conserved in the human neurotransmitter transporters.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711652/" 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/PMC3711652/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Zheng -- Zhen, Juan -- Karpowich, Nathan K -- Goetz, Regina M -- Law, Christopher J -- Reith, Maarten E A -- Wang, Da-Neng -- DA013261/DA/NIDA NIH HHS/ -- DA019676/DA/NIDA NIH HHS/ -- GM075026/GM/NIGMS NIH HHS/ -- GM075936/GM/NIGMS NIH HHS/ -- R01 DA013261/DA/NIDA NIH HHS/ -- R01 DA019676/DA/NIDA NIH HHS/ -- R01 DK053973/DK/NIDDK NIH HHS/ -- R21 DK060841/DK/NIDDK NIH HHS/ -- R21 GM075936/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM095315/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1390-3. Epub 2007 Aug 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17690258" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antidepressive Agents, Tricyclic/chemistry/*metabolism ; Bacterial Proteins/chemistry/*metabolism ; Binding Sites ; Caenorhabditis elegans Proteins/chemistry/metabolism ; Cell Line ; Conserved Sequence ; Crystallography, X-Ray ; Desipramine/chemistry/*metabolism ; Dopamine/chemistry/metabolism ; Dopamine Uptake Inhibitors/chemistry/metabolism ; Drosophila Proteins/chemistry/metabolism ; Humans ; Leucine/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Neurotransmitter Uptake Inhibitors/chemistry/*metabolism ; Norepinephrine/chemistry/metabolism ; Norepinephrine Plasma Membrane Transport Proteins/antagonists & ; inhibitors/chemistry/metabolism ; Plasma Membrane Neurotransmitter Transport Proteins/chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Sequence Homology, Amino Acid ; Serotonin/chemistry/metabolism ; Serotonin Uptake Inhibitors/chemistry/metabolism
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    Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-12-08
    Description: Many bacterial pathogens have long, slender pili through which they adhere to host cells. The crystal structure of the major pilin subunit from the Gram-positive human pathogen Streptococcus pyogenes at 2.2 angstroms resolution reveals an extended structure comprising two all-beta domains. The molecules associate in columns through the crystal, with each carboxyl terminus adjacent to a conserved lysine of the next molecule. This lysine forms the isopeptide bonds that link the subunits in native pili, validating the relevance of the crystal assembly. Each subunit contains two lysine-asparagine isopeptide bonds generated by an intramolecular reaction, and we find evidence for similar isopeptide bonds in other cell surface proteins of Gram-positive bacteria. The present structure explains the strength and stability of such Gram-positive pili and could facilitate vaccine development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, Hae Joo -- Coulibaly, Fasseli -- Clow, Fiona -- Proft, Thomas -- Baker, Edward N -- New York, N.Y. -- Science. 2007 Dec 7;318(5856):1625-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18063798" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Asparagine/chemistry ; Chemistry, Physical ; Crystallography, X-Ray ; Fimbriae Proteins/*chemistry ; Fimbriae, Bacterial/*chemistry/ultrastructure ; Hydrogen Bonding ; Lysine/chemistry ; Models, Molecular ; Molecular Sequence Data ; Peptides/chemistry ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Streptococcus pyogenes/*chemistry/metabolism/*ultrastructure
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  • 19
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    A membrane receptor for retinol binding protein mediates cellular uptake of vitamin A (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-01-27
    Description: Vitamin A has diverse biological functions. It is transported in the blood as a complex with retinol binding protein (RBP), but the molecular mechanism by which vitamin A is absorbed by cells from the vitamin A-RBP complex is not clearly understood. We identified in bovine retinal pigment epithelium cells STRA6, a multitransmembrane domain protein, as a specific membrane receptor for RBP. STRA6 binds to RBP with high affinity and has robust vitamin A uptake activity from the vitamin A-RBP complex. It is widely expressed in embryonic development and in adult organ systems. The RBP receptor represents a major physiological mediator of cellular vitamin A uptake.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kawaguchi, Riki -- Yu, Jiamei -- Honda, Jane -- Hu, Jane -- Whitelegge, Julian -- Ping, Peipei -- Wiita, Patrick -- Bok, Dean -- Sun, Hui -- 5T32EY07026/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2007 Feb 9;315(5813):820-5. Epub 2007 Jan 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, David Geffen School of Medicine at UCLA, 650 Charles E. Young Drive South, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17255476" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/metabolism ; Amino Acid Sequence ; Animals ; Blood-Retinal Barrier ; COS Cells ; Cattle ; Cell Line ; Cell Line, Tumor ; Cell Membrane/metabolism ; Cercopithecus aethiops ; Embryonic Development ; Endocytosis ; Humans ; Molecular Sequence Data ; Mutation, Missense ; Pigment Epithelium of Eye/*metabolism ; Placenta/metabolism ; Receptors, Cell Surface/*metabolism ; Retinal Vessels/metabolism ; Retinol-Binding Proteins/*metabolism ; Spleen/metabolism ; Transfection ; Vitamin A/*metabolism
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    A bacterial effector acts as a plant transcription factor and induces a cell size regulator (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-10-27
    Description: Pathogenicity of many Gram-negative bacteria relies on the injection of effector proteins by type III secretion into eukaryotic cells, where they modulate host signaling pathways to the pathogen's benefit. One such effector protein injected by Xanthomonas into plants is AvrBs3, which localizes to the plant cell nucleus and causes hypertrophy of plant mesophyll cells. We show that AvrBs3 induces the expression of a master regulator of cell size, upa20, which encodes a transcription factor containing a basic helix-loop-helix domain. AvrBs3 binds to a conserved element in the upa20 promoter via its central repeat region and induces gene expression through its activation domain. Thus, AvrBs3 and likely other members of this family provoke developmental reprogramming of host cells by mimicking eukaryotic transcription factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kay, Sabine -- Hahn, Simone -- Marois, Eric -- Hause, Gerd -- Bonas, Ulla -- New York, N.Y. -- Science. 2007 Oct 26;318(5850):648-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biology, Department of Genetics, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, D-06120 Halle (Saale), Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17962565" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/*physiology ; Basic Helix-Loop-Helix Transcription Factors/chemistry/genetics/*physiology ; Capsicum/cytology/*genetics/*microbiology ; Cell Enlargement ; Cell Size ; Chromatin Immunoprecipitation ; Gene Expression Regulation, Plant ; Gene Silencing ; Molecular Sequence Data ; Plant Leaves/cytology/genetics/metabolism ; Plant Proteins/chemistry/genetics/metabolism/*physiology ; Promoter Regions, Genetic ; Tobacco/genetics ; Transcription, Genetic ; Xanthomonas campestris/genetics/*metabolism/pathogenicity
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  • 21
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    Structural basis for substrate delivery by acyl carrier protein in the yeast fatty acid synthase (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-14
    Description: In the multifunctional fungal fatty acid synthase (FAS), the acyl carrier protein (ACP) domain shuttles reaction intermediates covalently attached to its prosthetic phosphopantetheine group between the different enzymatic centers of the reaction cycle. Here, we report the structure of the Saccharomyces cerevisiae FAS determined at 3.1 angstrom resolution with its ACP stalled at the active site of ketoacyl synthase. The ACP contacts the base of the reaction chamber through conserved, charge-complementary surfaces, which optimally position the ACP toward the catalytic cleft of ketoacyl synthase. The conformation of the prosthetic group suggests a switchblade mechanism for acyl chain delivery to the active site of the enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leibundgut, Marc -- Jenni, Simon -- Frick, Christian -- Ban, Nenad -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):288-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, 8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431182" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Carrier Protein/*chemistry/metabolism ; Acyltransferases/metabolism ; Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Fatty Acid Synthases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/*chemistry/metabolism
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    Conformational switching in the fungal light sensor Vivid (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-19
    Description: The Neurospora crassa photoreceptor Vivid tunes blue-light responses and modulates gating of the circadian clock. Crystal structures of dark-state and light-state Vivid reveal a light, oxygen, or voltage Per-Arnt-Sim domain with an unusual N-terminal cap region and a loop insertion that accommodates the flavin cofactor. Photoinduced formation of a cystein-flavin adduct drives flavin protonation to induce an N-terminal conformational change. A cysteine-to-serine substitution remote from the flavin adenine dinucleotide binding site decouples conformational switching from the flavin photocycle and prevents Vivid from sending signals in Neurospora. Key elements of this activation mechanism are conserved by other photosensors such as White Collar-1, ZEITLUPE, ENVOY, and flavin-binding, kelch repeat, F-BOX 1 (FKF1).〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682417/" 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/PMC3682417/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zoltowski, Brian D -- Schwerdtfeger, Carsten -- Widom, Joanne -- Loros, Jennifer J -- Bilwes, Alexandrine M -- Dunlap, Jay C -- Crane, Brian R -- GM079879-01/GM/NIGMS NIH HHS/ -- MH44651/MH/NIMH NIH HHS/ -- P01 GM068087/GM/NIGMS NIH HHS/ -- R01 GM034985/GM/NIGMS NIH HHS/ -- R01 GM034985-24/GM/NIGMS NIH HHS/ -- R37GM34985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 May 18;316(5827):1054-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17510367" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Amino Acid Sequence ; Amino Acid Substitution ; Binding Sites ; Crystallography, X-Ray ; Darkness ; Dimerization ; Flavin-Adenine Dinucleotide/chemistry ; Fungal Proteins/*chemistry/genetics/metabolism ; Light ; Molecular Sequence Data ; Mutagenesis ; Neurospora crassa/*chemistry ; Protein Conformation ; Protein Structure, Tertiary
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    DUBA: a deubiquitinase that regulates type I interferon production (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-10
    Description: Production of type I interferon (IFN-I) is a critical host defense triggered by pattern-recognition receptors (PRRs) of the innate immune system. Deubiquitinating enzyme A (DUBA), an ovarian tumor domain-containing deubiquitinating enzyme, was discovered in a small interfering RNA-based screen as a regulator of IFN-I production. Reduction of DUBA augmented the PRR-induced IFN-I response, whereas ectopic expression of DUBA had the converse effect. DUBA bound tumor necrosis factor receptor-associated factor 3 (TRAF3), an adaptor protein essential for the IFN-I response. TRAF3 is an E3 ubiquitin ligase that preferentially assembled lysine-63-linked polyubiquitin chains. DUBA selectively cleaved the lysine-63-linked polyubiquitin chains on TRAF3, resulting in its dissociation from the downstream signaling complex containing TANK-binding kinase 1. A discrete ubiquitin interaction motif within DUBA was required for efficient deubiquitination of TRAF3 and optimal suppression of IFN-I. Our data identify DUBA as a negative regulator of innate immune responses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kayagaki, Nobuhiko -- Phung, Qui -- Chan, Salina -- Chaudhari, Ruchir -- Quan, Casey -- O'Rourke, Karen M -- Eby, Michael -- Pietras, Eric -- Cheng, Genhong -- Bazan, J Fernando -- Zhang, Zemin -- Arnott, David -- Dixit, Vishva M -- New York, N.Y. -- Science. 2007 Dec 7;318(5856):1628-32. Epub 2007 Nov 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991829" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cell Line ; Endopeptidases/*metabolism ; Humans ; Interferon Type I/*biosynthesis/genetics ; Interferon-alpha/genetics ; Molecular Sequence Data ; NF-kappa B/metabolism ; Protein Structure, Tertiary ; RNA, Small Interfering ; Signal Transduction ; TNF Receptor-Associated Factor 3/metabolism ; Toll-Like Receptor 3/metabolism ; Ubiquitin/metabolism ; Ubiquitination
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  • 24
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    The after-hours mutant reveals a role for Fbxl3 in determining mammalian circadian period (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-28
    Description: By screening N-ethyl-N-nitrosourea-mutagenized animals for alterations in rhythms of wheel-running activity, we identified a mouse mutation, after hours (Afh). The mutation, a Cys(358)Ser substitution in Fbxl3, an F-box protein with leucine-rich repeats, results in long free-running rhythms of about 27 hours in homozygotes. Circadian transcriptional and translational oscillations are attenuated in Afh mice. The Afh allele significantly affected Per2 expression and delayed the rate of Cry protein degradation in Per2::Luciferase tissue slices. Our in vivo and in vitro studies reveal a central role for Fbxl3 in mammalian circadian timekeeping.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Godinho, Sofia I H -- Maywood, Elizabeth S -- Shaw, Linda -- Tucci, Valter -- Barnard, Alun R -- Busino, Luca -- Pagano, Michele -- Kendall, Rachel -- Quwailid, Mohamed M -- Romero, M Rosario -- O'neill, John -- Chesham, Johanna E -- Brooker, Debra -- Lalanne, Zuzanna -- Hastings, Michael H -- Nolan, Patrick M -- MC_U105170643/Medical Research Council/United Kingdom -- MC_U142684172/Medical Research Council/United Kingdom -- MC_U142684173/Medical Research Council/United Kingdom -- MC_U142684175/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 May 11;316(5826):897-900. Epub 2007 Apr 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17463252" target="_blank"〉PubMed〈/a〉
    Keywords: ARNTL Transcription Factors ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Basic Helix-Loop-Helix Transcription Factors/genetics/metabolism ; CLOCK Proteins ; COS Cells ; Cell Cycle Proteins/genetics/metabolism ; Cercopithecus aethiops ; *Circadian Rhythm/genetics ; Crosses, Genetic ; Cryptochromes ; F-Box Proteins/*genetics/*physiology ; Female ; Flavoproteins/genetics/metabolism ; Gene Expression Regulation ; Liver/metabolism ; Lung/metabolism ; Male ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C3H ; Molecular Sequence Data ; Nuclear Proteins/genetics/metabolism ; Period Circadian Proteins ; *Point Mutation ; Suprachiasmatic Nucleus/metabolism ; Trans-Activators/genetics/metabolism ; Transcription Factors/genetics/metabolism ; Transcription, Genetic
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    Structural insight into the transglycosylation step of bacterial cell-wall biosynthesis (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-10
    Description: Peptidoglycan glycosyltransferases (GTs) catalyze the polymerization step of cell-wall biosynthesis, are membrane-bound, and are highly conserved across all bacteria. Long considered the "holy grail" of antibiotic research, they represent an essential and easily accessible drug target for antibiotic-resistant bacteria, including methicillin-resistant Staphylococcus aureus. We have determined the 2.8 angstrom structure of a bifunctional cell-wall cross-linking enzyme, including its transpeptidase and GT domains, both unliganded and complexed with the substrate analog moenomycin. The peptidoglycan GTs adopt a fold distinct from those of other GT classes. The structures give insight into critical features of the catalytic mechanism and key interactions required for enzyme inhibition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lovering, Andrew L -- de Castro, Liza H -- Lim, Daniel -- Strynadka, Natalie C J -- New York, N.Y. -- Science. 2007 Mar 9;315(5817):1402-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, and Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17347437" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Aminoacyltransferases/*chemistry/metabolism ; Anti-Bacterial Agents/chemistry/metabolism ; Apoenzymes/chemistry ; Binding Sites ; Carbohydrate Conformation ; Carbohydrate Sequence ; Catalytic Domain ; Cell Wall/*metabolism ; Crystallography, X-Ray ; Enzyme Inhibitors/chemistry/metabolism/pharmacology ; Glycosylation ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/metabolism ; Oligosaccharides/chemistry/metabolism/pharmacology ; Penicillin-Binding Proteins/*chemistry/metabolism ; Peptidoglycan/*biosynthesis ; Peptidoglycan Glycosyltransferase/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Staphylococcus aureus/*enzymology/metabolism
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    Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-03
    Description: Acetylation of histone H3 lysine 56 (H3-K56) occurs in S phase, and cells lacking H3-K56 acetylation are sensitive to DNA-damaging agents. However, the histone acetyltransferase (HAT) that catalyzes global H3-K56 acetylation has not been found. Here we show that regulation of Ty1 transposition gene product 109 (Rtt109) is an H3-K56 HAT. Cells lacking Rtt109 or expressing rtt109 mutants with alterations at a conserved aspartate residue lose H3-K56 acetylation and exhibit increased sensitivity toward genotoxic agents, as well as elevated levels of spontaneous chromosome breaks. Thus, Rtt109, which shares no sequence homology with any other known HATs, is a unique HAT that acetylates H3-K56.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Han, Junhong -- Zhou, Hui -- Horazdovsky, Bruce -- Zhang, Kangling -- Xu, Rui-Ming -- Zhang, Zhiguo -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):653-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17272723" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Amino Acid Sequence ; Camptothecin/pharmacology ; Catalytic Domain ; Chromosome Breakage ; DNA Damage ; *DNA Replication ; Histone Acetyltransferases/chemistry/genetics/*metabolism ; Histones/*metabolism ; Hydroxyurea/pharmacology ; Lysine/*metabolism ; Methyl Methanesulfonate/pharmacology ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Mutagens/pharmacology ; Mutation ; Recombinant Proteins/metabolism ; S Phase ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid
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    Structure of the zinc transporter YiiP (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-25
    Description: YiiP is a membrane transporter that catalyzes Zn2+/H+ exchange across the inner membrane of Escherichia coli. Mammalian homologs of YiiP play critical roles in zinc homeostasis and cell signaling. Here, we report the x-ray structure of YiiP in complex with zinc at 3.8 angstrom resolution. YiiP is a homodimer held together in a parallel orientation through four Zn2+ ions at the interface of the cytoplasmic domains, whereas the two transmembrane domains swing out to yield a Y-shaped structure. In each protomer, the cytoplasmic domain adopts a metallochaperone-like protein fold; the transmembrane domain features a bundle of six transmembrane helices and a tetrahedral Zn2+ binding site located in a cavity that is open to both the membrane outer leaflet and the periplasm.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Min -- Fu, Dax -- R01 GM065137/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 21;317(5845):1746-8. Epub 2007 Aug 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17717154" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Escherichia coli/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Sequence Alignment ; Zinc/*chemistry/metabolism
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  • 28
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    Structure of C8alpha-MACPF reveals mechanism of membrane attack in complement immune defense (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-18
    Description: Membrane attack is important for mammalian immune defense against invading microorganisms and infected host cells. Proteins of the complement membrane attack complex (MAC) and the protein perforin share a common MACPF domain that is responsible for membrane insertion and pore formation. We determined the crystal structure of the MACPF domain of complement component C8alpha at 2.5 angstrom resolution and show that it is structurally homologous to the bacterial, pore-forming, cholesterol-dependent cytolysins. The structure displays two regions that (in the bacterial cytolysins) refold into transmembrane beta hairpins, forming the lining of a barrel pore. Local hydrophobicity explains why C8alpha is the first complement protein to insert into the membrane. The size of the MACPF domain is consistent with known C9 pore sizes. These data imply that these mammalian and bacterial cytolytic proteins share a common mechanism of membrane insertion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hadders, Michael A -- Beringer, Dennis X -- Gros, Piet -- New York, N.Y. -- Science. 2007 Sep 14;317(5844):1552-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17872444" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Membrane/immunology/metabolism ; Complement C8/*chemistry/immunology/*metabolism ; Complement Membrane Attack Complex/*chemistry/immunology/*metabolism ; Crystallography, X-Ray ; Cytotoxins/chemistry/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Membrane Glycoproteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Perforin ; Pore Forming Cytotoxic Proteins/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary
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  • 29
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    Chimeras of two isoprenoid synthases catalyze all four coupling reactions in isoprenoid biosynthesis (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-07
    Description: The carbon skeletons of over 55,000 naturally occurring isoprenoid compounds are constructed from four fundamental coupling reactions: chain elongation, cyclopropanation, branching, and cyclobutanation. Enzymes that catalyze chain elongation and cyclopropanation are well studied, whereas those that catalyze branching and cyclobutanation are unknown. We have catalyzed the four reactions with chimeric proteins generated by replacing segments of a chain-elongation enzyme with corresponding sequences from a cyclopropanation enzyme. Stereochemical and mechanistic considerations suggest that the four coupling enzymes could have evolved from a common ancestor through relatively small changes in the catalytic site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thulasiram, Hirekodathakallu V -- Erickson, Hans K -- Poulter, C Dale -- GM 21328/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Apr 6;316(5821):73-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, UT 84112, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17412950" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Artemisia/enzymology ; Catalysis ; Catalytic Domain ; Chrysanthemum cinerariifolium/enzymology ; Cyclopropanes/chemistry ; Evolution, Molecular ; Geranyltranstransferase/chemistry/genetics/*metabolism ; Kinetics ; Molecular Conformation ; Molecular Sequence Data ; Molecular Structure ; Mutagenesis, Site-Directed ; Recombinant Fusion Proteins/chemistry/metabolism ; Stereoisomerism ; Terpenes/chemistry/*metabolism
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  • 30
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    Structure of a tyrosine phosphatase adhesive interaction reveals a spacer-clamp mechanism (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-01
    Description: Cell-cell contacts are fundamental to multicellular organisms and are subject to exquisite levels of control. Human RPTPmu is a type IIB receptor protein tyrosine phosphatase that both forms an adhesive contact itself and is involved in regulating adhesion by dephosphorylating components of cadherin-catenin complexes. Here we describe a 3.1 angstrom crystal structure of the RPTPmu ectodomain that forms a homophilic trans (antiparallel) dimer with an extended and rigid architecture, matching the dimensions of adherens junctions. Cell surface expression of deletion constructs induces intercellular spacings that correlate with the ectodomain length. These data suggest that the RPTPmu ectodomain acts as a distance gauge and plays a key regulatory function, locking the phosphatase to its appropriate functional location.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aricescu, A Radu -- Siebold, Christian -- Choudhuri, Kaushik -- Chang, Veronica T -- Lu, Weixian -- Davis, Simon J -- van der Merwe, P Anton -- Jones, E Yvonne -- 081894/Wellcome Trust/United Kingdom -- G9722488/Medical Research Council/United Kingdom -- G9900061/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1217-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK Receptor Structure Research Group, University of Oxford, Henry Wellcome Building of Genomic Medicine, Division of Structural Biology, Roosevelt Drive, Oxford OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761881" target="_blank"〉PubMed〈/a〉
    Keywords: Adherens Junctions/chemistry/*physiology/ultrastructure ; Amino Acid Sequence ; Cell Adhesion ; Cell Adhesion Molecules/*chemistry/metabolism ; Cell Membrane/chemistry/enzymology ; Conserved Sequence ; Dimerization ; Fibronectins/chemistry ; Humans ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Immunoglobulins/chemistry ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Structure, Tertiary ; Protein Tyrosine Phosphatases/*chemistry/genetics/*metabolism ; Receptor-Like Protein Tyrosine Phosphatases, Class 2
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    JMJD6 is a histone arginine demethylase (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-10-20
    Description: Arginine methylation occurs on a number of proteins involved in a variety of cellular functions. Histone tails are known to be mono- and dimethylated on multiple arginine residues where they influence chromatin remodeling and gene expression. To date, no enzyme has been shown to reverse these regulatory modifications. We demonstrate that the Jumonji domain-containing 6 protein (JMJD6) is a JmjC-containing iron- and 2-oxoglutarate-dependent dioxygenase that demethylates histone H3 at arginine 2 (H3R2) and histone H4 at arginine 3 (H4R3) in both biochemical and cell-based assays. These findings may help explain the many developmental defects observed in the JMJD6(-/-) knockout mice.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Bingsheng -- Chen, Yue -- Zhao, Yingming -- Bruick, Richard K -- C06-RR15437-01/RR/NCRR NIH HHS/ -- CA107943/CA/NCI NIH HHS/ -- CA115962/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 19;318(5849):444-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17947579" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/*metabolism ; HeLa Cells ; Histones/*metabolism ; Humans ; Jumonji Domain-Containing Histone Demethylases ; Methylation ; Molecular Sequence Data ; Oxidation-Reduction ; Protein Processing, Post-Translational ; Receptors, Cell Surface/chemistry/genetics/*metabolism ; Recombinant Proteins/metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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    Ubiquitin-binding protein RAP80 mediates BRCA1-dependent DNA damage response (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-26
    Description: Mutations in the breast cancer susceptibility gene 1 (BRCA1) are associated with an increased risk of breast and ovarian cancers. BRCA1 participates in the cellular DNA damage response. We report the identification of receptor-associated protein 80 (RAP80) as a BRCA1-interacting protein in humans. RAP80 contains a tandem ubiquitin-interacting motif domain, which is required for its binding with ubiquitin in vitro and its damage-induced foci formation in vivo. Moreover, RAP80 specifically recruits BRCA1 to DNA damage sites and functions with BRCA1 in G2/M checkpoint control. Together, these results suggest the existence of a ubiquitination-dependent signaling pathway involved in the DNA damage response.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Hongtae -- Chen, Junjie -- Yu, Xiaochun -- R01CA089239/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2007 May 25;316(5828):1202-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Therapeutic Radiology, Yale University School of Medicine, Post Office Box 208040, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17525342" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; BRCA1 Protein/*metabolism ; Carrier Proteins/*metabolism ; Cell Cycle ; Cell Line, Tumor ; DNA/*metabolism/radiation effects ; *DNA Damage ; DNA Repair/*physiology ; HeLa Cells ; Humans ; Molecular Sequence Data ; Nuclear Proteins/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; RNA, Small Interfering ; Radiation, Ionizing ; Ubiquitin/*metabolism
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    Structural and regulatory genes required to make the gas dimethyl sulfide in bacteria (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-03
    Description: Dimethyl sulfide (DMS) is a key compound in global sulfur and carbon cycles. DMS oxidation products cause cloud nucleation and may affect weather and climate. DMS is generated largely by bacterial catabolism of dimethylsulfoniopropionate (DMSP), a secondary metabolite made by marine algae. We demonstrate that the bacterial gene dddD is required for this process and that its transcription is induced by the DMSP substrate. Cloned dddD from the marine bacterium Marinomonas and from two bacterial strains that associate with higher plants, the N(2)-fixing symbiont Rhizobium NGR234 and the root-colonizing Burkholderia cepacia AMMD, conferred to Escherichia coli the ability to make DMS from DMSP. The inferred enzymatic mechanism for DMS liberation involves an initial step in which DMSP is modified by addition of acyl coenzyme A, rather than the immediate release of DMS by a DMSP lyase, the previously suggested mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Todd, Jonathan D -- Rogers, Rachel -- Li, You Guo -- Wexler, Margaret -- Bond, Philip L -- Sun, Lei -- Curson, Andrew R J -- Malin, Gill -- Steinke, Michael -- Johnston, Andrew W B -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):666-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17272727" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/genetics/*metabolism ; Burkholderia cepacia/genetics/growth & development/metabolism ; Cloning, Molecular ; Coenzyme A-Transferases/genetics/*metabolism ; DNA Transposable Elements ; Escherichia coli/genetics/metabolism ; *Genes, Bacterial ; *Genes, Regulator ; Marinomonas/*genetics/growth & development/*metabolism ; Molecular Sequence Data ; Operon ; Oxidation-Reduction ; Phenotype ; Poaceae/microbiology ; Promoter Regions, Genetic ; Rhizobium/genetics/growth & development/metabolism ; Sulfides/*metabolism ; Sulfonium Compounds/metabolism ; Transformation, Bacterial
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    HIV-1 proviral DNA excision using an evolved recombinase (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-30
    Description: HIV-1 integrates into the host chromosome and persists as a provirus flanked by long terminal repeats (LTRs). To date, treatment regimens primarily target the virus enzymes or virus-cell fusion, but not the integrated provirus. We report here the substrate-linked protein evolution of a tailored recombinase that recognizes an asymmetric sequence within an HIV-1 LTR. This evolved recombinase efficiently excised integrated HIV proviral DNA from the genome of infected cells. Although a long way from use in the clinic, we speculate that this type of technology might be adapted in future antiretroviral therapies, among other possible uses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sarkar, Indrani -- Hauber, Ilona -- Hauber, Joachim -- Buchholz, Frank -- New York, N.Y. -- Science. 2007 Jun 29;316(5833):1912-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17600219" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; DNA Shuffling ; DNA, Viral/*metabolism ; *Directed Molecular Evolution ; Escherichia coli/genetics ; Gene Library ; Genome, Human ; *HIV Long Terminal Repeat ; HIV-1/*metabolism ; HeLa Cells ; Humans ; Integrases/*genetics/*metabolism ; Molecular Sequence Data ; Mutation ; Proviruses/metabolism ; Recombination, Genetic ; *Virus Integration
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    Interpreting sequences from mastodon and T. rex (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Asara, John M -- Garavelli, John S -- Slatter, David A -- Schweitzer, Mary H -- Freimark, Lisa M -- Phillips, Matthew -- Cantley, Lewis C -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1324-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17823333" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bone and Bones/chemistry ; Collagen/*chemistry ; *Dinosaurs ; *Elephants ; *Fossils ; Glycine/chemistry ; Mass Spectrometry ; Molecular Sequence Data ; Proline/chemistry ; Tandem Mass Spectrometry
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    Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-14
    Description: Fossilized bones from extinct taxa harbor the potential for obtaining protein or DNA sequences that could reveal evolutionary links to extant species. We used mass spectrometry to obtain protein sequences from bones of a 160,000- to 600,000-year-old extinct mastodon (Mammut americanum) and a 68-million-year-old dinosaur (Tyrannosaurus rex). The presence of T. rex sequences indicates that their peptide bonds were remarkably stable. Mass spectrometry can thus be used to determine unique sequences from ancient organisms from peptide fragmentation patterns, a valuable tool to study the evolution and adaptation of ancient taxa from which genomic sequences are unlikely to be obtained.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Asara, John M -- Schweitzer, Mary H -- Freimark, Lisa M -- Phillips, Matthew -- Cantley, Lewis C -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):280-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA. jasara@bidmc.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431180" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bone and Bones/*chemistry ; Collagen/chemistry ; *Dinosaurs ; *Elephants ; Evolution, Molecular ; *Fossils ; Humans ; *Mass Spectrometry ; Molecular Sequence Data ; Proteins/analysis/*chemistry ; Reptilian Proteins/analysis/*chemistry ; Sequence Alignment ; Sequence Analysis, Protein ; Struthioniformes
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    Structure and function of an essential component of the outer membrane protein assembly machine (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-19
    Description: Integral beta-barrel proteins are found in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. The machine that assembles these proteins contains an integral membrane protein, called YaeT in Escherichia coli, which has one or more polypeptide transport-associated (POTRA) domains. The crystal structure of a periplasmic fragment of YaeT reveals the POTRA domain fold and suggests a model for how POTRA domains can bind different peptide sequences, as required for a machine that handles numerous beta-barrel protein precursors. Analysis of POTRA domain deletions shows which are essential and provides a view of the spatial organization of this assembly machine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Seokhee -- Malinverni, Juliana C -- Sliz, Piotr -- Silhavy, Thomas J -- Harrison, Stephen C -- Kahne, Daniel -- GM34821/GM/NIGMS NIH HHS/ -- GM66174/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 17;317(5840):961-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702946" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/genetics/*metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Dimerization ; Escherichia coli/*chemistry/*metabolism ; Escherichia coli Proteins/*chemistry/genetics/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lipoproteins/chemistry/metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport
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    Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-01
    Description: The faithful duplication of genetic material depends on essential DNA replication initiation factors. Cellular initiators form higher-order assemblies on replication origins, using adenosine triphosphate (ATP) to locally remodel duplex DNA and facilitate proper loading of synthetic replisomal components. To better understand initiator function, we determined the 3.4 angstrom-resolution structure of an archaeal Cdc6/Orc1 heterodimer bound to origin DNA. The structure demonstrates that, in addition to conventional DNA binding elements, initiators use their AAA+ ATPase domains to recognize origin DNA. Together these interactions establish the polarity of initiator assembly on the origin and induce substantial distortions into origin DNA strands. Biochemical and comparative analyses indicate that AAA+/DNA contacts observed in the structure are dynamic and evolutionarily conserved, suggesting that the complex forms a core component of the basal initiation machinery.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dueber, Erin L Cunningham -- Corn, Jacob E -- Bell, Stephen D -- Berger, James M -- GM071747/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1210-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Miller Institute for Basic Research in Science, 2536 Channing Way 5190, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761879" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry ; Amino Acid Sequence ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; DNA, Archaeal/*chemistry/metabolism ; DNA, Single-Stranded/chemistry/metabolism ; Dimerization ; Helix-Turn-Helix Motifs ; Models, Molecular ; Nucleic Acid Conformation ; Origin Recognition Complex/*chemistry/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Replication Origin ; Sulfolobus solfataricus/*chemistry/metabolism
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    Crystal structures of the adenylate sensor from fission yeast AMP-activated protein kinase (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-10
    Description: The 5'-AMP (adenosine monophosphate)-activated protein kinase (AMPK) coordinates metabolic function with energy availability by responding to changes in intracellular ATP (adenosine triphosphate) and AMP concentrations. Here, we report crystal structures at 2.9 and 2.6 A resolution for ATP- and AMP-bound forms of a core alphabetagamma adenylate-binding domain from the fission yeast AMPK homolog. ATP and AMP bind competitively to a single site in the gamma subunit, with their respective phosphate groups positioned near function-impairing mutants. Unexpectedly, ATP binds without counterions, amplifying its electrostatic effects on a critical regulatory region where all three subunits converge.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Townley, Robert -- Shapiro, Lawrence -- New York, N.Y. -- Science. 2007 Mar 23;315(5819):1726-9. Epub 2007 Feb 8.〈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/17289942" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Binding, Competitive ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/metabolism ; Protein Kinases/*chemistry/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protein-Serine-Threonine Kinases/*chemistry/metabolism ; Schizosaccharomyces/*enzymology
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    Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-06
    Description: Telomeres, the DNA-protein complexes located at the end of linear eukaryotic chromosomes, are essential for chromosome stability. Until now, telomeres have been considered to be transcriptionally silent. We demonstrate that mammalian telomeres are transcribed into telomeric repeat-containing RNA (TERRA). TERRA molecules are heterogeneous in length, are transcribed from several subtelomeric loci toward chromosome ends, and localize to telomeres. We also show that suppressors with morphogenetic defects in genitalia (SMG) proteins, which are effectors of nonsense-mediated messenger RNA decay, are enriched at telomeres in vivo, negatively regulate TERRA association with chromatin, and protect chromosome ends from telomere loss. Thus, telomeres are actively transcribed into TERRA, and SMG factors represent a molecular link between TERRA regulation and the maintenance of telomere integrity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Azzalin, Claus M -- Reichenbach, Patrick -- Khoriauli, Lela -- Giulotto, Elena -- Lingner, Joachim -- New York, N.Y. -- Science. 2007 Nov 2;318(5851):798-801. Epub 2007 Oct 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Swiss Institute for Experimental Cancer Research (ISREC), CH-1066 Epalinges, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17916692" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Blotting, Northern ; Cells, Cultured ; Chromosomes, Human ; Chromosomes, Mammalian ; HeLa Cells ; Humans ; In Situ Hybridization, Fluorescence ; Mice ; Molecular Sequence Data ; Proteins/metabolism ; RNA/*genetics ; Repetitive Sequences, Nucleic Acid ; Telomerase/physiology ; Telomere/*genetics ; Transcription, Genetic ; Tumor Cells, Cultured
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    Beta-catenin defines head versus tail identity during planarian regeneration and homeostasis (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007
    Description: After amputation, freshwater planarians properly regenerate a head or tail from the resulting anterior or posterior wound. The mechanisms that differentiate anterior from posterior and direct the replacement of the appropriate missing body parts are unknown. We found that in the planarian Schmidtea mediterranea, RNA interference (RNAi) of beta-catenin or dishevelled causes the inappropriate regeneration of a head instead of a tail at posterior amputations. Conversely, RNAi of the beta-catenin antagonist adenomatous polyposis coli results in the regeneration of a tail at anterior wounds. In addition, the silencing of beta-catenin is sufficient to transform the tail of uncut adult animals into a head. We suggest that beta-catenin functions as a molecular switch to specify and maintain anteroposterior identity during regeneration and homeostasis in planarians.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755502/" 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/PMC2755502/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gurley, Kyle A -- Rink, Jochen C -- Sanchez Alvarado, Alejandro -- F32GM082016/GM/NIGMS NIH HHS/ -- R0-1 GM57260/GM/NIGMS NIH HHS/ -- R01 GM057260/GM/NIGMS NIH HHS/ -- R01 GM057260-08/GM/NIGMS NIH HHS/ -- T32CA093247/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2008 Jan 18;319(5861):323-7. Epub 2007 Dec 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology and Anatomy, Howard Hughes Medical Institute, University of Utah School of Medicine, 401 MREB, 20N 1900E, Salt Lake City, UT 84132, USA. sanchez@neuro.utah.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18063757" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/chemistry/genetics/physiology ; Adenomatous Polyposis Coli Protein/chemistry/physiology ; Amino Acid Sequence ; Animals ; Body Patterning ; Gene Expression Profiling ; Genes, APC ; Head ; Helminth Proteins/chemistry/genetics/physiology ; Homeostasis ; Molecular Sequence Data ; Phosphoproteins/chemistry/genetics/physiology ; Planarians/genetics/*physiology ; RNA Interference ; *Regeneration ; Signal Transduction ; Tail ; beta Catenin/chemistry/genetics/*physiology
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    The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-15
    Description: PIK3CA, one of the two most frequently mutated oncogenes in human tumors, codes for p110alpha, the catalytic subunit of a phosphatidylinositol 3-kinase, isoform alpha (PI3Kalpha, p110alpha/p85). Here, we report a 3.0 angstrom resolution structure of a complex between p110alpha and a polypeptide containing the p110alpha-binding domains of p85alpha, a protein required for its enzymatic activity. The structure shows that many of the mutations occur at residues lying at the interfaces between p110alpha and p85alpha or between the kinase domain of p110alpha and other domains within the catalytic subunit. Disruptions of these interactions are likely to affect the regulation of kinase activity by p85 or the catalytic activity of the enzyme, respectively. In addition to providing new insights about the structure of PI3Kalpha, these results suggest specific mechanisms for the effect of oncogenic mutations in p110alpha and p85alpha.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Chuan-Hsiang -- Mandelker, Diana -- Schmidt-Kittler, Oleg -- Samuels, Yardena -- Velculescu, Victor E -- Kinzler, Kenneth W -- Vogelstein, Bert -- Gabelli, Sandra B -- Amzel, L Mario -- CA 43460/CA/NCI NIH HHS/ -- GM 07184/GM/NIGMS NIH HHS/ -- GM066895/GM/NIGMS NIH HHS/ -- GM07309/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1744-8.〈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/18079394" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Molecular Sequence Data ; *Mutation ; Neoplasms/*genetics ; Phosphatidylinositol 3-Kinases/*chemistry/genetics/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/genetics/metabolism ; src Homology Domains
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    Abraxas and RAP80 form a BRCA1 protein complex required for the DNA damage response (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-26
    Description: The BRCT repeats of the breast and ovarian cancer predisposition protein BRCA1 are essential for tumor suppression. Phosphopeptide affinity proteomic analysis identified a protein, Abraxas, that directly binds the BRCA1 BRCT repeats through a phospho-Ser-X-X-Phe motif. Abraxas binds BRCA1 to the mutual exclusion of BACH1 (BRCA1-associated C-terminal helicase) and CtIP (CtBP-interacting protein), forming a third type of BRCA1 complex. Abraxas recruits the ubiquitin-interacting motif (UIM)-containing protein RAP80 to BRCA1. Both Abraxas and RAP80 were required for DNA damage resistance, G(2)-M checkpoint control, and DNA repair. RAP80 was required for optimal accumulation of BRCA1 on damaged DNA (foci) in response to ionizing radiation, and the UIM domains alone were capable of foci formation. The RAP80-Abraxas complex may help recruit BRCA1 to DNA damage sites in part through recognition of ubiquitinated proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3573690/" 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/PMC3573690/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Bin -- Matsuoka, Shuhei -- Ballif, Bryan A -- Zhang, Dong -- Smogorzewska, Agata -- Gygi, Steven P -- Elledge, Stephen J -- 1KO1, CA116275-01/CA/NCI NIH HHS/ -- 1U19A1067751/PHS HHS/ -- T32CA09216/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2007 May 25;316(5828):1194-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Center for Genetics and Genomics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17525340" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; BRCA1 Protein/*physiology ; Carrier Proteins/*physiology ; Cell Line, Tumor ; *DNA Damage ; *DNA Repair ; HeLa Cells ; Humans ; Mass Spectrometry ; Molecular Sequence Data ; Nuclear Proteins/*physiology ; Protein Binding ; Protein Structure, Tertiary
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    Structure of a site-2 protease family intramembrane metalloprotease (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-12-08
    Description: Regulated intramembrane proteolysis by members of the site-2 protease (S2P) family is an important signaling mechanism conserved from bacteria to humans. Here we report the crystal structure of the transmembrane core domain of an S2P metalloprotease from Methanocaldococcus jannaschii. The protease consists of six transmembrane segments, with the catalytic zinc atom coordinated by two histidine residues and one aspartate residue approximately 14 angstroms into the lipid membrane surface. The protease exhibits two distinct conformations in the crystals. In the closed conformation, the active site is surrounded by transmembrane helices and is impermeable to substrate peptide; water molecules gain access to zinc through a polar, central channel that opens to the cytosolic side. In the open conformation, transmembrane helices alpha1 and alpha6 separate from each other by 10 to 12 angstroms, exposing the active site to substrate entry. The structure reveals how zinc embedded in an integral membrane protein can catalyze peptide cleavage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feng, Liang -- Yan, Hanchi -- Wu, Zhuoru -- Yan, Nieng -- Wang, Zhe -- Jeffrey, Philip D -- Shi, Yigong -- New York, N.Y. -- Science. 2007 Dec 7;318(5856):1608-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18063795" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Archaeal Proteins/chemistry/metabolism ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Catalysis ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Membrane Proteins/*chemistry/metabolism ; Metalloendopeptidases/*chemistry/metabolism ; Methanococcus/*enzymology ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Water ; Zinc/chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Orchestration of the DNA-damage response by the RNF8 ubiquitin ligase (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-11-17
    Description: Cells respond to DNA double-strand breaks by recruiting factors such as the DNA-damage mediator protein MDC1, the p53-binding protein 1 (53BP1), and the breast cancer susceptibility protein BRCA1 to sites of damaged DNA. Here, we reveal that the ubiquitin ligase RNF8 mediates ubiquitin conjugation and 53BP1 and BRCA1 focal accumulation at sites of DNA lesions. Moreover, we establish that MDC1 recruits RNF8 through phosphodependent interactions between the RNF8 forkhead-associated domain and motifs in MDC1 that are phosphorylated by the DNA-damage activated protein kinase ataxia telangiectasia mutated (ATM). We also show that depletion of the E2 enzyme UBC13 impairs 53BP1 recruitment to sites of damage, which suggests that it cooperates with RNF8. Finally, we reveal that RNF8 promotes the G2/M DNA damage checkpoint and resistance to ionizing radiation. These results demonstrate how the DNA-damage response is orchestrated by ATM-dependent phosphorylation of MDC1 and RNF8-mediated ubiquitination.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430610/" 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/PMC2430610/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kolas, Nadine K -- Chapman, J Ross -- Nakada, Shinichiro -- Ylanko, Jarkko -- Chahwan, Richard -- Sweeney, Frederic D -- Panier, Stephanie -- Mendez, Megan -- Wildenhain, Jan -- Thomson, Timothy M -- Pelletier, Laurence -- Jackson, Stephen P -- Durocher, Daniel -- A5290/Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2007 Dec 7;318(5856):1637-40. Epub 2007 Nov 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto M5G1X5, Ontario, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18006705" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Ataxia Telangiectasia Mutated Proteins ; BRCA1 Protein/metabolism ; Cell Cycle Proteins/metabolism ; Cell Line, Tumor ; Cell Nucleus Structures/*genetics ; *DNA Breaks, Double-Stranded ; DNA Repair ; DNA-Binding Proteins/chemistry/*metabolism ; HeLa Cells ; Humans ; Intracellular Signaling Peptides and Proteins/metabolism ; Molecular Sequence Data ; Nuclear Proteins/chemistry/metabolism ; Phosphorylation ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/metabolism ; RNA, Small Interfering ; Trans-Activators/chemistry/metabolism ; Tumor Suppressor Proteins/metabolism ; Ubiquitin/metabolism ; Ubiquitin-Conjugating Enzymes/metabolism ; Ubiquitin-Protein Ligases/*metabolism ; Ubiquitination
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    A linear pentapeptide is a quorum-sensing factor required for mazEF-mediated cell death in Escherichia coli (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-10-27
    Description: mazEF is a toxin-antitoxin module located on many bacterial chromosomes, including those of pathogens. Here, we report that Escherichia coli mazEF-mediated cell death is a population phenomenon requiring a quorum-sensing molecule that we call the extracellular death factor (EDF). Structural analysis revealed that EDF is a linear pentapeptide, Asn-Asn-Trp-Asn-Asn. Each of the five amino acids of EDF is important for its activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kolodkin-Gal, Ilana -- Hazan, Ronen -- Gaathon, Ariel -- Carmeli, Shmuel -- Engelberg-Kulka, Hanna -- GM069509/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 26;318(5850):652-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17962566" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Apoptosis ; Aspartate-Ammonia Ligase/genetics/metabolism ; DNA-Binding Proteins/*physiology ; Endoribonucleases/*physiology ; Escherichia coli/cytology/growth & development/*physiology ; Escherichia coli Proteins/*physiology ; Microbial Viability ; Oligopeptides/chemistry/isolation & purification/*metabolism ; *Quorum Sensing
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  • 47
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    Sponge paleogenomics reveals an ancient role for carbonic anhydrase in skeletogenesis (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-06-02
    Description: Sponges (phylum Porifera) were prolific reef-building organisms during the Paleozoic and Mesozoic approximately 542 to 65 million years ago. These ancient animals inherited components of the first multicellular skeletogenic toolkit from the last common ancestor of the Metazoa. Using a paleogenomics approach, including gene- and protein-expression techniques and phylogenetic reconstruction, we show that a molecular component of this toolkit was the precursor to the alpha-carbonic anhydrases (alpha-CAs), a gene family used by extant animals in a variety of fundamental physiological processes. We used the coralline demosponge Astrosclera willeyana, a "living fossil" that has survived from the Mesozoic, to provide insight into the evolution of the ability to biocalcify, and show that the alpha-CA family expanded from a single ancestral gene through several independent gene-duplication events in sponges and eumetazoans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jackson, Daniel J -- Macis, Luciana -- Reitner, Joachim -- Degnan, Bernard M -- Worheide, Gert -- New York, N.Y. -- Science. 2007 Jun 29;316(5833):1893-5. Epub 2007 May 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Geoscience Centre Gottingen, Department of Geobiology, Goldschmidtstrasse 3, D-37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17540861" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Bicarbonates/metabolism ; *Calcification, Physiologic ; Calcium Carbonate/analysis/metabolism ; Carbonic Anhydrases/chemistry/*genetics/*metabolism ; Computational Biology ; Evolution, Molecular ; Gene Duplication ; Genes ; Genomics ; Molecular Sequence Data ; Porifera/anatomy & histology/enzymology/*genetics/*physiology ; Recombinant Proteins/chemistry/metabolism
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    An ancient mechanism controls the development of cells with a rooting function in land plants (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-06-09
    Description: Root hairs and rhizoids are cells with rooting functions in land plants. We describe two basic helix-loop-helix transcription factors that control root hair development in the sporophyte (2n) of the angiosperm Arabidopsis thaliana and rhizoid development in the gametophytes (n) of the bryophyte Physcomitrella patens. The phylogeny of land plants supports the hypothesis that early land plants were bryophyte-like and possessed a dominant gametophyte and later the sporophyte rose to dominance. If this hypothesis is correct, our data suggest that the increase in morphological complexity of the sporophyte body in the Paleozoic resulted at least in part from the recruitment of regulatory genes from gametophyte to sporophyte.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Menand, Benoit -- Yi, Keke -- Jouannic, Stefan -- Hoffmann, Laurent -- Ryan, Eoin -- Linstead, Paul -- Schaefer, Didier G -- Dolan, Liam -- BBS/E/J/0000A218/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 Jun 8;316(5830):1477-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Developmental Biology, John Innes Centre, Norwich NR47UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17556585" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/cytology/genetics/growth & development/*physiology ; Arabidopsis Proteins/genetics/*physiology ; Basic Helix-Loop-Helix Transcription Factors/genetics/*physiology ; Biological Evolution ; Bryopsida/cytology/genetics/growth & development/*physiology ; Diploidy ; Genes, Plant ; Haploidy ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plant Epidermis/cytology/physiology ; Plant Proteins/genetics/physiology ; Plant Roots/*cytology/growth & development ; Plants, Genetically Modified
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    High-throughput identification of catalytic redox-active cysteine residues (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-01-20
    Description: Cysteine (Cys) residues often play critical roles in proteins; however, identification of their specific functions has been limited to case-by-case experimental approaches. We developed a procedure for high-throughput identification of catalytic redox-active Cys in proteins by searching for sporadic selenocysteine-Cys pairs in sequence databases. This method is independent of protein family, structure, and taxon. We used it to selectively detect the majority of known proteins with redox-active Cys and to make additional predictions, one of which was verified. Rapid accumulation of sequence information from genomic and metagenomic projects should allow detection of many additional oxidoreductase families as well as identification of redox-active Cys in these proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fomenko, Dmitri E -- Xing, Weibing -- Adair, Blakely M -- Thomas, David J -- Gladyshev, Vadim N -- AG021518/AG/NIA NIH HHS/ -- GM061603/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Jan 19;315(5810):387-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17234949" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Archaeal Proteins/chemistry ; Bacterial Proteins/chemistry ; Base Sequence ; Catalysis ; Computational Biology ; Cysteine/analysis/*chemistry ; *Databases, Nucleic Acid ; *Databases, Protein ; Enzymes/*chemistry ; Eukaryotic Cells ; Evolution, Molecular ; Methyltransferases/chemistry ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/chemistry ; Proteins/*chemistry ; Selenocysteine/chemistry ; Selenoproteins/*chemistry
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  • 50
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    The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-11-10
    Description: Variants in the FTO (fat mass and obesity associated) gene are associated with increased body mass index in humans. Here, we show by bioinformatics analysis that FTO shares sequence motifs with Fe(II)- and 2-oxoglutarate-dependent oxygenases. We find that recombinant murine Fto catalyzes the Fe(II)- and 2OG-dependent demethylation of 3-methylthymine in single-stranded DNA, with concomitant production of succinate, formaldehyde, and carbon dioxide. Consistent with a potential role in nucleic acid demethylation, Fto localizes to the nucleus in transfected cells. Studies of wild-type mice indicate that Fto messenger RNA (mRNA) is most abundant in the brain, particularly in hypothalamic nuclei governing energy balance, and that Fto mRNA levels in the arcuate nucleus are regulated by feeding and fasting. Studies can now be directed toward determining the physiologically relevant FTO substrate and how nucleic acid methylation status is linked to increased fat mass.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668859/" 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/PMC2668859/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gerken, Thomas -- Girard, Christophe A -- Tung, Yi-Chun Loraine -- Webby, Celia J -- Saudek, Vladimir -- Hewitson, Kirsty S -- Yeo, Giles S H -- McDonough, Michael A -- Cunliffe, Sharon -- McNeill, Luke A -- Galvanovskis, Juris -- Rorsman, Patrik -- Robins, Peter -- Prieur, Xavier -- Coll, Anthony P -- Ma, Marcella -- Jovanovic, Zorica -- Farooqi, I Sadaf -- Sedgwick, Barbara -- Barroso, Ines -- Lindahl, Tomas -- Ponting, Chris P -- Ashcroft, Frances M -- O'Rahilly, Stephen -- Schofield, Christopher J -- 068086/Wellcome Trust/United Kingdom -- 077016/Wellcome Trust/United Kingdom -- G108/617/Medical Research Council/United Kingdom -- G9824984/Medical Research Council/United Kingdom -- MC_U137761446/Medical Research Council/United Kingdom -- U54 GM064346/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 30;318(5855):1469-72. Epub 2007 Nov 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, Oxon OX1 3TA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991826" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Brain/enzymology/metabolism ; Cell Nucleus/enzymology ; Computational Biology ; DNA/*metabolism ; DNA Methylation ; DNA, Single-Stranded/metabolism ; Eating ; Energy Metabolism ; Fasting ; Ferrous Compounds/metabolism ; Hypothalamus/enzymology/metabolism ; Ketoglutaric Acids/*metabolism ; Male ; Mice ; Mixed Function Oxygenases ; Molecular Sequence Data ; Oxo-Acid-Lyases/chemistry/*genetics/*metabolism ; RNA, Messenger/genetics/metabolism ; Recombinant Proteins/metabolism ; Succinic Acid/metabolism ; Thymine/analogs & derivatives/metabolism
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    Computational design of peptides that target transmembrane helices (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-03-31
    Description: A variety of methods exist for the design or selection of antibodies and other proteins that recognize the water-soluble regions of proteins; however, companion methods for targeting transmembrane (TM) regions are not available. Here, we describe a method for the computational design of peptides that target TM helices in a sequence-specific manner. To illustrate the method, peptides were designed that specifically recognize the TM helices of two closely related integrins (alphaIIbbeta3 and alphavbeta3) in micelles, bacterial membranes, and mammalian cells. These data show that sequence-specific recognition of helices in TM proteins can be achieved through optimization of the geometric complementarity of the target-host complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yin, Hang -- Slusky, Joanna S -- Berger, Bryan W -- Walters, Robin S -- Vilaire, Gaston -- Litvinov, Rustem I -- Lear, James D -- Caputo, Gregory A -- Bennett, Joel S -- DeGrado, William F -- 5T32 CA101968/CA/NCI NIH HHS/ -- 5T32 GM08275/GM/NIGMS NIH HHS/ -- GM54616/GM/NIGMS NIH HHS/ -- GM60610/GM/NIGMS NIH HHS/ -- HL40387/HL/NHLBI NIH HHS/ -- HL54500/HL/NHLBI NIH HHS/ -- T32 GM008275/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Mar 30;315(5820):1817-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17395823" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Motifs ; Amino Acid Sequence ; Blood Platelets/physiology ; Cell Membrane/*chemistry ; Databases, Protein ; Dimerization ; Escherichia coli/chemistry ; Fluorescence Resonance Energy Transfer ; Humans ; Integrin alphaVbeta3/*chemistry/metabolism ; Lipid Bilayers/chemistry ; Models, Molecular ; Molecular Sequence Data ; Optical Tweezers ; Osteopontin/metabolism ; Peptides/*chemistry/metabolism ; Platelet Adhesiveness ; Platelet Aggregation ; Platelet Glycoprotein GPIIb-IIIa Complex/*chemistry/metabolism ; *Protein Engineering ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Spectrum Analysis
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    Transcription. Seven ups the code (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-12-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Corden, Jeffry L -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1735-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Genetics, Johns Hopkins Medical School, Baltimore, MD 21205, USA. jcorden@jhmi.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079391" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Gene Expression Regulation ; Humans ; Mutation ; Phosphorylation ; Protein Structure, Tertiary ; RNA Polymerase II/chemistry/genetics/*metabolism ; Serine/metabolism ; Templates, Genetic ; *Transcription, Genetic
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    Emulating membrane protein evolution by rational design (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-01-27
    Description: How do integral membrane proteins evolve in size and complexity? Using the small multidrug-resistance protein EmrE from Escherichia coli as a model, we experimentally demonstrated that the evolution of membrane proteins composed of two homologous but oppositely oriented domains can occur in a small number of steps: An original dual-topology protein evolves, through a gene-duplication event, to a heterodimer formed by two oppositely oriented monomers. This simple evolutionary pathway can explain the frequent occurrence of membrane proteins with an internal pseudo-two-fold symmetry axis in the plane of the membrane.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rapp, Mikaela -- Seppala, Susanna -- Granseth, Erik -- von Heijne, Gunnar -- New York, N.Y. -- Science. 2007 Mar 2;315(5816):1282-4. Epub 2007 Jan 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17255477" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antiporters/*chemistry/genetics ; Cell Membrane/*chemistry ; Dimerization ; Directed Molecular Evolution ; Drug Resistance, Bacterial ; Escherichia coli/*chemistry/drug effects/genetics/growth & development ; Escherichia coli Proteins/*chemistry/genetics ; Ethidium/pharmacology ; *Evolution, Molecular ; Gene Duplication ; Membrane Transport Proteins/*chemistry/genetics ; Molecular Sequence Data ; Mutation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Recombinant Fusion Proteins/chemistry/metabolism
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    An X chromosome gene, WTX, is commonly inactivated in Wilms tumor (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-01-06
    Description: Wilms tumor is a pediatric kidney cancer associated with inactivation of the WT1 tumor-suppressor gene in 5 to 10% of cases. Using a high-resolution screen for DNA copy-number alterations in Wilms tumor, we identified somatic deletions targeting a previously uncharacterized gene on the X chromosome. This gene, which we call WTX, is inactivated in approximately one-third of Wilms tumors (15 of 51 tumors). Tumors with mutations in WTX lack WT1 mutations, and both genes share a restricted temporal and spatial expression pattern in normal renal precursors. In contrast to biallelic inactivation of autosomal tumor-suppressor genes, WTX is inactivated by a monoallelic "single-hit" event targeting the single X chromosome in tumors from males and the active X chromosome in tumors from females.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rivera, Miguel N -- Kim, Woo Jae -- Wells, Julie -- Driscoll, David R -- Brannigan, Brian W -- Han, Moonjoo -- Kim, James C -- Feinberg, Andrew P -- Gerald, William L -- Vargas, Sara O -- Chin, Lynda -- Iafrate, A John -- Bell, Daphne W -- Haber, Daniel A -- P01-CA101942/CA/NCI NIH HHS/ -- R37 CA054358/CA/NCI NIH HHS/ -- R37 CA054358-17/CA/NCI NIH HHS/ -- R37-CA058596/CA/NCI NIH HHS/ -- T32-CA009216/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):642-5. Epub 2007 Jan 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts General Hospital Cancer Center, Harvard Medical Center, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17204608" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing ; Alleles ; Amino Acid Sequence ; Animals ; Cell Line ; Chromosome Deletion ; Chromosomes, Human, X/*genetics ; Female ; Gene Expression ; *Gene Silencing ; *Genes, Wilms Tumor ; Heterozygote ; Humans ; In Situ Hybridization, Fluorescence ; Kidney/embryology/metabolism ; Kidney Neoplasms/*genetics ; Male ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Mutation ; Point Mutation ; Tumor Suppressor Proteins/chemistry/*genetics/physiology ; Wilms Tumor/*genetics ; beta Catenin/genetics
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    Free-solution, label-free molecular interactions studied by back-scattering interferometry (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-09-22
    Description: Free-solution, label-free molecular interactions were investigated with back-scattering interferometry in a simple optical train composed of a helium-neon laser, a microfluidic channel, and a position sensor. Molecular binding interactions between proteins, ions and protein, and small molecules and protein, were determined with high dynamic range dissociation constants (Kd spanning six decades) and unmatched sensitivity (picomolar Kd's and detection limits of 10,000s of molecules). With this technique, equilibrium dissociation constants were quantified for protein A and immunoglobulin G, interleukin-2 with its monoclonal antibody, and calmodulin with calcium ion Ca2+, a small molecule inhibitor, the protein calcineurin, and the M13 peptide. The high sensitivity of back-scattering interferometry and small volumes of microfluidics allowed the entire calmodulin assay to be performed with 200 picomoles of solute.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bornhop, Darryl J -- Latham, Joey C -- Kussrow, Amanda -- Markov, Dmitry A -- Jones, Richard D -- Sorensen, Henrik S -- R-01 EB0003537-01A2/EB/NIBIB NIH HHS/ -- T32 GM065086/GM/NIGMS NIH HHS/ -- T32-EY07135/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 21;317(5845):1732-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University, VU Station B 351822, Nashville, TN 37235-1822, USA. darryl.bornhop@vanderbilt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17885132" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Calcineurin/chemistry ; Calcium/chemistry ; Calmodulin/chemistry ; Dimethylpolysiloxanes ; Humans ; Immunoglobulin G/chemistry ; Interferometry/*methods ; Kinetics ; Molecular Sequence Data ; Myosin-Light-Chain Kinase/chemistry ; Peptide Fragments/chemistry ; *Protein Binding ; Rabbits ; Refractometry ; Silicones ; Solutions
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    Genomic minimalism in the early diverging intestinal parasite Giardia lamblia (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-29
    Description: The genome of the eukaryotic protist Giardia lamblia, an important human intestinal parasite, is compact in structure and content, contains few introns or mitochondrial relics, and has simplified machinery for DNA replication, transcription, RNA processing, and most metabolic pathways. Protein kinases comprise the single largest protein class and reflect Giardia's requirement for a complex signal transduction network for coordinating differentiation. Lateral gene transfer from bacterial and archaeal donors has shaped Giardia's genome, and previously unknown gene families, for example, cysteine-rich structural proteins, have been discovered. Unexpectedly, the genome shows little evidence of heterozygosity, supporting recent speculations that this organism is sexual. This genome sequence will not only be valuable for investigating the evolution of eukaryotes, but will also be applied to the search for new therapeutics for this parasite.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morrison, Hilary G -- McArthur, Andrew G -- Gillin, Frances D -- Aley, Stephen B -- Adam, Rodney D -- Olsen, Gary J -- Best, Aaron A -- Cande, W Zacheus -- Chen, Feng -- Cipriano, Michael J -- Davids, Barbara J -- Dawson, Scott C -- Elmendorf, Heidi G -- Hehl, Adrian B -- Holder, Michael E -- Huse, Susan M -- Kim, Ulandt U -- Lasek-Nesselquist, Erica -- Manning, Gerard -- Nigam, Anuranjini -- Nixon, Julie E J -- Palm, Daniel -- Passamaneck, Nora E -- Prabhu, Anjali -- Reich, Claudia I -- Reiner, David S -- Samuelson, John -- Svard, Staffan G -- Sogin, Mitchell L -- AI42488/AI/NIAID NIH HHS/ -- AI43273/AI/NIAID NIH HHS/ -- AI51687/AI/NIAID NIH HHS/ -- R01 AI043273/AI/NIAID NIH HHS/ -- R01 AI048082/AI/NIAID NIH HHS/ -- R01 HG004164/HG/NHGRI NIH HHS/ -- R01 HG004164-01/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 28;317(5846):1921-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Marine Biological Laboratory, Woods Hole, MA 02543-1015, USA. morrison@mbl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17901334" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; DNA Replication/genetics ; *Eukaryotic Cells ; Gene Transfer, Horizontal ; Genes, Protozoan ; *Genome, Protozoan ; Genomics ; Giardia lamblia/classification/*genetics/physiology ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Kinases/genetics/metabolism ; Protozoan Proteins/chemistry/genetics/metabolism ; RNA Processing, Post-Transcriptional ; Signal Transduction ; Transcription, Genetic
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    A conserved family of enzymes that phosphorylate inositol hexakisphosphate (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-07
    Description: Inositol pyrophosphates are a diverse group of high-energy signaling molecules whose cellular roles remain an active area of study. We report a previously uncharacterized class of inositol pyrophosphate synthase and find it is identical to yeast Vip1 and Asp1 proteins, regulators of actin-related protein-2/3 (ARP 2/3) complexes. Vip1 and Asp1 acted as enzymes that encode inositol hexakisphosphate (IP6) and inositol heptakisphosphate (IP7) kinase activities. Alterations in kinase activity led to defects in cell growth, morphology, and interactions with ARP complex members. The functionality of Asp1 and Vip1 may provide cells with increased signaling capacity through metabolism of IP6.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mulugu, Sashidhar -- Bai, Wenli -- Fridy, Peter C -- Bastidas, Robert J -- Otto, James C -- Dollins, D Eric -- Haystead, Timothy A -- Ribeiro, Anthony A -- York, John D -- 2-P30-CA14236-3/CA/NCI NIH HHS/ -- P30-CA-14236/CA/NCI NIH HHS/ -- R01-HL-55672/HL/NHLBI NIH HHS/ -- R33-DK-070272/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2007 Apr 6;316(5821):106-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Pharmacology and Cancer Biology, Duke University Medical Center, DUMC 3813, Durham, NC 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17412958" target="_blank"〉PubMed〈/a〉
    Keywords: Actin-Related Protein 3/metabolism ; Amino Acid Sequence ; Animals ; Catalytic Domain ; Chromatography, High Pressure Liquid ; Conserved Sequence ; Cytoskeletal Proteins/chemistry/genetics/isolation & purification/*metabolism ; Humans ; Inositol Phosphates/metabolism ; Molecular Sequence Data ; Phosphorylation ; Phosphotransferases (Phosphate Group Acceptor)/chemistry/genetics/isolation & ; purification/*metabolism ; Phytic Acid/*metabolism ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/isolation & purification/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/chemistry/genetics/isolation & ; purification/metabolism ; Schizosaccharomyces/cytology/*enzymology/genetics/growth & development ; Schizosaccharomyces pombe Proteins/chemistry/genetics/isolation & ; purification/*metabolism ; *Sequence Alignment ; Substrate Specificity ; Temperature
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    Regulation of CD8+ T cell development by thymus-specific proteasomes (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-06-02
    Description: Proteasomes are responsible for generating peptides presented by the class I major histocompatibility complex (MHC) molecules of the immune system. Here, we report the identification of a previously unrecognized catalytic subunit called beta5t. beta5t is expressed exclusively in cortical thymic epithelial cells, which are responsible for the positive selection of developing thymocytes. Although the chymotrypsin-like activity of proteasomes is considered to be important for the production of peptides with high affinities for MHC class I clefts, incorporation of beta5t into proteasomes in place of beta5 or beta5i selectively reduces this activity. We also found that beta5t-deficient mice displayed defective development of CD8(+) T cells in the thymus. Our results suggest a key role for beta5t in generating the MHC class I-restricted CD8(+) T cell repertoire during thymic selection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murata, Shigeo -- Sasaki, Katsuhiro -- Kishimoto, Toshihiko -- Niwa, Shin-Ichiro -- Hayashi, Hidemi -- Takahama, Yousuke -- Tanaka, Keiji -- New York, N.Y. -- Science. 2007 Jun 1;316(5829):1349-53.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Frontier Science, Core Technology and Research Center, Tokyo Metropolitan Institute of Medical Science, Bunkyo-ku, Tokyo 113-8613, Japan. smurata@rinshoken.or.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17540904" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Autoantigens/immunology/metabolism ; CD4-Positive T-Lymphocytes/cytology/immunology ; CD8-Positive T-Lymphocytes/cytology/*immunology ; Catalytic Domain ; Epithelial Cells/enzymology ; Green Fluorescent Proteins/genetics/metabolism ; Histocompatibility Antigens Class I/immunology/metabolism ; Humans ; Lymphopoiesis ; Molecular Sequence Data ; Peptides/chemistry/metabolism ; Proteasome Endopeptidase Complex/chemistry/genetics/*metabolism ; Spleen/cytology/immunology ; T-Lymphocyte Subsets/cytology/immunology ; Thymus Gland/*cytology/*enzymology/immunology
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    The phosphothreonine lyase activity of a bacterial type III effector family (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-02-17
    Description: Pathogenic bacteria use the type III secretion system to deliver effector proteins into host cells to modulate the host signaling pathways. In this study, the Shigella type III effector OspF was shown to inactivate mitogen-activated protein kinases (MAPKs) [extracellular signal-regulated kinases 1 and 2 (Erk1/2), c-Jun N-terminal kinase, and p38]. OspF irreversibly removed phosphate groups from the phosphothreonine but not from the phosphotyrosine residue in the activation loop of MAPKs. Mass spectrometry revealed a mass loss of 98 daltons in p-Erk2, due to the abstraction of the alpha proton concomitant with cleavage of the C-OP bond in the phosphothreonine residue. This unexpected enzymatic activity, termed phosphothreonine lyase, appeared specific for MAPKs and was shared by other OspF family members.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Hongtao -- Xu, Hao -- Zhou, Yan -- Zhang, Jie -- Long, Chengzu -- Li, Shuqin -- Chen, She -- Zhou, Jian-Min -- Shao, Feng -- New York, N.Y. -- Science. 2007 Feb 16;315(5814):1000-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute of Biological Sciences, Beijing, 102206, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17303758" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bacterial Proteins/genetics/*metabolism ; Cell Line ; HeLa Cells ; Humans ; JNK Mitogen-Activated Protein Kinases/antagonists & inhibitors/metabolism ; *MAP Kinase Signaling System ; Mitogen-Activated Protein Kinase 1/antagonists & inhibitors/metabolism ; Mitogen-Activated Protein Kinase 3/antagonists & inhibitors/metabolism ; Mitogen-Activated Protein Kinases/antagonists & inhibitors/*metabolism ; Molecular Sequence Data ; Mutagenesis ; NF-kappa B/metabolism ; Phosphoprotein Phosphatases/*metabolism ; Phosphorylation ; Salmonella typhimurium ; Shigella flexneri/*metabolism/physiology ; Tyrosine/metabolism ; p38 Mitogen-Activated Protein Kinases/antagonists & inhibitors/metabolism
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    Structure of the prefusion form of the vesicular stomatitis virus glycoprotein G (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-02-10
    Description: Glycoprotein G of the vesicular stomatitis virus triggers membrane fusion via a low pH-induced structural rearrangement. Despite the equilibrium between the pre- and postfusion states, the structure of the prefusion form, determined to 3.0 angstrom resolution, shows that the fusogenic transition entails an extensive structural reorganization of G. Comparison with the structure of the postfusion form suggests a pathway for the conformational change. In the prefusion form, G has the shape of a tripod with the fusion loops exposed, which point toward the viral membrane, and with the antigenic sites located at the distal end of the molecule. A large number of G glycoproteins, perhaps organized as in the crystals, act cooperatively to induce membrane merging.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roche, Stephane -- Rey, Felix A -- Gaudin, Yves -- Bressanelli, Stephane -- New York, N.Y. -- Science. 2007 Feb 9;315(5813):843-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS, Unite Mixte de Recherche (UMR) 2472, Institut National de la Recherche Agronomique (INRA), UMR 1157, Institut Federatif de Recherche 115, Laboratoire de Virologie Moleculaire et Structurale, 91198, Gif sur Yvette, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17289996" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallization ; Crystallography, X-Ray ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Membrane Fusion ; Membrane Glycoproteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Vesicular stomatitis Indiana virus/*chemistry ; Viral Envelope Proteins/*chemistry ; Viral Fusion Proteins/*chemistry
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    GE Prize-winning essay. Why Old World monkeys are resistant to HIV-1 (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-12-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stremlau, Matthew -- New York, N.Y. -- Science. 2007 Dec 7;318(5856):1565-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Global AIDS Coordinator's Office, State Department, Washington, DC 20522, USA. stremlauMH@state.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18063779" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Awards and Prizes ; Capsid/metabolism ; Carrier Proteins/chemistry/genetics/*physiology ; *Cercopithecidae ; HIV Infections/*immunology/virology ; HIV-1/*physiology ; Humans ; *Immunity, Innate ; Monkey Diseases/immunology/virology ; Protein Structure, Tertiary ; Simian Acquired Immunodeficiency Syndrome/immunology/virology ; Species Specificity ; Virus Replication ; Zinc Fingers
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    Natural selection favors a newly derived timeless allele in Drosophila melanogaster (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-06-30
    Description: Circadian and other natural clock-like endogenous rhythms may have evolved to anticipate regular temporal changes in the environment. We report that a mutation in the circadian clock gene timeless in Drosophila melanogaster has arisen and spread by natural selection relatively recently in Europe. We found that, when introduced into different genetic backgrounds, natural and artificial alleles of the timeless gene affect the incidence of diapause in response to changes in light and temperature. The natural mutant allele alters an important life history trait that may enhance the fly's adaptation to seasonal conditions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tauber, Eran -- Zordan, Mauro -- Sandrelli, Federica -- Pegoraro, Mirko -- Osterwalder, Nicolo -- Breda, Carlo -- Daga, Andrea -- Selmin, Alessandro -- Monger, Karen -- Benna, Clara -- Rosato, Ezio -- Kyriacou, Charalambos P -- Costa, Rodolfo -- New York, N.Y. -- Science. 2007 Jun 29;316(5833):1895-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, University of Leicester, Leicester LE1 7RH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17600215" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Animals ; Base Sequence ; Circadian Rhythm/genetics ; Drosophila Proteins/*genetics/physiology ; Drosophila melanogaster/*genetics/*physiology ; Europe ; Evolution, Molecular ; Female ; Geography ; Haplotypes ; Molecular Sequence Data ; Mutation ; *Photoperiod ; Phylogeny ; Polymorphism, Genetic ; Protein Isoforms/genetics/physiology ; Reproduction ; *Seasons ; *Selection, Genetic ; Temperature ; Transformation, Genetic
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    GNAT-like strategy for polyketide chain initiation (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-11-10
    Description: An unexpected biochemical strategy for chain initiation is described for the loading module of the polyketide synthase of curacin A, an anticancer lead derived from the marine cyanobacterium Lyngbya majuscula. A central GCN5-related N-acetyltransferase (GNAT) domain bears bifunctional decarboxylase/S-acetyltransferase activity, both unprecedented for the GNAT superfamily. A CurA loading tridomain, consisting of an adaptor domain, the GNAT domain, and an acyl carrier protein, was assessed biochemically, revealing that a domain showing homology to GNAT (GNAT(L)) catalyzes (i) decarboxylation of malonyl-coenzyme A (malonyl-CoA) to acetyl-CoA and (ii) direct S-acetyl transfer from acetyl-CoA to load an adjacent acyl carrier protein domain (ACP(L)). Moreover, the N-terminal adapter domain was shown to facilitate acetyl-group transfer. Crystal structures of GNAT(L) were solved at 1.95 angstroms (ligand-free form) and 2.75 angstroms (acyl-CoA complex), showing distinct substrate tunnels for acyl-CoA and holo-ACP(L) binding. Modeling and site-directed mutagenesis experiments demonstrated that histidine-389 and threonine-355, at the convergence of the CoA and ACP tunnels, participate in malonyl-CoA decarboxylation but not in acetyl-group transfer. Decarboxylation precedes acetyl-group transfer, leading to acetyl-ACP(L) as the key curacin A starter unit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gu, Liangcai -- Geders, Todd W -- Wang, Bo -- Gerwick, William H -- Hakansson, Kristina -- Smith, Janet L -- Sherman, David H -- DK42303/DK/NIDDK NIH HHS/ -- GM076477/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 9;318(5852):970-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991863" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl Coenzyme A/metabolism ; Acetyltransferases/*chemistry/*metabolism ; Acyl Carrier Protein/chemistry/metabolism ; Amino Acid Sequence ; Carboxy-Lyases/chemistry/metabolism ; Crystallography, X-Ray ; Cyanobacteria/*enzymology/genetics ; Cyclopropanes/*metabolism ; Decarboxylation ; Malonyl Coenzyme A/metabolism ; Models, Molecular ; Molecular Sequence Data ; Polyketide Synthases/*chemistry/genetics/*metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Thiazoles/*metabolism
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    Transposase-derived transcription factors regulate light signaling in Arabidopsis (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-11-24
    Description: Plants use light to optimize growth and development. The photoreceptor phytochrome A (phyA) mediates various far-red light-induced responses. We show that Arabidopsis FHY3 and FAR1, which encode two proteins related to Mutator-like transposases, act together to modulate phyA signaling by directly activating the transcription of FHY1 and FHL, whose products are essential for light-induced phyA nuclear accumulation and subsequent light responses. FHY3 and FAR1 have separable DNA binding and transcriptional activation domains that are highly conserved in Mutator-like transposases. Further, expression of FHY3 and FAR1 is negatively regulated by phyA signaling. We propose that FHY3 and FAR1 represent transcription factors that have been co-opted from an ancient Mutator-like transposase(s) to modulate phyA-signaling homeostasis in higher plants.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2151751/" 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/PMC2151751/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, Rongcheng -- Ding, Lei -- Casola, Claudio -- Ripoll, Daniel R -- Feschotte, Cedric -- Wang, Haiyang -- R01 GM077582/GM/NIGMS NIH HHS/ -- R01 GM077582-01A1/GM/NIGMS NIH HHS/ -- R01 GM77582-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 23;318(5854):1302-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Boyce Thompson Institute for Plant Research (BTI), Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18033885" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Cell Nucleus/metabolism ; Gene Expression Regulation, Plant ; *Light ; Molecular Sequence Data ; Mutation ; Nuclear Proteins/chemistry/genetics/*metabolism ; Phylogeny ; Phytochrome/chemistry/genetics/*metabolism ; Phytochrome A/metabolism ; Promoter Regions, Genetic ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; *Signal Transduction ; Transcription Factors/genetics/metabolism ; Transcriptional Activation ; Transposases/chemistry/genetics/metabolism
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    A common fold mediates vertebrate defense and bacterial attack (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-08-25
    Description: Proteins containing membrane attack complex/perforin (MACPF) domains play important roles in vertebrate immunity, embryonic development, and neural-cell migration. In vertebrates, the ninth component of complement and perforin form oligomeric pores that lyse bacteria and kill virus-infected cells, respectively. However, the mechanism of MACPF function is unknown. We determined the crystal structure of a bacterial MACPF protein, Plu-MACPF from Photorhabdus luminescens, to 2.0 angstrom resolution. The MACPF domain reveals structural similarity with poreforming cholesterol-dependent cytolysins (CDCs) from Gram-positive bacteria. This suggests that lytic MACPF proteins may use a CDC-like mechanism to form pores and disrupt cell membranes. Sequence similarity between bacterial and vertebrate MACPF domains suggests that the fold of the CDCs, a family of proteins important for bacterial pathogenesis, is probably used by vertebrates for defense against infection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosado, Carlos J -- Buckle, Ashley M -- Law, Ruby H P -- Butcher, Rebecca E -- Kan, Wan-Ting -- Bird, Catherina H -- Ung, Kheng -- Browne, Kylie A -- Baran, Katherine -- Bashtannyk-Puhalovich, Tanya A -- Faux, Noel G -- Wong, Wilson -- Porter, Corrine J -- Pike, Robert N -- Ellisdon, Andrew M -- Pearce, Mary C -- Bottomley, Stephen P -- Emsley, Jonas -- Smith, A Ian -- Rossjohn, Jamie -- Hartland, Elizabeth L -- Voskoboinik, Ilia -- Trapani, Joseph A -- Bird, Phillip I -- Dunstone, Michelle A -- Whisstock, James C -- New York, N.Y. -- Science. 2007 Sep 14;317(5844):1548-51. Epub 2007 Aug 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17717151" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bacterial Proteins/*chemistry/metabolism ; Complement Membrane Attack Complex/chemistry/metabolism ; Crystallography, X-Ray ; Cytotoxins/chemistry ; Membrane Glycoproteins/chemistry/genetics/metabolism ; Molecular Sequence Data ; Perforin ; Photorhabdus/*chemistry ; Pore Forming Cytotoxic Proteins/chemistry/genetics/metabolism ; *Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Vertebrates
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    Structure of a NHEJ polymerase-mediated DNA synaptic complex (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-20
    Description: Nonhomologous end joining (NHEJ) is a critical DNA double-strand break (DSB) repair pathway required to maintain genome stability. Many prokaryotes possess a minimalist NHEJ apparatus required to repair DSBs during stationary phase, composed of two conserved core proteins, Ku and ligase D (LigD). The crystal structure of Mycobacterium tuberculosis polymerase domain of LigD mediating the synapsis of two noncomplementary DNA ends revealed a variety of interactions, including microhomology base pairing, mismatched and flipped-out bases, and 3' termini forming hairpin-like ends. Biochemical and biophysical studies confirmed that polymerase-induced end synapsis also occurs in solution. We propose that this DNA synaptic structure reflects an intermediate bridging stage of the NHEJ process, before end processing and ligation, with both the polymerase and the DNA sequence playing pivotal roles in determining the sequential order of synapsis and remodeling before end joining.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brissett, Nigel C -- Pitcher, Robert S -- Juarez, Raquel -- Picher, Angel J -- Green, Andrew J -- Dafforn, Timothy R -- Fox, Gavin C -- Blanco, Luis -- Doherty, Aidan J -- BB/D522746/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G120/738/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 Oct 19;318(5849):456-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17947582" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Crystallography, X-Ray ; DNA Ligases/*chemistry/genetics/metabolism ; *DNA Repair ; DNA, Bacterial/*chemistry/metabolism ; Dimerization ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Mycobacterium tuberculosis/*chemistry/enzymology/genetics/metabolism ; Protein Conformation ; Protein Structure, Tertiary
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    A slicer-mediated mechanism for repeat-associated siRNA 5' end formation in Drosophila (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-27
    Description: In Drosophila, repeat-associated small interfering RNAs (rasiRNAs) are produced in the germ line by a Dicer-independent pathway and function through the PIWI subfamily of Argonautes to ensure silencing of retrotransposons. We sequenced small RNAs associated with the PIWI subfamily member AGO3. Although other members of PIWI, Aubergine (Aub) and Piwi, associated with rasiRNAs derived mainly from the antisense strand of retrotransposons, AGO3-associated rasiRNAs arose mainly from the sense strand. Aub- and Piwi-associated rasiRNAs showed a strong preference for uracil at their 5' ends, and AGO3-associated rasiRNAs showed a strong preference for adenine at nucleotide 10. Comparisons between AGO3- and Aub-associated rasiRNAs revealed pairs of rasiRNAs showing complementarities in their first 10 nucleotides. Aub and AGO3 exhibited Slicer activity in vitro. These data support a model in which formation of a 5' terminus within rasiRNA precursors is guided by rasiRNAs originating from transcripts of the other strand in concert with the Slicer activity of PIWI.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gunawardane, Lalith S -- Saito, Kuniaki -- Nishida, Kazumichi M -- Miyoshi, Keita -- Kawamura, Yoshinori -- Nagami, Tomoko -- Siomi, Haruhiko -- Siomi, Mikiko C -- New York, N.Y. -- Science. 2007 Mar 16;315(5818):1587-90. Epub 2007 Feb 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genome Research, University of Tokushima, Tokushima 770-8503, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17322028" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Argonaute Proteins ; Drosophila Proteins/chemistry/genetics/*metabolism ; Drosophila melanogaster/embryology/*genetics/metabolism ; Female ; Gene Library ; Male ; Models, Genetic ; Molecular Sequence Data ; Ovary/metabolism ; Peptide Initiation Factors/chemistry/genetics/*metabolism ; Proteins/genetics/metabolism ; RNA Interference ; RNA, Small Interfering/chemistry/genetics/*metabolism ; RNA-Induced Silencing Complex ; Recombinant Fusion Proteins/metabolism ; Retroelements ; Testis/metabolism
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    Boron-toxicity tolerance in barley arising from efflux transporter amplification (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-01
    Description: Both limiting and toxic soil concentrations of the essential micronutrient boron represent major limitations to crop production worldwide. We identified Bot1, a BOR1 ortholog, as the gene responsible for the superior boron-toxicity tolerance of the Algerian barley landrace Sahara 3771 (Sahara). Bot1 was located at the tolerance locus by high-resolution mapping. Compared to intolerant genotypes, Sahara contains about four times as many Bot1 gene copies, produces substantially more Bot1 transcript, and encodes a Bot1 protein with a higher capacity to provide tolerance in yeast. Bot1 transcript levels identified in barley tissues are consistent with a role in limiting the net entry of boron into the root and in the disposal of boron from leaves via hydathode guttation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sutton, Tim -- Baumann, Ute -- Hayes, Julie -- Collins, Nicholas C -- Shi, Bu-Jun -- Schnurbusch, Thorsten -- Hay, Alison -- Mayo, Gwenda -- Pallotta, Margaret -- Tester, Mark -- Langridge, Peter -- New York, N.Y. -- Science. 2007 Nov 30;318(5855):1446-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Private Mail Bag 1, Glen Osmond, South Australia 5064, Australia. tim.sutton@acpfg.com.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18048688" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Biological Transport ; Boron/metabolism/*toxicity ; Boron Compounds/*metabolism/*toxicity ; Chromosome Mapping ; *Genes, Plant ; Hordeum/*drug effects/*genetics/metabolism ; Membrane Transport Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Plant Lectins/genetics/metabolism ; Plant Proteins/chemistry/genetics/metabolism ; Plant Roots/genetics/metabolism ; Quantitative Trait Loci ; Saccharomyces cerevisiae/genetics/growth & development/metabolism ; Transcription, Genetic
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    GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-27
    Description: The beta2-adrenergic receptor (beta2AR) is a well-studied prototype for heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) that respond to diffusible hormones and neurotransmitters. To overcome the structural flexibility of the beta2AR and to facilitate its crystallization, we engineered a beta2AR fusion protein in which T4 lysozyme (T4L) replaces most of the third intracellular loop of the GPCR ("beta2AR-T4L") and showed that this protein retains near-native pharmacologic properties. Analysis of adrenergic receptor ligand-binding mutants within the context of the reported high-resolution structure of beta2AR-T4L provides insights into inverse-agonist binding and the structural changes required to accommodate catecholamine agonists. Amino acids known to regulate receptor function are linked through packing interactions and a network of hydrogen bonds, suggesting a conformational pathway from the ligand-binding pocket to regions that interact with G proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosenbaum, Daniel M -- Cherezov, Vadim -- Hanson, Michael A -- Rasmussen, Soren G F -- Thian, Foon Sun -- Kobilka, Tong Sun -- Choi, Hee-Jung -- Yao, Xiao-Jie -- Weis, William I -- Stevens, Raymond C -- Kobilka, Brian K -- F32 GM082028/GM/NIGMS NIH HHS/ -- NS028471/NS/NINDS NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM62411/GM/NIGMS NIH HHS/ -- R01 GM056169/GM/NIGMS NIH HHS/ -- R21 GM075811/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 23;318(5854):1266-73. Epub 2007 Oct 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17962519" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenergic beta-Agonists/chemistry/metabolism ; Adrenergic beta-Antagonists/chemistry/metabolism ; Amino Acid Sequence ; Bacteriophage T4/enzymology ; Binding Sites ; Cell Line ; Cell Membrane/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Drug Inverse Agonism ; Humans ; Immunoglobulin Fab Fragments/chemistry/metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Muramidase/chemistry/metabolism ; Propanolamines/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Adrenergic, beta-2/*chemistry/*metabolism ; Recombinant Fusion Proteins/chemistry/metabolism
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    Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-07
    Description: Although highly homologous, the spliceosomal hPrp31 and the nucleolar Nop56 and Nop58 (Nop56/58) proteins recognize different ribonucleoprotein (RNP) particles. hPrp31 interacts with complexes containing the 15.5K protein and U4 or U4atac small nuclear RNA (snRNA), whereas Nop56/58 associate with 15.5K-box C/D small nucleolar RNA complexes. We present structural and biochemical analyses of hPrp31-15.5K-U4 snRNA complexes that show how the conserved Nop domain in hPrp31 maintains high RNP binding selectivity despite relaxed RNA sequence requirements. The Nop domain is a genuine RNP binding module, exhibiting RNA and protein binding surfaces. Yeast two-hybrid analyses suggest a link between retinitis pigmentosa and an aberrant hPrp31-hPrp6 interaction that blocks U4/U6-U5 tri-snRNP formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Sunbin -- Li, Ping -- Dybkov, Olexandr -- Nottrott, Stephanie -- Hartmuth, Klaus -- Luhrmann, Reinhard -- Carlomagno, Teresa -- Wahl, Markus C -- New York, N.Y. -- Science. 2007 Apr 6;316(5821):115-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Abteilung Zellulare Biochemie, Max-Planck-Institut fur Biophysikalische Chemie, Am Fassberg 11, D-37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17412961" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Amino Acid Substitution ; Carrier Proteins/chemistry/metabolism ; Eye Proteins/*chemistry/*metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Small Nuclear/*chemistry/*metabolism ; RNA-Binding Proteins ; Retinitis Pigmentosa/genetics ; Ribonucleoprotein, U4-U6 Small Nuclear/*chemistry/*metabolism ; Transcription Factors
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    Structure of Galphaq-p63RhoGEF-RhoA complex reveals a pathway for the activation of RhoA by GPCRs (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-22
    Description: The guanine nucleotide exchange factor p63RhoGEF is an effector of the heterotrimeric guanine nucleotide-binding protein (G protein) Galphaq and thereby links Galphaq-coupled receptors (GPCRs) to the activation of the small-molecular-weight G protein RhoA. We determined the crystal structure of the Galphaq-p63RhoGEF-RhoA complex, detailing the interactions of Galphaq with the Dbl and pleckstrin homology (DH and PH) domains of p63RhoGEF. These interactions involve the effector-binding site and the C-terminal region of Galphaq and appear to relieve autoinhibition of the catalytic DH domain by the PH domain. Trio, Duet, and p63RhoGEF are shown to constitute a family of Galphaq effectors that appear to activate RhoA both in vitro and in intact cells. We propose that this structure represents the crux of an ancient signal transduction pathway that is expected to be important in an array of physiological processes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lutz, Susanne -- Shankaranarayanan, Aruna -- Coco, Cassandra -- Ridilla, Marc -- Nance, Mark R -- Vettel, Christiane -- Baltus, Doris -- Evelyn, Chris R -- Neubig, Richard R -- Wieland, Thomas -- Tesmer, John J G -- HL071818/HL/NHLBI NIH HHS/ -- HL086865/HL/NHLBI NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Dec 21;318(5858):1923-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty Mannheim, University of Heidelberg, Maybachstrasse 14, D-68169 Mannheim, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18096806" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Cell Line ; Crystallography, X-Ray ; GTP-Binding Protein alpha Subunits, Gq-G11/*chemistry/metabolism ; Guanine Nucleotide Exchange Factors/*chemistry/metabolism ; Humans ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rho Guanine Nucleotide Exchange Factors ; Signal Transduction ; rhoA GTP-Binding Protein/*chemistry/metabolism
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    The evolution of selfing in Arabidopsis thaliana (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-07-28
    Description: Unlike most of its close relatives, Arabidopsis thaliana is capable of self-pollination. In other members of the mustard family, outcrossing is ensured by the complex self-incompatibility (S) locus,which harbors multiple diverged specificity haplotypes that effectively prevent selfing. We investigated the role of the S locus in the evolution of and transition to selfing in A. thaliana. We found that the S locus of A. thaliana harbored considerable diversity, which is an apparent remnant of polymorphism in the outcrossing ancestor. Thus, the fixation of a single inactivated S-locus allele cannot have been a key step in the transition to selfing. An analysis of the genome-wide pattern of linkage disequilibrium suggests that selfing most likely evolved roughly a million years ago or more.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tang, Chunlao -- Toomajian, Christopher -- Sherman-Broyles, Susan -- Plagnol, Vincent -- Guo, Ya-Long -- Hu, Tina T -- Clark, Richard M -- Nasrallah, June B -- Weigel, Detlef -- Nordborg, Magnus -- GM62932/GM/NIGMS NIH HHS/ -- P50 HG002790/HG/NHGRI NIH HHS/ -- R01 GM062932/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 24;317(5841):1070-2. Epub 2007 Jul 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17656687" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Arabidopsis/*genetics/*physiology ; Arabidopsis Proteins/*genetics ; *Biological Evolution ; Chromosomes, Artificial, Bacterial ; *Genes, Plant ; Genetic Drift ; Haplotypes ; Linkage Disequilibrium ; Molecular Sequence Data ; Nuclear Proteins/*genetics ; Plant Proteins/*genetics ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Protein Kinases/*genetics ; *Pseudogenes ; Reproduction/physiology
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    A -defensin mutation causes black coat color in domestic dogs (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-20
    Description: Genetic analysis of mammalian color variation has provided fundamental insight into human biology and disease. In most vertebrates, two key genes, Agouti and Melanocortin 1 receptor (Mc1r), encode a ligand-receptor system that controls pigment type-switching, but in domestic dogs, a third gene is implicated, the K locus, whose genetic characteristics predict a previously unrecognized component of the melanocortin pathway. We identify the K locus as beta-defensin 103 (CBD103) and show that its protein product binds with high affinity to the Mc1r and has a simple and strong effect on pigment type-switching in domestic dogs and transgenic mice. These results expand the functional role of beta-defensins, a protein family previously implicated in innate immunity, and identify an additional class of ligands for signaling through melanocortin receptors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906624/" 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/PMC2906624/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Candille, Sophie I -- Kaelin, Christopher B -- Cattanach, Bruce M -- Yu, Bin -- Thompson, Darren A -- Nix, Matthew A -- Kerns, Julie A -- Schmutz, Sheila M -- Millhauser, Glenn L -- Barsh, Gregory S -- R01 DK064265/DK/NIDDK NIH HHS/ -- R01 DK064265-08/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 30;318(5855):1418-23. Epub 2007 Oct 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Genetics and Pediatrics, Stanford University, Stanford, CA, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17947548" target="_blank"〉PubMed〈/a〉
    Keywords: Agouti Signaling Protein/genetics/metabolism ; Amino Acid Sequence ; Animals ; Cell Line ; Chromosome Mapping ; Dogs/*genetics/metabolism ; Female ; Hair Color/*genetics ; Haplotypes ; Humans ; Keratinocytes/metabolism ; Male ; Mice ; Mice, Transgenic ; Molecular Sequence Data ; Mutation ; Polymorphism, Genetic ; Receptor, Melanocortin, Type 1/*metabolism ; Sequence Analysis, DNA ; Sequence Deletion ; Signal Transduction ; Skin/metabolism ; beta-Defensins/chemistry/*genetics/*metabolism
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    Serine-7 of the RNA polymerase II CTD is specifically required for snRNA gene expression (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-15
    Description: RNA polymerase II (Pol II) transcribes genes that encode proteins and noncoding small nuclear RNAs (snRNAs). The carboxyl-terminal repeat domain (CTD) of the largest subunit of mammalian RNA Pol II, comprising tandem repeats of the heptapeptide consensus Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7, is required for expression of both gene types. We show that mutation of serine-7 to alanine causes a specific defect in snRNA gene expression. We also present evidence that phosphorylation of serine-7 facilitates interaction with the snRNA gene-specific Integrator complex. These findings assign a biological function to this amino acid and highlight a gene type-specific requirement for a residue within the CTD heptapeptide, supporting the existence of a CTD code.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2263945/" 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/PMC2263945/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Egloff, Sylvain -- O'Reilly, Dawn -- Chapman, Rob D -- Taylor, Alice -- Tanzhaus, Katrin -- Pitts, Laura -- Eick, Dirk -- Murphy, Shona -- 072107/Wellcome Trust/United Kingdom -- 081312/Wellcome Trust/United Kingdom -- G0400653/Medical Research Council/United Kingdom -- G0400653(71330)/Medical Research Council/United Kingdom -- G9826944/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1777-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079403" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine ; Amino Acid Sequence ; Cell Line ; Consensus Sequence ; *Gene Expression Regulation ; Heterogeneous-Nuclear Ribonucleoproteins/genetics ; Humans ; Mutation ; Oligopeptides/chemistry/metabolism ; Phosphorylation ; Protein Structure, Tertiary ; Protein Subunits/genetics/metabolism ; RNA Polymerase II/chemistry/genetics/*metabolism ; RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics/metabolism ; RNA, Small Nuclear/*genetics ; Serine/*metabolism ; Templates, Genetic ; *Transcription, Genetic
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    Cross-species identification of Mendel's I locus (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-01-06
    Description: A key gene involved in plant senescence, mutations of which partially disable chlorophyll catabolism and confer stay-green leaf and cotyledon phenotypes, has been identified in Pisum sativum, Arabidopsis thaliana, and Festuca pratensis by using classical and molecular genetics and comparative genomics. A stay-green locus in F. pratensis is syntenically equivalent to a similar stay-green locus on rice chromosome 9. Functional testing in Arabidopsis of a homolog of the rice candidate gene revealed (i) senescence-associated gene expression and (ii) a stay-green phenotype after RNA interference silencing. Genetic mapping in pea demonstrated cosegregation with the yellow/green cotyledon polymorphism (I/i) first reported by Gregor Mendel in 1866.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armstead, Ian -- Donnison, Iain -- Aubry, Sylvain -- Harper, John -- Hortensteiner, Stefan -- James, Caron -- Mani, Jan -- Moffet, Matt -- Ougham, Helen -- Roberts, Luned -- Thomas, Ann -- Weeden, Norman -- Thomas, Howard -- King, Ian -- New York, N.Y. -- Science. 2007 Jan 5;315(5808):73.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Grassland and Environmental Research, Aberystwyth SY23 3EB, UK. ian.armstead@bbsrc.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17204643" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/*genetics/physiology ; Arabidopsis Proteins/genetics ; Chlorophyll/analysis/*metabolism ; Chromosome Mapping ; Cotyledon/physiology ; Festuca/*genetics/physiology ; Gene Expression Regulation, Plant ; *Genes, Plant ; Molecular Sequence Data ; Peas/*genetics/physiology ; Phenotype ; Plant Leaves/physiology ; RNA Interference
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    Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7 (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-15
    Description: RNA polymerase II is distinguished by its large carboxyl-terminal repeat domain (CTD), composed of repeats of the consensus heptapeptide Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Differential phosphorylation of serine-2 and serine-5 at the 5' and 3' regions of genes appears to coordinate the localization of transcription and RNA processing factors to the elongating polymerase complex. Using monoclonal antibodies, we reveal serine-7 phosphorylation on transcribed genes. This position does not appear to be phosphorylated in CTDs of less than 20 consensus repeats. The position of repeats where serine-7 is substituted influenced the appearance of distinct phosphorylated forms, suggesting functional differences between CTD regions. Our results indicate that restriction of serine-7 epitopes to the Linker-proximal region limits CTD phosphorylation patterns and is a requirement for optimal gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chapman, Rob D -- Heidemann, Martin -- Albert, Thomas K -- Mailhammer, Reinhard -- Flatley, Andrew -- Meisterernst, Michael -- Kremmer, Elisabeth -- Eick, Dirk -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1780-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Clinical Molecular Biology and Tumour Genetics, GSF-Research Center of Environment and Health, Munich Center for Integrated Protein Science (CiPSM), Marchioninistrasse 25, 81377 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079404" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal ; Cell Line, Tumor ; Chromatin Immunoprecipitation ; Epitopes ; *Gene Expression Regulation ; Genes, T-Cell Receptor beta ; Humans ; Molecular Sequence Data ; Oligopeptides/chemistry/metabolism ; Phosphorylation ; Protein Subunits/chemistry/immunology/metabolism ; RNA Polymerase II/chemistry/genetics/immunology/*metabolism ; Serine/*metabolism ; *Transcription, Genetic
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  • 77
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    Crystal structure of an ancient protein: evolution by conformational epistasis (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-19
    Description: The structural mechanisms by which proteins have evolved new functions are known only indirectly. We report x-ray crystal structures of a resurrected ancestral protein-the approximately 450 million-year-old precursor of vertebrate glucocorticoid (GR) and mineralocorticoid (MR) receptors. Using structural, phylogenetic, and functional analysis, we identify the specific set of historical mutations that recapitulate the evolution of GR's hormone specificity from an MR-like ancestor. These substitutions repositioned crucial residues to create new receptor-ligand and intraprotein contacts. Strong epistatic interactions occur because one substitution changes the conformational position of another site. "Permissive" mutations-substitutions of no immediate consequence, which stabilize specific elements of the protein and allow it to tolerate subsequent function-switching changes-played a major role in determining GR's evolutionary trajectory.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519897/" 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/PMC2519897/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ortlund, Eric A -- Bridgham, Jamie T -- Redinbo, Matthew R -- Thornton, Joseph W -- F32-GM074398/GM/NIGMS NIH HHS/ -- R01 GM081592/GM/NIGMS NIH HHS/ -- R01 GM081592-01/GM/NIGMS NIH HHS/ -- R01 GM081592-02/GM/NIGMS NIH HHS/ -- R01-DK622229/DK/NIDDK NIH HHS/ -- R01-GM081592/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 14;317(5844):1544-8. Epub 2007 Aug 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702911" target="_blank"〉PubMed〈/a〉
    Keywords: Aldosterone/metabolism ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Crystallography, X-Ray ; Epistasis, Genetic ; *Evolution, Molecular ; Humans ; Hydrocortisone/metabolism ; Ligands ; Likelihood Functions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Glucocorticoid/*chemistry/*genetics/metabolism ; Receptors, Mineralocorticoid/*chemistry/*genetics/metabolism
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  • 78
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    Comment on "Obestatin, a peptide encoded by the ghrelin gene, opposes ghrelin's effects on food intake" (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-10
    Description: Zhang et al. (Research Articles, 11 November 2005, p. 996) reported that obestatin, a peptide derived from the ghrelin precursor, activated the orphan G protein-coupled receptor GPR39. However, we found that I125-obestatin does not bind GPR39 and observed no effects of obestatin on GPR39-transfected cells in various functional assays (cyclic adenosine monophosphate production, calcium mobilization, and GPR39 internalization). Our results indicate that obestatin is not the cognate ligand for GPR39.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chartrel, N -- Alvear-Perez, R -- Leprince, J -- Iturrioz, X -- Reaux-Le Goazigo, A -- Audinot, V -- Chomarat, P -- Coge, F -- Nosjean, O -- Rodriguez, M -- Galizzi, J P -- Boutin, J A -- Vaudry, H -- Llorens-Cortes, C -- New York, N.Y. -- Science. 2007 Feb 9;315(5813):766; author reply 766.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut National de la Sante et de la Recherche Medicale (INSERM), U413, Laboratory of Cellular and Molecular Neuroendocrinology, and European Institute for Peptide Research (IFRMP 23), University of Rouen, 76821 Mont-Saint-Aignan, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17289961" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; CHO Cells ; Calcium/metabolism ; Cell Membrane/metabolism ; Colforsin/pharmacology ; Cricetinae ; Cricetulus ; Cyclic AMP/metabolism ; Ghrelin ; Humans ; Ligands ; Molecular Sequence Data ; Peptide Hormones/genetics/*metabolism/pharmacology ; Pituitary Gland/cytology/metabolism ; Protein Binding ; Receptors, G-Protein-Coupled/genetics/*metabolism ; Transfection
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  • 79
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    Differential antigen processing by dendritic cell subsets in vivo (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-01-06
    Description: Dendritic cells (DCs) process and present self and foreign antigens to induce tolerance or immunity. In vitro models suggest that induction of immunity is controlled by regulating the presentation of antigen, but little is known about how DCs control antigen presentation in vivo. To examine antigen processing and presentation in vivo, we specifically targeted antigens to two major subsets of DCs by using chimeric monoclonal antibodies. Unlike CD8+ DCs that express the cell surface protein CD205, CD8- DCs, which are positive for the 33D1 antigen, are specialized for presentation on major histocompatibility complex (MHC) class II. This difference in antigen processing is intrinsic to the DC subsets and is associated with increased expression of proteins involved in MHC processing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dudziak, Diana -- Kamphorst, Alice O -- Heidkamp, Gordon F -- Buchholz, Veit R -- Trumpfheller, Christine -- Yamazaki, Sayuri -- Cheong, Cheolho -- Liu, Kang -- Lee, Han-Woong -- Park, Chae Gyu -- Steinman, Ralph M -- Nussenzweig, Michel C -- New York, N.Y. -- Science. 2007 Jan 5;315(5808):107-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17204652" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Monoclonal/immunology ; *Antigen Presentation ; Antigens, CD/analysis/immunology ; Antigens, CD8/analysis/immunology ; Base Sequence ; Dendritic Cells/*immunology ; Histocompatibility Antigens Class I/immunology ; Histocompatibility Antigens Class II/immunology ; Lectins, C-Type/analysis/immunology ; Lymphocyte Activation ; Mice ; Mice, Inbred C3H ; Mice, Inbred C57BL ; Mice, Transgenic ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Receptors, Cell Surface/analysis/immunology ; T-Lymphocytes/immunology
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  • 80
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    Smed-betacatenin-1 is required for anteroposterior blastema polarity in planarian regeneration (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007
    Description: Planarian flatworms can regenerate heads at anterior-facing wounds and tails at posterior-facing wounds throughout the body. How this regeneration polarity is specified has been a classic problem for more than a century. We identified a planarian gene, Smed-betacatenin-1, that controls regeneration polarity. Posterior-facing blastemas regenerate a head instead of a tail in Smed-betacatenin-1(RNAi) animals. Smed-betacatenin-1 is required after wounding and at any posterior-facing wound for polarity. Additionally, intact Smed-betacatenin-1(RNAi) animals display anteriorization during tissue turnover. Five Wnt genes and a secreted Frizzled-related Wnt antagonist-like gene are expressed in domains along the anteroposterior axis that reset to new positions during regeneration, which suggests that Wnts control polarity through Smed-betacatenin-1. Our data suggest that beta-catenin specifies the posterior character of the anteroposterior axis throughout the Bilateria and specifies regeneration polarity in planarians.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Petersen, Christian P -- Reddien, Peter W -- New York, N.Y. -- Science. 2008 Jan 18;319(5861):327-30. Epub 2007 Dec 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18063755" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Body Patterning ; Gene Expression ; Genes, Helminth ; Head ; Helminth Proteins/chemistry/genetics/physiology ; Homeostasis ; Molecular Sequence Data ; Photoreceptor Cells, Invertebrate/physiology ; Planarians/cytology/genetics/*physiology ; RNA Interference ; *Regeneration ; Signal Transduction ; Wnt Proteins/genetics/physiology ; beta Catenin/chemistry/genetics/*physiology
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  • 81
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    Cloned viral protein vaccine for foot-and-mouth disease: responses in cattle and swine (1981)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1981-12-04
    Description: A DNA sequence coding for the immunogenic capsid protein VP3 of foot-and-mouth disease virus A12, prepared from the virion RNA, was ligated to a plasmid designed to express a chimeric protein from the Escherichia coli tryptophan promoter-operator system. When Escherichia coli transformed with this plasmid was grown in tryptophan-depleted media, approximately 17 percent of the total cellular protein was found to be an insoluble and stable chimeric protein. The purified chimeric protein competed equally on a molar basis with VP3 for specific antibodies to foot-and-mouth disease virus. When inoculated into six cattle and two swine, this protein elicited high levels of neutralizing antibody and protection against challenge with foot-and-mouth disease virus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kleid, D G -- Yansura, D -- Small, B -- Dowbenko, D -- Moore, D M -- Grubman, M J -- McKercher, P D -- Morgan, D O -- Robertson, B H -- Bachrach, H L -- New York, N.Y. -- Science. 1981 Dec 4;214(4525):1125-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6272395" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibody Formation ; Base Sequence ; Cattle ; Cattle Diseases/*prevention & control ; *Cloning, Molecular ; DNA Restriction Enzymes ; DNA, Recombinant/metabolism ; Foot-and-Mouth Disease/*prevention & control ; Immunity, Cellular ; Protein Biosynthesis ; Swine ; Swine Diseases/*prevention & control ; Transcription, Genetic ; *Vaccines ; Viral Proteins/genetics/*therapeutic use
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  • 82
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    Calcitonin messenger RNA encodes multiple polypeptides in a single precursor (1981)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1981-07-24
    Description: Recombinant DNA techniques were used to analyze the structure of the messenger RNA encoding a precursor of calcitonin, a small calcium-regulating hormone of 32 amino acids. Analyses of the nucleotide sequences of cloned complementary DNA's comprising the entire coding sequence of the messenger RNA revealed that calcitonin is flanked at both its amino and carboxyl termini by peptide extensions linked to the hormone by short sequences of basic amino acids. The location of glycine next to the carboxyl terminal prolinamide of calcitonin is consistent with indications that glycine is required for the enzymatic amidation of proline to the prolinamide. During cellular biosynthesis, calcitonin arises from a large precursor protein by cleavages at both amino and carboxyl terminal residues of the hormone. These findings raise questions concerning the regulation of these cleavages and the potential biological functions of the precursor extensions derived from these cleavages.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacobs, J W -- Goodman, R H -- Chin, W W -- Dee, P C -- Habener, J F -- Bell, N H -- Potts, J T Jr -- AM 27781-01/AM/NIADDK NIH HHS/ -- New York, N.Y. -- Science. 1981 Jul 24;213(4506):457-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6264603" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Calcitonin/*genetics ; Cloning, Molecular ; DNA Restriction Enzymes ; DNA, Recombinant/*metabolism ; Macromolecular Substances ; Neoplasms, Experimental/metabolism ; Nucleic Acid Hybridization ; Peptide Biosynthesis ; Plants/metabolism ; Protein Biosynthesis ; RNA, Messenger/*genetics ; Rats ; Thyroid Neoplasms/metabolism ; Triticum/metabolism
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  • 83
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    Determination of nucleotide sequences in DNA (1981)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1981-12-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanger, F -- New York, N.Y. -- Science. 1981 Dec 11;214(4526):1205-10.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7302589" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bacteriophages/genetics ; *Base Sequence ; Cloning, Molecular ; DNA/*genetics ; DNA, Mitochondrial/genetics ; DNA, Single-Stranded/genetics ; DNA-Directed DNA Polymerase ; Humans ; Protein Biosynthesis ; Templates, Genetic
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  • 84
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    Pituitary gastrins occur in corticotrophs and melanotrophs (1981)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1981-08-14
    Description: The gut hormone gastrin was identified in pituitary cells containing adrenocorticotropic hormone and alpha-melanocyte--stimulating hormone by region-specific immunocytochemistry and radioimmunoassay. Smaller amounts of gastrin were found in nerve fibers of the neural lobe and pituitary stalk. Since adrenocorticotropic hormone--like peptides occur in antropyloric gastrin cells, these data indicate a considerable similarity in peptide composition of pituitary and gastrointestinal endocrine cells and reinforces questions of multiple hormone production.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Larsson, L I -- Rehfeld, J F -- New York, N.Y. -- Science. 1981 Aug 14;213(4509):768-70.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6266012" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenocorticotropic Hormone/metabolism ; Amino Acid Sequence ; Animals ; Cats ; Gastrins/genetics/*metabolism ; Histocytochemistry ; Melanocyte-Stimulating Hormones/metabolism ; Pituitary Gland/cytology/*metabolism ; Radioimmunoassay ; Swine
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  • 85
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    Species restriction of a monoclonal antibody reacting with residues 130 to 137 in encephalitogenic myelin basic protein (1981)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1981-10-02
    Description: A monoclonal antibody (immunoglobulin G1) has been produced that reacts against myelin basic protein present in or extracted from the brains of many mammals-with certain important exceptions. Because of known species differences in amino acid sequences of basic protein and of certain peptide fragments, the binding site for this particular antibody appeared likely to include residues 130 to 137. Confirmation of this hypothesis was obtained by amino acid composition of the major immunoreactive peptides produced by thermolysin digestion of human basic protein and isolated by high-performance liquid chromatography.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sires, L R -- Hruby, S -- Alvord, E C Jr -- Hellstrom, I -- Hellstrom, K E -- Kies, M W -- Martemspm, R -- Deibler, G E -- Beckman, E D -- Casnellie, J E -- CA-19148/CA/NCI NIH HHS/ -- CA-25558/CA/NCI NIH HHS/ -- CA-26584/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1981 Oct 2;214(4516):87-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6169147" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Monoclonal ; Cattle ; Chickens ; Epitopes ; Guinea Pigs ; Humans ; Macaca ; Myelin Basic Protein/*immunology ; Peptide Fragments/immunology ; Rabbits ; Rats ; Species Specificity
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  • 86
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    Biology of hepatitis B virus (1981)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1981-07-24
    Description: Immunochemical investigations of the viral antigens and molecular characterization of the viral DNA have elucidated the nature of the hepatitis B virus infection underlying acute, chronic, and oncogenic disorders of the liver in man. Cloning and sequencing of viral DNA have made possible studies on the structure of the genome and on certain aspects of the biology of the virus, hitherto constrained for a lack of tissue culture systems and laboratory animal models useful in its propagation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tiollais, P -- Charnay, P -- Vyas, G N -- New York, N.Y. -- Science. 1981 Jul 24;213(4506):406-11.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6264599" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA Restriction Enzymes ; Genes, Viral ; Hepatitis B/microbiology ; Hepatitis B Surface Antigens/*analysis ; Hepatitis B virus/*genetics/immunology ; Humans ; Viral Proteins
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  • 87
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    Characterization of a 41-residue ovine hypothalamic peptide that stimulates secretion of corticotropin and beta-endorphin (1981)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1981-09-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vale, W -- Spiess, J -- Rivier, C -- Rivier, J -- AM 18811/AM/NIADDK NIH HHS/ -- AM 20917/AM/NIADDK NIH HHS/ -- AM 26741/AM/NIADDK NIH HHS/ -- New York, N.Y. -- Science. 1981 Sep 18;213(4514):1394-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6267699" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenocorticotropic Hormone/*secretion ; Amino Acid Sequence ; Amphibian Proteins ; Angiotensinogen ; Animals ; Corticotropin-Releasing Hormone/*isolation & purification ; Endorphins/*secretion ; Hypothalamo-Hypophyseal System/physiology ; Peptide Hormones ; Peptides ; Pituitary Gland, Anterior/*secretion ; Pituitary Hormone-Releasing Hormones/*isolation & purification ; Radioimmunoassay ; Sheep ; Structure-Activity Relationship
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  • 88
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    Influence of calcium ion on the binding of fibrin amino terminal peptides to fibrinogen (1981)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1981-04-24
    Description: The affinity of the amino terminal tetrapeptide of the beta chain of fibrin, Gly-His-Arg-Pro, for fibrinogen dramatically increases in the presence of 2 millimolar calcium ion. In contrast, there is no significant increase in the affinity of peptides beginning with the amino terminal sequence of the fibrin alpha chain, Gly-Pro-Arg, in the presence of calcium ions, although the number of binding sites increases. In the latter case, the increased number of sites is due to the alpha chain analogs binding to the site ordinarily occupied by the beta chain analogs. These results indicate that structures at the amino terminus of the fibrin beta chain play a more important role in fibrin polymerization when calcium ions are present.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laudano, A P -- Doolittle, R F -- AM-07233/AM/NIADDK NIH HHS/ -- HE-18, 576/PHS HHS/ -- New York, N.Y. -- Science. 1981 Apr 24;212(4493):457-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7209542" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Calcium/*pharmacology ; Fibrin/*metabolism ; Fibrinogen/*metabolism ; Humans ; Peptide Fragments/metabolism ; Protein Binding/drug effects
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  • 89
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    Primary structure of a large aminoacyl-tRNA synthetase (1981)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1981-09-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Putney, S D -- Royal, N J -- Neuman de Vegvar, H -- Herlihy, W C -- Biemann, K -- Schimmel, P -- GM05472/GM/NIGMS NIH HHS/ -- GM23562/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1981 Sep 25;213(4515):1497-501.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7025207" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine-tRNA Ligase/*genetics ; Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/*genetics ; Base Sequence ; Escherichia coli/*enzymology ; Genes ; Mass Spectrometry ; Peptide Fragments/analysis
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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