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  • Binding Sites  (98)
  • American Association for the Advancement of Science (AAAS)  (98)
  • American Institute of Physics (AIP)
  • Oxford University Press
  • 2010-2014  (32)
  • 1995-1999
  • 1990-1994  (66)
  • 2011  (32)
  • 1992  (66)
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Publisher
  • American Association for the Advancement of Science (AAAS)  (98)
  • American Institute of Physics (AIP)
  • Oxford University Press
  • Nature Publishing Group (NPG)  (36)
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  • 2010-2014  (32)
  • 1995-1999
  • 1990-1994  (66)
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  • 1
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    A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-03-12
    Description: Disruption of the circadian clock exacerbates metabolic diseases, including obesity and diabetes. We show that histone deacetylase 3 (HDAC3) recruitment to the genome displays a circadian rhythm in mouse liver. Histone acetylation is inversely related to HDAC3 binding, and this rhythm is lost when HDAC3 is absent. Although amounts of HDAC3 are constant, its genomic recruitment in liver corresponds to the expression pattern of the circadian nuclear receptor Rev-erbalpha. Rev-erbalpha colocalizes with HDAC3 near genes regulating lipid metabolism, and deletion of HDAC3 or Rev-erbalpha in mouse liver causes hepatic steatosis. Thus, genomic recruitment of HDAC3 by Rev-erbalpha directs a circadian rhythm of histone acetylation and gene expression required for normal hepatic lipid homeostasis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389392/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389392/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feng, Dan -- Liu, Tao -- Sun, Zheng -- Bugge, Anne -- Mullican, Shannon E -- Alenghat, Theresa -- Liu, X Shirley -- Lazar, Mitchell A -- DK19525/DK/NIDDK NIH HHS/ -- DK43806/DK/NIDDK NIH HHS/ -- DK45586/DK/NIDDK NIH HHS/ -- DK49210/DK/NIDDK NIH HHS/ -- HG4069/HG/NHGRI NIH HHS/ -- P30 DK019525/DK/NIDDK NIH HHS/ -- R01 DK045586/DK/NIDDK NIH HHS/ -- R37 DK043806/DK/NIDDK NIH HHS/ -- R37 DK043806-20/DK/NIDDK NIH HHS/ -- RC1 DK086239/DK/NIDDK NIH HHS/ -- RC1DK08623/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2011 Mar 11;331(6022):1315-9. doi: 10.1126/science.1198125.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21393543" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Chromatin Immunoprecipitation ; Chronobiology Disorders/genetics/metabolism ; *Circadian Clocks ; *Circadian Rhythm ; DNA/metabolism ; Epigenesis, Genetic ; Fatty Liver/*metabolism ; Gene Expression Regulation ; *Genome ; Histone Deacetylases/*metabolism ; Histones/metabolism ; Homeostasis ; *Lipid Metabolism ; Lipogenesis/genetics ; Liver/*metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Molecular Sequence Data ; Nuclear Receptor Co-Repressor 1/metabolism ; Nuclear Receptor Subfamily 1, Group D, Member 1/genetics/metabolism ; RNA Polymerase II/metabolism ; Up-Regulation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Computational design of proteins targeting the conserved stem region of influenza hemagglutinin (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-14
    Description: We describe a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions between disembodied amino acid residues and the target surface are identified and used to anchor de novo designed interfaces. The method was used to design proteins that bind a conserved surface patch on the stem of the influenza hemagglutinin (HA) from the 1918 H1N1 pandemic virus. After affinity maturation, two of the designed proteins, HB36 and HB80, bind H1 and H5 HAs with low nanomolar affinity. Further, HB80 inhibits the HA fusogenic conformational changes induced at low pH. The crystal structure of HB36 in complex with 1918/H1 HA revealed that the actual binding interface is nearly identical to that in the computational design model. Such designed binding proteins may be useful for both diagnostics and therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164876/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164876/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fleishman, Sarel J -- Whitehead, Timothy A -- Ekiert, Damian C -- Dreyfus, Cyrille -- Corn, Jacob E -- Strauch, Eva-Maria -- Wilson, Ian A -- Baker, David -- AI057141/AI/NIAID NIH HHS/ -- AI058113/AI/NIAID NIH HHS/ -- GM080209/GM/NIGMS NIH HHS/ -- P01 AI058113/AI/NIAID NIH HHS/ -- P01 AI058113-07/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 May 13;332(6031):816-21. doi: 10.1126/science.1202617.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21566186" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Binding Sites ; Computational Biology ; *Computer Simulation ; Hemagglutinin Glycoproteins, Influenza Virus/chemistry/*metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; *Models, Molecular ; Molecular Sequence Data ; Mutation ; Peptide Library ; Protein Binding ; Protein Conformation ; *Protein Engineering ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Proteins/*chemistry/genetics/*metabolism ; Software
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Crystal structure of the dynein motor domain (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-02-19
    Description: Dyneins are microtubule-based motor proteins that power ciliary beating, transport intracellular cargos, and help to construct the mitotic spindle. Evolved from ring-shaped hexameric AAA-family adenosine triphosphatases (ATPases), dynein's large size and complexity have posed challenges for understanding its structure and mechanism. Here, we present a 6 angstrom crystal structure of a functional dimer of two ~300-kilodalton motor domains of yeast cytoplasmic dynein. The structure reveals an unusual asymmetric arrangement of ATPase domains in the ring-shaped motor domain, the manner in which the mechanical element interacts with the ATPase ring, and an unexpected interaction between two coiled coils that create a base for the microtubule binding domain. The arrangement of these elements provides clues as to how adenosine triphosphate-driven conformational changes might be transmitted across the motor domain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169322/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169322/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, Andrew P -- Cho, Carol -- Jin, Lan -- Vale, Ronald D -- MC_UP_A025_1011/Medical Research Council/United Kingdom -- R01 GM097312/GM/NIGMS NIH HHS/ -- R01 GM097312-01/GM/NIGMS NIH HHS/ -- R01 GM097312-02/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Mar 4;331(6021):1159-65. doi: 10.1126/science.1202393. Epub 2011 Feb 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California-San Francisco, 600 16th Street, San Francisco, CA 94158, USA. cartera@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21330489" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Allosteric Regulation ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Cytoplasmic Dyneins/*chemistry/*metabolism ; Methionine/chemistry ; Microtubules/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry ; Saccharomyces cerevisiae Proteins/*chemistry/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    A cell cycle phosphoproteome of the yeast centrosome (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-06-28
    Description: Centrosomes organize the bipolar mitotic spindle, and centrosomal defects cause chromosome instability. Protein phosphorylation modulates centrosome function, and we provide a comprehensive map of phosphorylation on intact yeast centrosomes (18 proteins). Mass spectrometry was used to identify 297 phosphorylation sites on centrosomes from different cell cycle stages. We observed different modes of phosphoregulation via specific protein kinases, phosphorylation site clustering, and conserved phosphorylated residues. Mutating all eight cyclin-dependent kinase (Cdk)-directed sites within the core component, Spc42, resulted in lethality and reduced centrosomal assembly. Alternatively, mutation of one conserved Cdk site within gamma-tubulin (Tub4-S360D) caused mitotic delay and aberrant anaphase spindle elongation. Our work establishes the extent and complexity of this prominent posttranslational modification in centrosome biology and provides specific examples of phosphorylation control in centrosome function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825980/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825980/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keck, Jamie M -- Jones, Michele H -- Wong, Catherine C L -- Binkley, Jonathan -- Chen, Daici -- Jaspersen, Sue L -- Holinger, Eric P -- Xu, Tao -- Niepel, Mario -- Rout, Michael P -- Vogel, Jackie -- Sidow, Arend -- Yates, John R 3rd -- Winey, Mark -- F32 GM086038/GM/NIGMS NIH HHS/ -- GM51312/GM/NIGMS NIH HHS/ -- MOP-64404/Canadian Institutes of Health Research/Canada -- P41 RR011823/RR/NCRR NIH HHS/ -- R01 GM051312/GM/NIGMS NIH HHS/ -- R01 GM051312-16/GM/NIGMS NIH HHS/ -- R01 GM051312-16S1/GM/NIGMS NIH HHS/ -- R01 GM062427/GM/NIGMS NIH HHS/ -- R01 HG003039/HG/NHGRI NIH HHS/ -- T32 GM008759/GM/NIGMS NIH HHS/ -- U54 RR022220/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2011 Jun 24;332(6037):1557-61. doi: 10.1126/science.1205193.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21700874" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; CDC2 Protein Kinase/metabolism ; *Cell Cycle ; Centrosome/*metabolism/ultrastructure ; Cytoskeletal Proteins/genetics/metabolism ; Fungal Proteins/chemistry/metabolism ; Fungi/metabolism ; G1 Phase ; Mitosis ; Mutation ; Phosphoproteins/genetics/metabolism ; Phosphorylation ; Protein Processing, Post-Translational ; Proteome/*metabolism ; Saccharomyces cerevisiae/cytology/genetics/growth & development/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Spindle Apparatus/metabolism/ultrastructure ; Tubulin/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 5
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    Cardiac myosin activation: a potential therapeutic approach for systolic heart failure (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-03-19
    Description: Decreased cardiac contractility is a central feature of systolic heart failure. Existing drugs increase cardiac contractility indirectly through signaling cascades but are limited by their mechanism-related adverse effects. To avoid these limitations, we previously developed omecamtiv mecarbil, a small-molecule, direct activator of cardiac myosin. Here, we show that it binds to the myosin catalytic domain and operates by an allosteric mechanism to increase the transition rate of myosin into the strongly actin-bound force-generating state. Paradoxically, it inhibits adenosine 5'-triphosphate turnover in the absence of actin, which suggests that it stabilizes an actin-bound conformation of myosin. In animal models, omecamtiv mecarbil increases cardiac function by increasing the duration of ejection without changing the rates of contraction. Cardiac myosin activation may provide a new therapeutic approach for systolic heart failure.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090309/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090309/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Malik, Fady I -- Hartman, James J -- Elias, Kathleen A -- Morgan, Bradley P -- Rodriguez, Hector -- Brejc, Katjusa -- Anderson, Robert L -- Sueoka, Sandra H -- Lee, Kenneth H -- Finer, Jeffrey T -- Sakowicz, Roman -- Baliga, Ramesh -- Cox, David R -- Garard, Marc -- Godinez, Guillermo -- Kawas, Raja -- Kraynack, Erica -- Lenzi, David -- Lu, Pu Ping -- Muci, Alexander -- Niu, Congrong -- Qian, Xiangping -- Pierce, Daniel W -- Pokrovskii, Maria -- Suehiro, Ion -- Sylvester, Sheila -- Tochimoto, Todd -- Valdez, Corey -- Wang, Wenyue -- Katori, Tatsuo -- Kass, David A -- Shen, You-Tang -- Vatner, Stephen F -- Morgans, David J -- 1-R43-HL-66647-1/HL/NHLBI NIH HHS/ -- R01 HL106511/HL/NHLBI NIH HHS/ -- R43 HL066647/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2011 Mar 18;331(6023):1439-43. doi: 10.1126/science.1200113.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Preclinical Research and Development, Cytokinetics, Inc., South San Francisco, CA 94080, USA. fmalik@cytokinetics.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21415352" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/metabolism ; Actins/metabolism ; Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Adrenergic beta-Agonists/pharmacology ; Allosteric Regulation ; Animals ; Binding Sites ; Calcium/metabolism ; Cardiac Myosins/chemistry/*metabolism ; Cardiac Output/drug effects ; Dogs ; Female ; Heart Failure, Systolic/*drug therapy/physiopathology ; Isoproterenol/pharmacology ; Male ; Myocardial Contraction/*drug effects ; Myocytes, Cardiac/*drug effects/physiology ; Phosphates/metabolism ; Protein Binding ; Protein Conformation ; Protein Isoforms/chemistry/metabolism ; Rats ; Rats, Sprague-Dawley ; Urea/*analogs & derivatives/chemistry/metabolism/pharmacology ; Ventricular Function, Left/drug effects
    Print ISSN: 0036-8075
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  • 6
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    Proteoglycan-specific molecular switch for RPTPsigma clustering and neuronal extension (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-04-02
    Description: Heparan and chondroitin sulfate proteoglycans (HSPGs and CSPGs, respectively) regulate numerous cell surface signaling events, with typically opposite effects on cell function. CSPGs inhibit nerve regeneration through receptor protein tyrosine phosphatase sigma (RPTPsigma). Here we report that RPTPsigma acts bimodally in sensory neuron extension, mediating CSPG inhibition and HSPG growth promotion. Crystallographic analyses of a shared HSPG-CSPG binding site reveal a conformational plasticity that can accommodate diverse glycosaminoglycans with comparable affinities. Heparan sulfate and analogs induced RPTPsigma ectodomain oligomerization in solution, which was inhibited by chondroitin sulfate. RPTPsigma and HSPGs colocalize in puncta on sensory neurons in culture, whereas CSPGs occupy the extracellular matrix. These results lead to a model where proteoglycans can exert opposing effects on neuronal extension by competing to control the oligomerization of a common receptor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154093/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154093/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coles, Charlotte H -- Shen, Yingjie -- Tenney, Alan P -- Siebold, Christian -- Sutton, Geoffrey C -- Lu, Weixian -- Gallagher, John T -- Jones, E Yvonne -- Flanagan, John G -- Aricescu, A Radu -- 090532/Wellcome Trust/United Kingdom -- 10976/Cancer Research UK/United Kingdom -- EY11559/EY/NEI NIH HHS/ -- G0700232/Medical Research Council/United Kingdom -- G0900084/Medical Research Council/United Kingdom -- HD29417/HD/NICHD NIH HHS/ -- R01 EY011559/EY/NEI NIH HHS/ -- R01 EY011559-19/EY/NEI NIH HHS/ -- R37 HD029417/HD/NICHD NIH HHS/ -- R37 HD029417-20/HD/NICHD NIH HHS/ -- Cancer Research UK/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2011 Apr 22;332(6028):484-8. doi: 10.1126/science.1200840. Epub 2011 Mar 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21454754" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Axons/*physiology ; Binding Sites ; Cell Membrane/metabolism ; Cells, Cultured ; Chondroitin Sulfate Proteoglycans/chemistry/*metabolism ; Chondroitin Sulfates/chemistry/metabolism ; Crystallography, X-Ray ; Extracellular Matrix ; Ganglia, Spinal ; Glypicans/metabolism ; Growth Cones/metabolism ; Heparan Sulfate Proteoglycans/chemistry/*metabolism ; Heparitin Sulfate/analogs & derivatives/chemistry/metabolism ; Humans ; Mice ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Neurites/physiology ; Neurocan/metabolism ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; Receptor-Like Protein Tyrosine Phosphatases, Class 2/*chemistry/*metabolism ; Sensory Receptor Cells/*physiology
    Print ISSN: 0036-8075
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  • 7
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    The structure of the kinesin-1 motor-tail complex reveals the mechanism of autoinhibition (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-13
    Description: When not transporting cargo, kinesin-1 is autoinhibited by binding of a tail region to the motor domains, but the mechanism of inhibition is unclear. We report the crystal structure of a motor domain dimer in complex with its tail domain at 2.2 angstroms and compare it with a structure of the motor domain alone at 2.7 angstroms. These structures indicate that neither an induced conformational change nor steric blocking is the cause of inhibition. Instead, the tail cross-links the motor domains at a second position, in addition to the coiled coil. This "double lockdown," by cross-linking at two positions, prevents the movement of the motor domains that is needed to undock the neck linker and release adenosine diphosphate. This autoinhibition mechanism could extend to some other kinesins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339660/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339660/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaan, Hung Yi Kristal -- Hackney, David D -- Kozielski, Frank -- NS058848/NS/NINDS NIH HHS/ -- R01 NS058848/NS/NINDS NIH HHS/ -- R01 NS058848-01A2/NS/NINDS NIH HHS/ -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2011 Aug 12;333(6044):883-5. doi: 10.1126/science.1204824.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21836017" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Drosophila Proteins/*antagonists & inhibitors/*chemistry/metabolism ; Hydrogen Bonding ; Kinesin/*antagonists & inhibitors/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Cartilage acidic protein-1B (LOTUS), an endogenous Nogo receptor antagonist for axon tract formation (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-06
    Description: Neural circuitry formation depends on the molecular control of axonal projection during development. By screening with fluorophore-assisted light inactivation in the developing mouse brain, we identified cartilage acidic protein-1B as a key molecule for lateral olfactory tract (LOT) formation and named it LOT usher substance (LOTUS). We further identified Nogo receptor-1 (NgR1) as a LOTUS-binding protein. NgR1 is a receptor of myelin-derived axon growth inhibitors, such as Nogo, which prevent neural regeneration in the adult. LOTUS suppressed Nogo-NgR1 binding and Nogo-induced growth cone collapse. A defasciculated LOT was present in lotus-deficient mice but not in mice lacking both lotus- and ngr1. These findings suggest that endogenous antagonism of NgR1 by LOTUS is crucial for normal LOT formation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244695/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244695/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sato, Yasufumi -- Iketani, Masumi -- Kurihara, Yuji -- Yamaguchi, Megumi -- Yamashita, Naoya -- Nakamura, Fumio -- Arie, Yuko -- Kawasaki, Takahiko -- Hirata, Tatsumi -- Abe, Takaya -- Kiyonari, Hiroshi -- Strittmatter, Stephen M -- Goshima, Yoshio -- Takei, Kohtaro -- R37 NS033020/NS/NINDS NIH HHS/ -- R37 NS033020-19/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2011 Aug 5;333(6043):769-73. doi: 10.1126/science.1204144.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Pharmacology and Neurobiology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21817055" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axons/*physiology ; Binding Sites ; Calcium-Binding Proteins/chemistry/genetics/*metabolism ; Cell Line ; Cells, Cultured ; GPI-Linked Proteins/genetics/metabolism ; Growth Cones/metabolism ; Humans ; Immunohistochemistry ; Ligands ; Mice ; Mice, Inbred ICR ; Myelin Proteins/genetics/*metabolism ; Olfactory Pathways/*cytology/*growth & development/metabolism ; Prosencephalon/embryology/metabolism ; Protein Binding ; Receptors, Cell Surface/genetics/*metabolism ; Signal Transduction
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  • 9
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    Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 A resolution (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-11-19
    Description: Gene silencing is essential for regulating cell fate in eukaryotes. Altered chromatin architectures contribute to maintaining the silenced state in a variety of species. The silent information regulator (Sir) proteins regulate mating type in Saccharomyces cerevisiae. One of these proteins, Sir3, interacts directly with the nucleosome to help generate silenced domains. We determined the crystal structure of a complex of the yeast Sir3 BAH (bromo-associated homology) domain and the nucleosome core particle at 3.0 angstrom resolution. We see multiple molecular interactions between the protein surfaces of the nucleosome and the BAH domain that explain numerous genetic mutations. These interactions are accompanied by structural rearrangements in both the nucleosome and the BAH domain. The structure explains how covalent modifications on H4K16 and H3K79 regulate formation of a silencing complex that contains the nucleosome as a central component.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098850/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098850/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armache, Karim-Jean -- Garlick, Joseph D -- Canzio, Daniele -- Narlikar, Geeta J -- Kingston, Robert E -- GM043901/GM/NIGMS NIH HHS/ -- P41 RR012408/RR/NCRR NIH HHS/ -- R01 GM043901/GM/NIGMS NIH HHS/ -- R37 GM048405/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Nov 18;334(6058):977-82. doi: 10.1126/science.1210915.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22096199" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; *Gene Silencing ; Histones/*chemistry/metabolism ; Hydrogen Bonding ; Methylation ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Mutant Proteins/chemistry/metabolism ; Nucleosomes/*chemistry/metabolism/ultrastructure ; Physicochemical Processes ; Protein Folding ; *Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/chemistry/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; Silent Information Regulator Proteins, Saccharomyces ; cerevisiae/*chemistry/genetics/metabolism ; Static Electricity
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  • 10
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    Unfolded proteins are Ire1-activating ligands that directly induce the unfolded protein response (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-20
    Description: The unfolded protein response (UPR) detects the accumulation of unfolded proteins in the endoplasmic reticulum (ER) and adjusts the protein-folding capacity to the needs of the cell. Under conditions of ER stress, the transmembrane protein Ire1 oligomerizes to activate its cytoplasmic kinase and ribonuclease domains. It is unclear what feature of ER stress Ire1 detects. We found that the core ER-lumenal domain (cLD) of yeast Ire1 binds to unfolded proteins in yeast cells and to peptides primarily composed of basic and hydrophobic residues in vitro. Mutation of amino acid side chains exposed in a putative peptide-binding groove of Ire1 cLD impaired peptide binding. Peptide binding caused Ire1 cLD oligomerization in vitro, suggesting that direct binding to unfolded proteins activates the UPR.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202989/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202989/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gardner, Brooke M -- Walter, Peter -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 30;333(6051):1891-4. doi: 10.1126/science.1209126. Epub 2011 Aug 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21852455" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cathepsin A/chemistry/metabolism ; Endoplasmic Reticulum/*metabolism ; Fluorescence Polarization ; Fungal Proteins/chemistry/metabolism ; Glutathione Transferase/metabolism ; HSP70 Heat-Shock Proteins/chemistry/metabolism ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Membrane Glycoproteins/*chemistry/*metabolism ; Mutant Proteins/chemistry/metabolism ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein-Serine-Threonine Kinases/*chemistry/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Stress, Physiological ; *Unfolded Protein Response
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  • 11
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    NMR detection of structures in the HIV-1 5'-leader RNA that regulate genome packaging (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-10-15
    Description: The 5'-leader of the HIV-1 genome regulates multiple functions during viral replication via mechanisms that have yet to be established. We developed a nuclear magnetic resonance approach that enabled direct detection of structural elements within the intact leader (712-nucleotide dimer) that are critical for genome packaging. Residues spanning the gag start codon (AUG) form a hairpin in the monomeric leader and base pair with residues of the unique-5' region (U5) in the dimer. U5:AUG formation promotes dimerization by displacing and exposing a dimer-promoting hairpin and enhances binding by the nucleocapsid (NC) protein, which is the cognate domain of the viral Gag polyprotein that directs packaging. Our findings support a packaging mechanism in which translation, dimerization, NC binding, and packaging are regulated by a common RNA structural switch.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3335204/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3335204/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Kun -- Heng, Xiao -- Garyu, Lianko -- Monti, Sarah -- Garcia, Eric L -- Kharytonchyk, Siarhei -- Dorjsuren, Bilguujin -- Kulandaivel, Gowry -- Jones, Simonne -- Hiremath, Atheeth -- Divakaruni, Sai Sachin -- LaCotti, Courtney -- Barton, Shawn -- Tummillo, Daniel -- Hosic, Azra -- Edme, Kedy -- Albrecht, Sara -- Telesnitsky, Alice -- Summers, Michael F -- 2T34 GM008663/GM/NIGMS NIH HHS/ -- R01 GM042561/GM/NIGMS NIH HHS/ -- R01 GM042561-21/GM/NIGMS NIH HHS/ -- R01 GM042561-22/GM/NIGMS NIH HHS/ -- R01 GM042561-23/GM/NIGMS NIH HHS/ -- R01 GM042561-24/GM/NIGMS NIH HHS/ -- R01 GM42561/GM/NIGMS NIH HHS/ -- R25 GM055036/GM/NIGMS NIH HHS/ -- R25 GM055036-14/GM/NIGMS NIH HHS/ -- R25 GM055036-15/GM/NIGMS NIH HHS/ -- R25 GM055036-16/GM/NIGMS NIH HHS/ -- R25 GM55036/GM/NIGMS NIH HHS/ -- T34 GM008663/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Oct 14;334(6053):242-5. doi: 10.1126/science.1210460.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21998393" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions ; Base Pairing ; Binding Sites ; Codon, Initiator ; Dimerization ; Genes, gag ; *Genome, Viral ; HIV-1/*genetics/*physiology ; Human Immunodeficiency Virus Proteins/metabolism ; Mutagenesis, Site-Directed ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Conformation ; Nucleocapsid Proteins/metabolism ; Protein Binding ; Protein Biosynthesis ; RNA, Viral/*chemistry/*genetics ; *Virus Assembly ; gag Gene Products, Human Immunodeficiency Virus/metabolism
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  • 12
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    AMPK is a direct adenylate charge-regulated protein kinase (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-06-18
    Description: The adenosine monophosphate (AMP)-activated protein kinase (AMPK) regulates whole-body and cellular energy balance in response to energy demand and supply. AMPK is an alphabetagamma heterotrimer activated by decreasing concentrations of adenosine triphosphate (ATP) and increasing AMP concentrations. AMPK activation depends on phosphorylation of the alpha catalytic subunit on threonine-172 (Thr(172)) by kinases LKB1 or CaMKKbeta, and this is promoted by AMP binding to the gamma subunit. AMP sustains activity by inhibiting dephosphorylation of alpha-Thr(172), whereas ATP promotes dephosphorylation. Adenosine diphosphate (ADP), like AMP, bound to gamma sites 1 and 3 and stimulated alpha-Thr(172) phosphorylation. However, in contrast to AMP, ADP did not directly activate phosphorylated AMPK. In this way, both ADP/ATP and AMP/ATP ratios contribute to AMPK regulation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oakhill, Jonathan S -- Steel, Rohan -- Chen, Zhi-Ping -- Scott, John W -- Ling, Naomi -- Tam, Shanna -- Kemp, Bruce E -- New York, N.Y. -- Science. 2011 Jun 17;332(6036):1433-5. doi: 10.1126/science.1200094.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Protein Chemistry and Metabolism, St. Vincent's Institute of Medical Research, University of Melbourne, 41 Victoria Parade, Fitzroy 3065, Victoria, Australia. joakhill@svi.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21680840" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases/chemistry/*metabolism ; Adenosine Diphosphate/*metabolism ; Adenosine Monophosphate/*metabolism ; Adenosine Triphosphate/*metabolism ; Animals ; Binding Sites ; COS Cells ; Calcium-Calmodulin-Dependent Protein Kinase Kinase/metabolism ; Cercopithecus aethiops ; Enzyme Activation ; Myristic Acid/metabolism ; Phosphorylation ; Protein Subunits/chemistry/metabolism ; Protein-Serine-Threonine Kinases/metabolism ; Recombinant Fusion Proteins/metabolism ; Threonine/metabolism
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  • 13
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    Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-07-19
    Description: Passive transfer of broadly neutralizing HIV antibodies can prevent infection, which suggests that vaccines that elicit such antibodies would be protective. Thus far, however, few broadly neutralizing HIV antibodies that occur naturally have been characterized. To determine whether these antibodies are part of a larger group of related molecules, we cloned 576 new HIV antibodies from four unrelated individuals. All four individuals produced expanded clones of potent broadly neutralizing CD4-binding-site antibodies that mimic binding to CD4. Despite extensive hypermutation, the new antibodies shared a consensus sequence of 68 immunoglobulin H (IgH) chain amino acids and arise independently from two related IgH genes. Comparison of the crystal structure of one of the antibodies to the broadly neutralizing antibody VRC01 revealed conservation of the contacts to the HIV spike.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351836/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351836/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scheid, Johannes F -- Mouquet, Hugo -- Ueberheide, Beatrix -- Diskin, Ron -- Klein, Florian -- Oliveira, Thiago Y K -- Pietzsch, John -- Fenyo, David -- Abadir, Alexander -- Velinzon, Klara -- Hurley, Arlene -- Myung, Sunnie -- Boulad, Farid -- Poignard, Pascal -- Burton, Dennis R -- Pereyra, Florencia -- Ho, David D -- Walker, Bruce D -- Seaman, Michael S -- Bjorkman, Pamela J -- Chait, Brian T -- Nussenzweig, Michel C -- P01 AI081677/AI/NIAID NIH HHS/ -- P30 AI060354/AI/NIAID NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- RR00862/RR/NCRR NIH HHS/ -- RR022220/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1633-7. doi: 10.1126/science.1207227. Epub 2011 Jul 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764753" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Neutralizing/*chemistry/*immunology/metabolism ; Antibody Affinity ; Antibody Specificity ; Antigens, CD4/immunology/*metabolism ; Binding Sites ; Binding Sites, Antibody ; Cloning, Molecular ; Consensus Sequence ; Crystallography, X-Ray ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/*chemistry/*immunology/metabolism ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; Humans ; Immunoglobulin Fab Fragments/chemistry ; Immunoglobulin Heavy Chains/chemistry ; Immunoglobulin Light Chains/chemistry ; Molecular Mimicry ; Molecular Sequence Data ; Mutation ; Protein Conformation
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  • 14
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    The crystal structure of the signal recognition particle in complex with its receptor (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-02-19
    Description: Cotranslational targeting of membrane and secretory proteins is mediated by the universally conserved signal recognition particle (SRP). Together with its receptor (SR), SRP mediates the guanine triphosphate (GTP)-dependent delivery of translating ribosomes bearing signal sequences to translocons on the target membrane. Here, we present the crystal structure of the SRP:SR complex at 3.9 angstrom resolution and biochemical data revealing that the activated SRP:SR guanine triphosphatase (GTPase) complex binds the distal end of the SRP hairpin RNA where GTP hydrolysis is stimulated. Combined with previous findings, these results suggest that the SRP:SR GTPase complex initially assembles at the tetraloop end of the SRP RNA and then relocalizes to the opposite end of the RNA. This rearrangement provides a mechanism for coupling GTP hydrolysis to the handover of cargo to the translocon.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758919/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758919/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ataide, Sandro F -- Schmitz, Nikolaus -- Shen, Kuang -- Ke, Ailong -- Shan, Shu-ou -- Doudna, Jennifer A -- Ban, Nenad -- GM078024/GM/NIGMS NIH HHS/ -- R01 GM078024/GM/NIGMS NIH HHS/ -- R01 GM086766/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Feb 18;331(6019):881-6. doi: 10.1126/science.1196473.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, Eidgenossische Technische Hochschule Zurich (ETH Zurich), Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21330537" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Base Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Enzyme Activation ; Escherichia coli/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; GTP Phosphohydrolases/chemistry/metabolism ; Guanosine Triphosphate/analogs & derivatives/chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Biological ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; Protein Transport ; RNA, Bacterial/*chemistry/metabolism ; Receptors, Cytoplasmic and Nuclear/*chemistry/metabolism ; Ribosomal Proteins/chemistry/metabolism ; Ribosomes/metabolism ; Signal Recognition Particle/*chemistry/metabolism
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  • 15
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    A crystal structure of the complex between human complement receptor 2 and its ligand C3d (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-04-30
    Description: The interaction of complement receptor 2 (CR2)--which is present on B cells and follicular dendritic cells--with its antigen-bound ligand C3d results in an enhanced antibody response, thus providing an important link between the innate and adaptive immune systems. Although a cocrystal structure of a complex between C3d and the ligand-binding domains of CR2 has been published, several aspects of this structure, including the position in C3d of the binding interface, remained controversial because of disagreement with biochemical data. We now report a cocrystal structure of a CR2(SCR1-2):C3d complex at 3.2 angstrom resolution in which the interaction interfaces differ markedly from the previously published structure and are consistent with the biochemical data. It is likely that, in the previous structure, the interaction was influenced by the presence of zinc acetate additive in the crystallization buffer, leading to a nonphysiological complex. Detailed knowledge of the binding interface now at hand gives the potential to exploit the interaction in vaccine design or in therapeutics directed against autoreactive B cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van den Elsen, Jean M H -- Isenman, David E -- New York, N.Y. -- Science. 2011 Apr 29;332(6029):608-11. doi: 10.1126/science.1201954.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK. bssjmhve@bath.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21527715" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Complement C3d/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Mutagenesis, Site-Directed ; Protein Binding ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Receptors, Complement 3d/*chemistry/genetics/metabolism ; Zinc Acetate
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  • 16
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    Crystal structure of the maltose transporter in a pretranslocation intermediate state (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-05-14
    Description: Adenosine triphosphate (ATP)-binding cassette (ABC) transporters convert chemical energy from ATP hydrolysis to mechanical work for substrate translocation. They function by alternating between two states, exposing the substrate-binding site to either side of the membrane. A key question that remains to be addressed is how substrates initiate the transport cycle. Using x-ray crystallography, we have captured the maltose transporter in an intermediate step between the inward- and outward-facing states. We show that interactions with substrate-loaded maltose-binding protein in the periplasm induce a partial closure of the MalK dimer in the cytoplasm. ATP binding to this conformation then promotes progression to the outward-facing state. These results, interpreted in light of biochemical and functional studies, provide a structural basis to understand allosteric communication in ABC transporters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oldham, Michael L -- Chen, Jue -- GM070515/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Jun 3;332(6034):1202-5. doi: 10.1126/science.1200767. Epub 2011 May 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, Howard Hughes Medical Institute, West Lafayette, IN 47907, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21566157" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Binding Sites ; Biological Transport, Active ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; Hydrogen Bonding ; Maltose/metabolism ; Maltose-Binding Proteins/chemistry/metabolism ; Models, Biological ; Models, Molecular ; Monosaccharide Transport Proteins/*chemistry/metabolism ; Periplasm/metabolism ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 17
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    A diiron protein autogenerates a valine-phenylalanine cross-link (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-21
    Description: All known internal covalent cross-links in proteins involve functionalized groups having oxygen, nitrogen, or sulfur atoms present to facilitate their formation. Here, we report a carbon-carbon cross-link between two unfunctionalized side chains. This valine-phenyalanine cross-link, produced in an oxygen-dependent reaction, is generated by its own carboxylate-bridged diiron center and serves to stabilize the metallocenter. This finding opens the door to new types of posttranslational modifications, and it demonstrates new catalytic potential of diiron centers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736988/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736988/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cooley, Richard B -- Rhoads, Timothy W -- Arp, Daniel J -- Karplus, P Andrew -- ES00210/ES/NIEHS NIH HHS/ -- GM R01-083136/GM/NIGMS NIH HHS/ -- R01 GM083136/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 May 20;332(6032):929. doi: 10.1126/science.1205687.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, 2011 Agriculture and Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21596985" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Cyanophora/*chemistry/metabolism ; Iron/*chemistry ; Metalloproteins/*chemistry/metabolism ; Oxygen/chemistry ; Phenylalanine/*chemistry ; Plant Proteins/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Valine/*chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 18
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    How a DNA polymerase clamp loader opens a sliding clamp (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-12-24
    Description: Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of adenosine triphosphatases (ATPases). We present structures for the ATP-bound state of the clamp loader complex from bacteriophage T4, bound to an open clamp and primer-template DNA. The clamp loader traps a spiral conformation of the open clamp so that both the loader and the clamp match the helical symmetry of DNA. One structure reveals that ATP has been hydrolyzed in one subunit and suggests that clamp closure and ejection of the loader involves disruption of the ATP-dependent match in symmetry. The structures explain how synergy among the loader, the clamp, and DNA can trigger ATP hydrolysis and release of the closed clamp on DNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281585/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281585/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelch, Brian A -- Makino, Debora L -- O'Donnell, Mike -- Kuriyan, John -- F32 GM087888/GM/NIGMS NIH HHS/ -- F32 GM087888-02/GM/NIGMS NIH HHS/ -- F32-087888/PHS HHS/ -- R01 GM038839/GM/NIGMS NIH HHS/ -- R01 GM038839-26/GM/NIGMS NIH HHS/ -- R01 GM045547/GM/NIGMS NIH HHS/ -- R01 GM045547-20/GM/NIGMS NIH HHS/ -- R01-GM308839/GM/NIGMS NIH HHS/ -- R01-GM45547/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Dec 23;334(6063):1675-80. doi: 10.1126/science.1211884.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22194570" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Bacteriophage T4 ; Binding Sites ; Crystallography, X-Ray ; DNA, A-Form/*chemistry/metabolism ; DNA, Viral/*chemistry/metabolism ; DNA-Directed DNA Polymerase/chemistry/*metabolism ; Hydrolysis ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Static Electricity ; Templates, Genetic ; Trans-Activators/*chemistry/metabolism ; Viral Proteins/*chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 19
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    Chromosome organization by a nucleoid-associated protein in live bacteria (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-10
    Description: Bacterial chromosomes are confined in submicrometer-sized nucleoids. Chromosome organization is facilitated by nucleoid-associated proteins (NAPs), but the mechanisms of action remain elusive. In this work, we used super-resolution fluorescence microscopy, in combination with a chromosome-conformation capture assay, to study the distributions of major NAPs in live Escherichia coli cells. Four NAPs--HU, Fis, IHF, and StpA--were largely scattered throughout the nucleoid. In contrast, H-NS, a global transcriptional silencer, formed two compact clusters per chromosome, driven by oligomerization of DNA-bound H-NS through interactions mediated by the amino-terminal domain of the protein. H-NS sequestered the regulated operons into these clusters and juxtaposed numerous DNA segments broadly distributed throughout the chromosome. Deleting H-NS led to substantial chromosome reorganization. These observations demonstrate that H-NS plays a key role in global chromosome organization in bacteria.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329943/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329943/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Wenqin -- Li, Gene-Wei -- Chen, Chongyi -- Xie, X Sunney -- Zhuang, Xiaowei -- GM 096450/GM/NIGMS NIH HHS/ -- R01 GM096450/GM/NIGMS NIH HHS/ -- R01 GM096450-03/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 9;333(6048):1445-9. doi: 10.1126/science.1204697.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21903814" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Division ; Chromosomes, Bacterial/*metabolism/*ultrastructure ; DNA, Bacterial/chemistry/*metabolism ; DNA-Binding Proteins/metabolism ; Escherichia coli K12/genetics/metabolism/*ultrastructure ; Escherichia coli Proteins/chemistry/genetics/*metabolism ; Factor For Inversion Stimulation Protein/metabolism ; Fimbriae Proteins/chemistry/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Genetic Loci ; Genome, Bacterial ; Integration Host Factors/metabolism ; Molecular Chaperones/metabolism ; Nucleic Acid Conformation ; Operon ; Protein Multimerization ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/chemistry/genetics/*metabolism
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  • 20
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    Biochemistry. KSR plays CRAF-ty (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shi, Fumin -- Lemmon, Mark A -- New York, N.Y. -- Science. 2011 May 27;332(6033):1043-4. doi: 10.1126/science.1208063.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, and Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, 422 Curie Boulevard, Philadelphia, PA 19104-6059, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21617065" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Animals ; Binding Sites ; Catalytic Domain ; Cell Membrane/enzymology ; Enzyme Activation ; Extracellular Signal-Regulated MAP Kinases/*metabolism ; Humans ; *MAP Kinase Signaling System ; Mitogen-Activated Protein Kinase Kinases/*metabolism ; Mutation ; Phosphorylation ; Protein Conformation ; Protein Kinases/chemistry/genetics/*metabolism ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proto-Oncogene Proteins B-raf/antagonists & inhibitors/*metabolism ; Proto-Oncogene Proteins c-raf/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 21
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    Increasing the potency and breadth of an HIV antibody by using structure-based rational design (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-10-29
    Description: Antibodies against the CD4 binding site (CD4bs) on the HIV-1 spike protein gp120 can show exceptional potency and breadth. We determined structures of NIH45-46, a more potent clonal variant of VRC01, alone and bound to gp120. Comparisons with VRC01-gp120 revealed that a four-residue insertion in heavy chain complementarity-determining region 3 (CDRH3) contributed to increased interaction between NIH45-46 and the gp120 inner domain, which correlated with enhanced neutralization. We used structure-based design to create NIH45-46(G54W), a single substitution in CDRH2 that increases contact with the gp120 bridging sheet and improves breadth and potency, critical properties for potential clinical use, by an order of magnitude. Together with the NIH45-46-gp120 structure, these results indicate that gp120 inner domain and bridging sheet residues should be included in immunogens to elicit CD4bs antibodies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232316/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232316/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Diskin, Ron -- Scheid, Johannes F -- Marcovecchio, Paola M -- West, Anthony P Jr -- Klein, Florian -- Gao, Han -- Gnanapragasam, Priyanthi N P -- Abadir, Alexander -- Seaman, Michael S -- Nussenzweig, Michel C -- Bjorkman, Pamela J -- P01 AI081677-01/AI/NIAID NIH HHS/ -- RR00862/RR/NCRR NIH HHS/ -- RR022220/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Dec 2;334(6060):1289-93. doi: 10.1126/science.1213782. Epub 2011 Oct 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22033520" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Amino Acid Sequence ; Antibodies, Neutralizing/chemistry/*immunology/metabolism ; Antibody Affinity ; Antigens, CD4/chemistry/metabolism ; Binding Sites ; Complementarity Determining Regions ; Crystallography, X-Ray ; HIV Antibodies/chemistry/*immunology/metabolism ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV-1/*immunology ; Humans ; Hydrophobic and Hydrophilic Interactions ; Immunoglobulin Fab Fragments/chemistry/immunology/metabolism ; Immunoglobulin Heavy Chains/chemistry/immunology/metabolism ; Molecular Mimicry ; Molecular Sequence Data ; Mutant Proteins/chemistry/immunology/metabolism ; Protein Conformation ; *Protein Engineering ; Protein Structure, Tertiary
    Print ISSN: 0036-8075
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  • 22
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    Structural basis for tail-anchored membrane protein biogenesis by the Get3-receptor complex (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-07-02
    Description: Tail-anchored (TA) proteins are involved in cellular processes including trafficking, degradation, and apoptosis. They contain a C-terminal membrane anchor and are posttranslationally delivered to the endoplasmic reticulum (ER) membrane by the Get3 adenosine triphosphatase interacting with the hetero-oligomeric Get1/2 receptor. We have determined crystal structures of Get3 in complex with the cytosolic domains of Get1 and Get2 in different functional states at 3.0, 3.2, and 4.6 angstrom resolution. The structural data, together with biochemical experiments, show that Get1 and Get2 use adjacent, partially overlapping binding sites and that both can bind simultaneously to Get3. Docking to the Get1/2 complex allows for conformational changes in Get3 that are required for TA protein insertion. These data suggest a molecular mechanism for nucleotide-regulated delivery of TA proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601824/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601824/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stefer, Susanne -- Reitz, Simon -- Wang, Fei -- Wild, Klemens -- Pang, Yin-Yuin -- Schwarz, Daniel -- Bomke, Jorg -- Hein, Christopher -- Lohr, Frank -- Bernhard, Frank -- Denic, Vladimir -- Dotsch, Volker -- Sinning, Irmgard -- R01 GM099943/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Aug 5;333(6043):758-62. doi: 10.1126/science.1207125. Epub 2011 Jun 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, Goethe University, D-60325 Frankfurt am Main, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21719644" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Vesicular Transport/*chemistry/*metabolism ; Adenosine Triphosphatases/*chemistry/*metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Cytosol/chemistry ; Endoplasmic Reticulum/metabolism ; Guanine Nucleotide Exchange Factors/*chemistry/*metabolism ; Membrane Proteins/*chemistry/*metabolism ; Microsomes/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Saccharomyces cerevisiae/*chemistry/metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/*metabolism
    Print ISSN: 0036-8075
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  • 23
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    AIDS/HIV. Converging on an HIV vaccine (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korber, Bette -- Gnanakaran, S -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1589-90. doi: 10.1126/science.1211919.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Theoretical Biology and Biophysics, T6, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. btk@lanl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21921189" target="_blank"〉PubMed〈/a〉
    Keywords: *AIDS Vaccines ; Antibodies, Neutralizing/chemistry/*immunology/metabolism ; Antibody Affinity ; Antigens, CD4/chemistry/immunology/metabolism ; Binding Sites ; Binding Sites, Antibody ; Complementarity Determining Regions/genetics ; Crystallography, X-Ray ; Epitopes ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/chemistry/*immunology/metabolism ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; Humans ; Models, Molecular ; Molecular Mimicry ; Protein Conformation
    Print ISSN: 0036-8075
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    Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-13
    Description: Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516815/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516815/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Xueling -- Zhou, Tongqing -- Zhu, Jiang -- Zhang, Baoshan -- Georgiev, Ivelin -- Wang, Charlene -- Chen, Xuejun -- Longo, Nancy S -- Louder, Mark -- McKee, Krisha -- O'Dell, Sijy -- Perfetto, Stephen -- Schmidt, Stephen D -- Shi, Wei -- Wu, Lan -- Yang, Yongping -- Yang, Zhi-Yong -- Yang, Zhongjia -- Zhang, Zhenhai -- Bonsignori, Mattia -- Crump, John A -- Kapiga, Saidi H -- Sam, Noel E -- Haynes, Barton F -- Simek, Melissa -- Burton, Dennis R -- Koff, Wayne C -- Doria-Rose, Nicole A -- Connors, Mark -- NISC Comparative Sequencing Program -- Mullikin, James C -- Nabel, Gary J -- Roederer, Mario -- Shapiro, Lawrence -- Kwong, Peter D -- Mascola, John R -- 5U19 AI 067854-06/AI/NIAID NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- U19 AI067854/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1593-602. doi: 10.1126/science.1207532. Epub 2011 Aug 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21835983" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Amino Acid Sequence ; Antibodies, Neutralizing/*chemistry/genetics/*immunology/isolation & purification ; Antibody Affinity ; Antibody Specificity ; Antigens, CD4/metabolism ; Base Sequence ; Binding Sites ; Binding Sites, Antibody ; Complementarity Determining Regions/genetics ; Crystallography, X-Ray ; Epitopes ; *Evolution, Molecular ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/*chemistry/genetics/*immunology/isolation & purification ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; HIV-1/chemistry/*immunology ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoglobulin Fab Fragments/chemistry/immunology ; Immunoglobulin Heavy Chains/chemistry/immunology ; Immunoglobulin J-Chains/genetics ; Immunoglobulin Light Chains/chemistry/immunology ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Sequence Analysis, DNA
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  • 25
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    Structures of C3b in complex with factors B and D give insight into complement convertase formation (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-01-06
    Description: Activation of the complement cascade induces inflammatory responses and marks cells for immune clearance. In the central complement-amplification step, a complex consisting of surface-bound C3b and factor B is cleaved by factor D to generate active convertases on targeted surfaces. We present crystal structures of the pro-convertase C3bB at 4 angstrom resolution and its complex with factor D at 3.5 angstrom resolution. Our data show how factor B binding to C3b forms an open "activation" state of C3bB. Factor D specifically binds the open conformation of factor B through a site distant from the catalytic center and is activated by the substrate, which displaces factor D's self-inhibitory loop. This concerted proteolytic mechanism, which is cofactor-dependent and substrate-induced, restricts complement amplification to C3b-tagged target cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087196/" 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/PMC3087196/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Forneris, Federico -- Ricklin, Daniel -- Wu, Jin -- Tzekou, Apostolia -- Wallace, Rachel S -- Lambris, John D -- Gros, Piet -- AI030040/AI/NIAID NIH HHS/ -- AI068730/AI/NIAID NIH HHS/ -- AI072106/AI/NIAID NIH HHS/ -- GM062134/GM/NIGMS NIH HHS/ -- P01 AI068730/AI/NIAID NIH HHS/ -- P01 AI068730-04/AI/NIAID NIH HHS/ -- R01 AI030040/AI/NIAID NIH HHS/ -- R01 AI030040-14/AI/NIAID NIH HHS/ -- R01 AI072106/AI/NIAID NIH HHS/ -- R01 AI072106-04/AI/NIAID NIH HHS/ -- R01 GM062134/GM/NIGMS NIH HHS/ -- R01 GM062134-08/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1816-20. doi: 10.1126/science.1195821.〈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/21205667" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalytic Domain ; Complement C3 Convertase, Alternative Pathway/*chemistry/metabolism ; Complement C3b/*chemistry/metabolism ; Complement Factor B/*chemistry/metabolism ; Complement Factor D/*chemistry/metabolism ; Complement Pathway, Alternative ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Mutant Proteins/chemistry ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary
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  • 26
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    Mass spectrometry of intact V-type ATPases reveals bound lipids and the effects of nucleotide binding (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-10-25
    Description: The ability of electrospray to propel large viruses into a mass spectrometer is established and is rationalized by analogy to the atmospheric transmission of the common cold. Much less clear is the fate of membrane-embedded molecular machines in the gas phase. Here we show that rotary adenosine triphosphatases (ATPases)/synthases from Thermus thermophilus and Enterococcus hirae can be maintained intact with membrane and soluble subunit interactions preserved in vacuum. Mass spectra reveal subunit stoichiometries and the identity of tightly bound lipids within the membrane rotors. Moreover, subcomplexes formed in solution and gas phases reveal the regulatory effects of nucleotide binding on both ATP hydrolysis and proton translocation. Consequently, we can link specific lipid and nucleotide binding with distinct regulatory roles.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927129/" 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/PMC3927129/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Min -- Morgner, Nina -- Barrera, Nelson P -- Politis, Argyris -- Isaacson, Shoshanna C -- Matak-Vinkovic, Dijana -- Murata, Takeshi -- Bernal, Ricardo A -- Stock, Daniela -- Robinson, Carol V -- 088150/Wellcome Trust/United Kingdom -- 099141/Wellcome Trust/United Kingdom -- G1000819/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2011 Oct 21;334(6054):380-5. doi: 10.1126/science.1210148.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22021858" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/*metabolism ; Adenosine Triphosphate/*metabolism ; Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; Cardiolipins/analysis/metabolism ; Enterococcus/enzymology ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Mass Spectrometry ; Membrane Lipids/analysis/*metabolism ; Models, Molecular ; Phosphatidylethanolamines/analysis/metabolism ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Spectrometry, Mass, Electrospray Ionization ; Thermus thermophilus/*enzymology ; Vacuolar Proton-Translocating ATPases/*chemistry/*metabolism
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  • 27
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    Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-13
    Description: Ribosome assembly in eukaryotes requires approximately 200 essential assembly factors (AFs) and occurs through ordered events that initiate in the nucleolus and culminate in the cytoplasm. Here, we present the electron cryo-microscopy (cryo-EM) structure of a late cytoplasmic 40S ribosome assembly intermediate from Saccharomyces cerevisiae at 18 angstrom resolution. We obtained cryo-EM reconstructions of preribosomal complexes lacking individual components to define the positions of all seven AFs bound to this intermediate. These late-binding AFs are positioned to prevent each step in the translation initiation pathway. Together, they obstruct the binding sites for initiation factors, prevent the opening of the messenger RNA channel, block 60S subunit joining, and disrupt the decoding site. These redundant mechanisms probably ensure that pre-40S particles do not enter the translation pathway, which would result in their rapid degradation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402165/" 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/PMC3402165/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strunk, Bethany S -- Loucks, Cherisse R -- Su, Min -- Vashisth, Harish -- Cheng, Shanshan -- Schilling, Justin -- Brooks, Charles L 3rd -- Karbstein, Katrin -- Skiniotis, Georgios -- P41 RR012255/RR/NCRR NIH HHS/ -- R01 GM086451/GM/NIGMS NIH HHS/ -- R01-GM086451/GM/NIGMS NIH HHS/ -- RR12255/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2011 Sep 9;333(6048):1449-53. doi: 10.1126/science.1208245. Epub 2011 Aug 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chemical Biology Doctoral Program, 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/21835981" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cryoelectron Microscopy ; Eukaryotic Initiation Factor-1/chemistry/metabolism ; Eukaryotic Initiation Factor-3/chemistry/metabolism ; Image Processing, Computer-Assisted ; Methyltransferases/chemistry/metabolism ; Models, Molecular ; Nuclear Proteins/chemistry/metabolism ; *Peptide Chain Initiation, Translational ; Protein-Serine-Threonine Kinases/chemistry/metabolism ; RNA, Fungal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Ribosomal Proteins/chemistry/metabolism ; Ribosome Subunits, Small, Eukaryotic/chemistry/*metabolism/ultrastructure ; Saccharomyces cerevisiae/chemistry/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/*metabolism
    Print ISSN: 0036-8075
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  • 28
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    Physiology. Crise de foie, redux? (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-03-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moore, David D -- New York, N.Y. -- Science. 2011 Mar 11;331(6022):1275-6. doi: 10.1126/science.1203194.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA. moore@bcm.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21393533" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Chronobiology Disorders/*metabolism ; *Circadian Clocks ; *Circadian Rhythm ; DNA/metabolism ; Epigenesis, Genetic ; Fatty Liver/*metabolism ; Gene Expression Regulation ; Histone Deacetylases/*metabolism ; Histones/metabolism ; *Lipid Metabolism ; Lipogenesis ; Liver/*metabolism ; Mice ; Nuclear Receptor Co-Repressor 1/metabolism ; Nuclear Receptor Subfamily 1, Group D, Member 1/*metabolism
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  • 29
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    Structure of the FANCI-FANCD2 complex: insights into the Fanconi anemia DNA repair pathway (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-07-19
    Description: Fanconi anemia is a cancer predisposition syndrome caused by defects in the repair of DNA interstrand cross-links (ICLs). Central to this pathway is the Fanconi anemia I-Fanconi anemia D2 (FANCI-FANCD2) (ID) complex, which is activated by DNA damage-induced phosphorylation and monoubiquitination. The 3.4 angstrom crystal structure of the ~300 kilodalton ID complex reveals that monoubiquitination and regulatory phosphorylation sites map to the I-D interface, suggesting that they occur on monomeric proteins or an opened-up complex and that they may serve to stabilize I-D heterodimerization. The 7.8 angstrom electron-density map of FANCI-DNA crystals and in vitro data show that each protein has binding sites for both single- and double-stranded DNA, suggesting that the ID complex recognizes DNA structures that result from the encounter of replication forks with an ICL.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310437/" 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/PMC3310437/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joo, Woo -- Xu, Guozhou -- Persky, Nicole S -- Smogorzewska, Agata -- Rudge, Derek G -- Buzovetsky, Olga -- Elledge, Stephen J -- Pavletich, Nikola P -- R01 GM044664/GM/NIGMS NIH HHS/ -- R01 GM044664-10/GM/NIGMS NIH HHS/ -- R37 GM044664/GM/NIGMS NIH HHS/ -- T32 CA009216/CA/NCI NIH HHS/ -- T32 CA009216-32/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Jul 15;333(6040):312-6. doi: 10.1126/science.1205805.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764741" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; *DNA Repair ; DNA, Single-Stranded/chemistry/metabolism ; Fanconi Anemia/genetics ; Fanconi Anemia Complementation Group D2 Protein/*chemistry/metabolism ; Fanconi Anemia Complementation Group Proteins/*chemistry/metabolism ; Hydrophobic and Hydrophilic Interactions ; Mice ; Models, Molecular ; Molecular Sequence Data ; Phosphorylation ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Static Electricity ; Ubiquitin/chemistry ; Ubiquitination
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  • 30
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    Structure of an agonist-bound human A2A adenosine receptor (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-03-12
    Description: Activation of G protein-coupled receptors upon agonist binding is a critical step in the signaling cascade for this family of cell surface proteins. We report the crystal structure of the A(2A) adenosine receptor (A(2A)AR) bound to an agonist UK-432097 at 2.7 angstrom resolution. Relative to inactive, antagonist-bound A(2A)AR, the agonist-bound structure displays an outward tilt and rotation of the cytoplasmic half of helix VI, a movement of helix V, and an axial shift of helix III, resembling the changes associated with the active-state opsin structure. Additionally, a seesaw movement of helix VII and a shift of extracellular loop 3 are likely specific to A(2A)AR and its ligand. The results define the molecule UK-432097 as a "conformationally selective agonist" capable of receptor stabilization in a specific active-state configuration.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3086811/" 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/PMC3086811/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Fei -- Wu, Huixian -- Katritch, Vsevolod -- Han, Gye Won -- Jacobson, Kenneth A -- Gao, Zhan-Guo -- Cherezov, Vadim -- Stevens, Raymond C -- GM075915/GM/NIGMS NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- R01 GM089857/GM/NIGMS NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- U54 GM094618-01/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2011 Apr 15;332(6027):322-7. doi: 10.1126/science.1202793. Epub 2011 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21393508" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/*analogs & derivatives/chemistry/metabolism ; Adenosine A2 Receptor Agonists/chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Opsins/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Receptor, Adenosine A2A/*chemistry/*metabolism ; Rhodopsin/chemistry/metabolism ; Triazines/chemistry/metabolism ; Triazoles/chemistry/metabolism
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    Chemoenzymatic synthesis of homogeneous ultralow molecular weight heparins (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-10-29
    Description: Ultralow molecular weight (ULMW) heparins are sulfated glycans that are clinically used to treat thrombotic disorders. ULMW heparins range from 1500 to 3000 daltons, corresponding from 5 to 10 saccharide units. The commercial drug Arixtra (fondaparinux sodium) is a structurally homogeneous ULMW heparin pentasaccharide that is synthesized through a lengthy chemical process. Here, we report 10- and 12-step chemoenzymatic syntheses of two structurally homogeneous ULMW heparins (MW = 1778.5 and 1816.5) in 45 and 37% overall yield, respectively, starting from a simple disaccharide. These ULMW heparins display excellent in vitro anticoagulant activity and comparable pharmacokinetic properties to Arixtra, as demonstrated in a rabbit model. The chemoenzymatic approach is scalable and shows promise for a more efficient route to synthesize this important class of medicinal agent.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3425363/" 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/PMC3425363/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Yongmei -- Masuko, Sayaka -- Takieddin, Majde -- Xu, Haoming -- Liu, Renpeng -- Jing, Juliana -- Mousa, Shaker A -- Linhardt, Robert J -- Liu, Jian -- AI074775/AI/NIAID NIH HHS/ -- AI50050/AI/NIAID NIH HHS/ -- GM38060/GM/NIGMS NIH HHS/ -- HL094463/HL/NHLBI NIH HHS/ -- HL096972/HL/NHLBI NIH HHS/ -- HL62244/HL/NHLBI NIH HHS/ -- R01 AI050050/AI/NIAID NIH HHS/ -- R01 GM038060/GM/NIGMS NIH HHS/ -- R01 HL062244/HL/NHLBI NIH HHS/ -- R01 HL094463/HL/NHLBI NIH HHS/ -- R01 HL096972/HL/NHLBI NIH HHS/ -- R21 AI074775/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2011 Oct 28;334(6055):498-501. doi: 10.1126/science.1207478.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, 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/22034431" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anticoagulants/*chemical synthesis/chemistry/pharmacokinetics/pharmacology ; Antithrombins/chemistry/metabolism ; Binding Sites ; Chemical Processes ; Glycosyltransferases/metabolism ; Heparin, Low-Molecular-Weight/*chemical ; synthesis/chemistry/pharmacokinetics/pharmacology ; Molecular Structure ; Molecular Weight ; N-Acetylglucosaminyltransferases/metabolism ; Oligosaccharides/chemistry ; Polysaccharides/chemistry/pharmacokinetics/pharmacology ; Rabbits ; Racemases and Epimerases/metabolism ; Spectrometry, Mass, Electrospray Ionization ; Substrate Specificity ; Sulfotransferases/metabolism
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  • 32
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    Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6 (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-11-05
    Description: Protein synthesis in all organisms is catalyzed by ribosomes. In comparison to their prokaryotic counterparts, eukaryotic ribosomes are considerably larger and are subject to more complex regulation. The large ribosomal subunit (60S) catalyzes peptide bond formation and contains the nascent polypeptide exit tunnel. We present the structure of the 60S ribosomal subunit from Tetrahymena thermophila in complex with eukaryotic initiation factor 6 (eIF6), cocrystallized with the antibiotic cycloheximide (a eukaryotic-specific inhibitor of protein synthesis), at a resolution of 3.5 angstroms. The structure illustrates the complex functional architecture of the eukaryotic 60S subunit, which comprises an intricate network of interactions between eukaryotic-specific ribosomal protein features and RNA expansion segments. It reveals the roles of eukaryotic ribosomal protein elements in the stabilization of the active site and the extent of eukaryotic-specific differences in other functional regions of the subunit. Furthermore, it elucidates the molecular basis of the interaction with eIF6 and provides a structural framework for further studies of ribosome-associated diseases and the role of the 60S subunit in the initiation of protein synthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klinge, Sebastian -- Voigts-Hoffmann, Felix -- Leibundgut, Marc -- Arpagaus, Sofia -- Ban, Nenad -- New York, N.Y. -- Science. 2011 Nov 18;334(6058):941-8. doi: 10.1126/science.1211204. Epub 2011 Nov 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22052974" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/metabolism ; Base Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Cycloheximide/metabolism ; Eukaryotic Initiation Factors/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptide Chain Initiation, Translational ; Protein Conformation ; Protein Structure, Secondary ; Protozoan Proteins/chemistry/metabolism ; RNA, Protozoan/chemistry/metabolism ; RNA, Ribosomal/chemistry/metabolism ; RNA, Ribosomal, 5.8S/chemistry/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosome Subunits, Large, Eukaryotic/*chemistry/metabolism/ultrastructure ; Tetrahymena thermophila/*chemistry/metabolism
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  • 33
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    Cooperativity induced by a single mutation at the subunit interface of a dimeric enzyme: glutathione reductase (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-11-13
    Description: When glycine418 of Escherichia coli glutathione reductase, which is in a closely packed region of the dimer interface, is replaced with a bulky tryptophan residue, the enzyme becomes highly cooperative (Hill coefficient 1.76) for glutathione binding. The cooperativity is lost when the mutant subunit is hybridized with a wild-type subunit to create a heterodimer. The mutation appears to disrupt atomic packing at the dimer interface, which induces a change of kinetic mechanism. A single mutation in a region of the protein remote from the active site can thus act as a molecular switch to confer cooperativity on an enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scrutton, N S -- Deonarain, M P -- Berry, A -- Perham, R N -- New York, N.Y. -- Science. 1992 Nov 13;258(5085):1140-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Cambridge, United Kingdom.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1439821" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Escherichia coli/*enzymology/genetics ; Genes, Bacterial ; Glutathione/metabolism ; Glutathione Reductase/*chemistry/genetics/metabolism ; Glycine/chemistry ; Kinetics ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; *Mutagenesis, Site-Directed ; NADP/metabolism ; Plasmids ; Protein Multimerization ; Tryptophan/chemistry
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  • 34
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    Recognition of tRNA precursors: a role for the intron (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-03-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abelson, J -- New York, N.Y. -- Science. 1992 Mar 13;255(5050):1390.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, Pasadena 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1542787" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Endoribonucleases/*metabolism ; Introns/*physiology ; RNA Precursors/*metabolism ; RNA Splicing/*physiology ; RNA, Transfer/*metabolism
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  • 35
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    Repression of the insulin-like growth factor II gene by the Wilms tumor suppressor WT1 (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-07-31
    Description: The Wilms tumor suppressor gene wt1 encodes a zinc finger DNA binding protein, WT1, that functions as a transcriptional repressor. The fetal mitogen insulin-like growth factor II (IGF-II) is overexpressed in Wilms tumors and may have autocrine effects in tumor progression. The major fetal IGF-II promoter was defined in transient transfection assays as a region spanning from nucleotides -295 to +135, relative to the transcription start site. WT1 bound to multiple sites in this region and functioned as a potent repressor of IGF-II transcription in vivo. Maximal repression was dependent on the presence of WT1 binding sites on each side of the transcriptional initiation site. These findings provide a molecular basis for overexpression of IGF-II in Wilms tumors and suggest that WT1 negatively regulates blastemal cell proliferation by limiting the production of a fetal growth factor in the developing vertebrate kidney.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Drummond, I A -- Madden, S L -- Rohwer-Nutter, P -- Bell, G I -- Sukhatme, V P -- Rauscher, F J 3rd -- CA 10817/CA/NCI NIH HHS/ -- CA 47983/CA/NCI NIH HHS/ -- CA 52009/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Jul 31;257(5070):674-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of Chicago, IL 60637.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1323141" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Blotting, Northern ; DNA/chemistry/metabolism ; DNA-Binding Proteins/*metabolism ; Deoxyribonuclease I/metabolism ; *Gene Expression Regulation, Neoplastic ; Genes, Wilms Tumor/*physiology ; Humans ; Insulin-Like Growth Factor II/*genetics ; Kidney/embryology/metabolism ; Mice ; Molecular Sequence Data ; Promoter Regions, Genetic ; Rats ; Sequence Homology, Nucleic Acid ; Transfection ; WT1 Proteins ; Wilms Tumor/genetics/metabolism ; Zinc Fingers
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  • 36
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    Sequence discrimination by alternatively spliced isoforms of a DNA binding zinc finger domain (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-09-25
    Description: Two major developmentally regulated isoforms of the Drosophila chorion transcription factor CF2 differ by an extra zinc finger within the DNA binding domain. The preferred DNA binding sites were determined and are distinguished by an internal duplication of TAT in the site recognized by the isoform with the extra finger. The results are consistent with modular interactions between zinc fingers and trinucleotides and also suggest rules for recognition of AT-rich DNA sites by zinc finger proteins. The results show how modular finger interactions with trinucleotides can be used, in conjunction with alternative splicing, to alter the binding specificity and increase the spectrum of sites recognized by a DNA binding domain. Thus, CF2 may potentially regulate distinct sets of target genes during development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gogos, J A -- Hsu, T -- Bolton, J -- Kafatos, F C -- New York, N.Y. -- Science. 1992 Sep 25;257(5078):1951-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Developmental Biology, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1290524" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; DNA-Binding Proteins/*metabolism ; *Drosophila Proteins ; Drosophila melanogaster/genetics ; Hydrogen Bonding ; Molecular Sequence Data ; Oligodeoxyribonucleotides/chemistry/metabolism ; Protein Binding ; *Regulatory Sequences, Nucleic Acid ; Structure-Activity Relationship ; Transcription Factors/*metabolism ; *Zinc Fingers
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    Actin constitution: guaranteeing the right to assemble (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wertman, K F -- Drubin, D G -- GM42759/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Oct 30;258(5083):759-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1439782" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/*chemistry/genetics/metabolism ; Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Models, Molecular ; Molecular Structure ; Mutation ; Rabbits ; Tetrahymena/chemistry
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    Pseudo--half-knot formation with RNA (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-14
    Description: A pseudo--half-knot can be formed by binding an oligonucleotide asymmetrically to an RNA hairpin loop. This binding motif was used to target the human immunodeficiency virus TAR element, an important viral RNA structure that is the receptor for Tat, the major viral transactivator protein. Oligonucleotides complementary to different halves of the TAR structure bound with greater affinity than molecules designed to bind symmetrically around the hairpin. The pseudo--half-knot--forming oligonucleotides altered the TAR structure so that specific recognition and binding of a Tat-derived peptide was disrupted. This general binding motif may be used to disrupt the structure of regulatory RNA hairpins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ecker, D J -- Vickers, T A -- Bruice, T W -- Freier, S M -- Jenison, R D -- Manoharan, M -- Zounes, M -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):958-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉ISIS Pharmaceuticals, Carlsbad, CA 92008.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1502560" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; DNA, Viral/metabolism ; Gene Products, tat/metabolism ; HIV/*genetics ; Kinetics ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Oligoribonucleotides/*chemistry ; RNA, Viral/*chemistry/genetics/metabolism ; tat Gene Products, Human Immunodeficiency Virus
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  • 39
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    Spatial control of the gap gene knirps in the Drosophila embryo by posterior morphogen system (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-02-21
    Description: The gap genes of Drosophila are the first zygotic genes to respond to the maternal positional signals and establish the body pattern along the anterior-posterior axis. The gap gene knirps, required for patterning in the posterior region of the embryo, can be activated throughout the wild-type embryo and is normally repressed from the anterior and posterior sides. These results provide direct molecular evidence that the posterior morphogen system interacts in a fundamentally different manner than do hunchback and bicoid, which are responsible for anterior pattern formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pankratz, M J -- Busch, M -- Hoch, M -- Seifert, E -- Jackle, H -- New York, N.Y. -- Science. 1992 Feb 21;255(5047):986-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck Institut fur Biophysikalische Chemie, Abteilung Molekulare Entwicklungsbiologie, Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1546296" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Cloning, Molecular ; Drosophila melanogaster/embryology/*genetics ; Gene Expression Regulation ; Genes ; Molecular Sequence Data ; Morphogenesis ; Regulatory Sequences, Nucleic Acid
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    Nucleotide-iron-sulfur cluster signal transduction in the nitrogenase iron-protein: the role of Asp125 (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-11-06
    Description: Electron transfer in nitrogenase involves a gating process initiated by MgATP (magnesium adenosine triphosphate) binding to Fe-protein. The redox site, an 4Fe:4S cluster, is structurally separated from the MgATP binding site. For MgATP hydrolysis to be coupled to electron transfer, a signal transduction mechanism is proposed that is similar to that in guanosine triphosphatase proteins. Based on the three-dimensional structure of Fe-protein, Asp125 is likely to be part of a putative transduction path. Altered Fe-protein with Glu replacing Asp has been prepared and retains the ability for the initial nucleotide-dependent conformational change. However, either MgADP or MgATP can induce the shift and Mg binding to the nucleotide is no longer essential.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wolle, D -- Dean, D R -- Howard, J B -- New York, N.Y. -- Science. 1992 Nov 6;258(5084):992-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Minnesota, Minneapolis 55455.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1359643" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/*metabolism ; Aspartic Acid/*metabolism ; Azotobacter vinelandii/enzymology ; Binding Sites ; Crystallization ; Electron Transport ; Glutamates ; Glutamic Acid ; Iron-Sulfur Proteins/*metabolism ; Molecular Structure ; Mutagenesis, Site-Directed ; Nitrogenase/chemistry/genetics/*metabolism ; Protein Conformation ; Signal Transduction/*physiology
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    Overlapping but nonidentical binding sites on CD2 for CD58 and a second ligand CD59 (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-06-26
    Description: The interaction of the T cell glycoprotein CD2 with one ligand, CD58, contributes to T cell function. We have identified CD59, a glycoprotein with complement-inhibitory function, as a second physiological ligand for CD2. Antibodies to CD59 inhibit CD2-dependent T cell activation in murine T cell hybridomas expressing human CD2. In an in vitro binding assay with purified CD58 and CD59, CD2+ cells bind not only immobilized CD58 but also CD59. With two complementary approaches, it was demonstrated that the binding sites on CD2 for CD58 and CD59 are overlapping but nonidentical. These observations suggest that direct interactions between CD2 and both CD58 and CD59 contribute to T cell activation and adhesion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hahn, W C -- Menu, E -- Bothwell, A L -- Sims, P J -- Bierer, B E -- AI28554/AI/NIAID NIH HHS/ -- HL36061/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1992 Jun 26;256(5065):1805-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Pediatric Oncology, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, MA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1377404" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD/*metabolism ; Antigens, CD2 ; Antigens, CD58 ; Antigens, CD59 ; Antigens, Differentiation, T-Lymphocyte/*metabolism ; Binding Sites ; Dose-Response Relationship, Drug ; Humans ; Hybridomas ; Immunity, Cellular ; In Vitro Techniques ; Membrane Glycoproteins/*metabolism ; Mice ; Receptors, Antigen, T-Cell/*physiology ; Receptors, Immunologic/*metabolism ; T-Lymphocytes/immunology
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    Predicted structural similarities of the DNA binding domains of c-Myc and endonuclease Eco RI (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-24
    Description: The c-Myc oncoprotein belongs to a family of proteins whose DNA binding domains contain a basic region-helix-loop-helix (bHLH) motif. Systematic mutagenesis of c-Myc revealed that dimerized bHLH motifs formed a parallel four-helix bundle with the amino termini of helices 1 and 2 directed toward the inner and outer nucleotides of the DNA binding site, respectively. Both the basic region and the carboxyl-terminal end of the loop contributed to DNA binding specificity. The DNA binding domain of c-Myc may therefore be structurally similar to that of restriction endonuclease Eco RI.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Halazonetis, T D -- Kandil, A N -- New York, N.Y. -- Science. 1992 Jan 24;255(5043):464-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cancer Research, Merck Sharp and Dohme Research Laboratories, West Point, PA 19486.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1734524" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; DNA-Binding Proteins/*chemistry ; Deoxyribonuclease EcoRI/*chemistry ; Humans ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Proto-Oncogene Proteins c-myc/*chemistry ; Sequence Alignment ; Transcription Factors/chemistry
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    Dimerization of a specific DNA-binding protein on the DNA (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-10
    Description: Many specific DNA-binding proteins bind to sites with dyad symmetry, and the bound form of the protein is a dimer. For some proteins, dimers form in solution and bind to DNA. LexA repressor of Escherichia coli has been used to test an alternative binding model in which two monomers bind sequentially. This model predicts that a repressor monomer should bind with high specificity to an isolated operator half-site. Monomer binding to a half-site was observed. A second monomer bound to an intact operator far more tightly than the first monomer; this cooperativity arose from protein-protein contacts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, B -- Little, J W -- GM24178/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Jan 10;255(5041):203-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Arizona, Tucson 85721.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1553548" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*metabolism ; Base Sequence ; Binding Sites ; DNA, Bacterial/*metabolism ; DNA-Binding Proteins/*metabolism ; Deoxyribonucleases ; Escherichia coli/*metabolism ; Kinetics ; Macromolecular Substances ; Models, Structural ; Molecular Sequence Data ; Oligodeoxyribonucleotides/metabolism ; Operon ; Rec A Recombinases/genetics ; Repressor Proteins/metabolism ; *Serine Endopeptidases
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    Modulation of the dimerization of a transcriptional antiterminator protein by phosphorylation (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-09-04
    Description: The transcriptional antiterminator protein BglG inhibits transcription termination of the bgl operon in Escherichia coli when it is in the nonphosphorylated state. The BglG protein is now shown to exist in two configurations, an active, dimeric nonphosphorylated form and an inactive, monomeric phosphorylated form. The migration of BglG on native polyacrylamide gels was consistent with it existing as a dimer when nonphosphorylated and as a monomer when phosphorylated. Only the nonphosphorylated dimer was found to bind to the target RNA. When the dimerization domain of the lambda repressor was replaced with BglG, the resulting chimera behaved like an intact lambda repressor in its ability to repress lambda gene expression, which suggests that BglG dimerizes in vivo. Repression by the lambda-BglG hybrid was significantly reduced by BglF, the BglG kinase, an effect that was relieved by conditions that stimulate dephosphorylation of BglG by BglF. These results suggest that the phosphorylation and the dephosphorylation of BglG regulate its activity by controlling its dimeric state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Amster-Choder, O -- Wright, A -- New York, N.Y. -- Science. 1992 Sep 4;257(5075):1395-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Microbiology, Tufts University Health Sciences Campus, Boston, MA 02111.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1382312" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Bacteriophage lambda/genetics ; Binding Sites ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/metabolism ; Macromolecular Substances ; Molecular Weight ; Operon ; Phosphorylation ; RNA/metabolism ; RNA-Binding Proteins/*chemistry/metabolism ; Repressor Proteins/metabolism ; Structure-Activity Relationship ; Transcription, Genetic
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    Identification of a protein that binds to the SH3 region of Abl and is similar to Bcr and GAP-rho (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-07
    Description: A Src homology 3 (SH3) region is a sequence of approximately 50 amino acids found in many nonreceptor tyrosine kinases and other proteins. Deletion of the SH3 region from the protein encoded by the c-abl proto-oncogene activates the protein's transforming capacity, thereby suggesting the participation of the SH3 region in the negative regulation of transformation. A complementary DNA was isolated that encoded a protein, 3BP-1, to which the SH3 region of Abl bound with high specificity and to which SH3 regions from other proteins bound differentially. The sequence of the 3BP-1 protein is similar to that of a COOH-terminal segment of Bcr and to guanosine triphosphatase-activating protein (GAP)-rho, which suggests that it might have GAP activity for Ras-related proteins. The 3BP-1 protein may therefore be a mediator of SH3 function in transformation inhibition and may link tyrosine kinases to Ras-related proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cicchetti, P -- Mayer, B J -- Thiel, G -- Baltimore, D -- A107233/PHS HHS/ -- CA 08875/CA/NCI NIH HHS/ -- CA51462/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Aug 7;257(5071):803-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rockefeller University, New York, NY 10021.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1379745" target="_blank"〉PubMed〈/a〉
    Keywords: 3T3 Cells ; Amino Acid Sequence ; Animals ; Binding Sites ; Chimera ; Cloning, Molecular ; GTPase-Activating Proteins ; Gene Library ; *Genes, abl ; *Genes, src ; Glutathione Transferase/genetics/metabolism ; Mice ; Molecular Sequence Data ; Oncogene Proteins/genetics/*metabolism ; Plasmids ; Polymerase Chain Reaction/methods ; Prosencephalon/physiology ; Protein-Tyrosine Kinases/*metabolism ; Proteins/*metabolism ; *Proto-Oncogene Proteins ; Proto-Oncogene Proteins c-abl/genetics/*metabolism ; Proto-Oncogene Proteins c-bcr ; Proto-Oncogene Proteins pp60(c-src)/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Restriction Mapping ; Rho Factor/*metabolism ; Sequence Homology, Nucleic Acid ; ras GTPase-Activating Proteins
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    Converting trypsin to chymotrypsin: the role of surface loops (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-03-06
    Description: Trypsin (Tr) and chymotrypsin (Ch) have similar tertiary structures, yet Tr cleaves peptides at arginine and lysine residues and Ch prefers large hydrophobic residues. Although replacement of the S1 binding site of Tr with the analogous residues of Ch is sufficient to transfer Ch specificity for ester hydrolysis, specificity for amide hydrolysis is not transferred. Trypsin is converted to a Ch-like protease when the binding pocket alterations are further modified by exchange of the Ch surface loops 185 through 188 and 221 through 225 for the analogous Tr loops. These loops are not structural components of either the S1 binding site or the extended substrate binding sites. This mutant enzyme is equivalent to Ch in its catalytic rate, but its substrate binding is impaired. Like Ch, this mutant utilizes extended substrate binding to accelerate catalysis, and substrate discrimination occurs during the acylation step rather than in substrate binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hedstrom, L -- Szilagyi, L -- Rutter, W J -- DK21344/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 Mar 6;255(5049):1249-53.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hormone Research Institute, University of California, San Francisco 94143-0534.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1546324" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Chymotrypsin/*chemistry/metabolism ; Hydrolysis ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Mutagenesis, Site-Directed ; Protein Conformation ; Substrate Specificity ; Trypsin/*chemistry/genetics/metabolism
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    Cloning of a subunit of yeast RNA polymerase II transcription factor b and CTD kinase (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-09-04
    Description: Yeast RNA polymerase II initiation factor b copurifies with three polypeptides of 85, 73, and 50 kilodaltons and with a protein kinase that phosphorylates the carboxyl-terminal repeat domain (CTD) of the largest polymerase subunit. The gene that encodes the 73-kilodalton polypeptide, designated TFB1, was cloned and found to be essential for cell growth. The deduced protein sequence exhibits no similarity to those of protein kinases. However, the sequence is similar to that of the 62-kilodalton subunit of the HeLa transcription factor BFT2, suggesting that this factor is the human counterpart of yeast factor b. Immunoprecipitation experiments using antibodies to the TFB1 gene product demonstrate that the transcriptional and CTD kinase activities of factor b are closely associated with an oligomer of the three polypeptides. Photoaffinity labeling with 3'-O-(4-benzoyl)benzoyl-ATP (adenosine triphosphate) identified an ATP-binding site in the 85-kilodalton polypeptide, suggesting that the 85-kilodalton subunit contains the catalytic domain of the kinase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gileadi, O -- Feaver, W J -- Kornberg, R D -- GM-36659/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Sep 4;257(5075):1389-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Sherman Fairchild Center, Stanford University Medical School, CA 94305.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1445600" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Affinity Labels ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; *Cloning, Molecular ; Immunosorbent Techniques ; Molecular Sequence Data ; Phosphorylation ; Protein Kinases/chemistry/*genetics/metabolism ; RNA Polymerase II/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; *Saccharomyces cerevisiae Proteins ; Sequence Homology, Nucleic Acid ; Transcription Factors/chemistry/*genetics ; *Transcription Factors, General ; *Transcription Factors, TFII ; *Transcriptional Elongation Factors
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    Tertiary structure around the guanosine-binding site of the Tetrahymena ribozyme (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-24
    Description: A cleavage reagent directed to the active site of the Tetrahymena catalytic RNA was synthesized by derivatization of the guanosine substrate with a metal chelator. When complexed with iron(II), this reagent cleaved the RNA in five regions. Cleavage at adenosine 207, which is far from the guanosine-binding site in the primary and secondary structure, provides a constraint for the higher order folding of the RNA. This cleavage site constitutes physical evidence for a key feature of the Michel-Westhof model. Targeting a reactive entity to a specific site should be generally useful for determining proximity within folded RNA molecules or ribonucleoprotein complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, J F -- Cech, T R -- New York, N.Y. -- Science. 1992 Apr 24;256(5056):526-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1315076" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Edetic Acid/metabolism ; Free Radicals ; Guanosine/*metabolism ; Guanosine Monophosphate/metabolism ; Iron/metabolism ; Iron Chelating Agents/metabolism ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Nucleic Acid Conformation ; Pentetic Acid/metabolism ; RNA, Catalytic/*chemistry/metabolism ; Tetrahymena/*chemistry
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    Interaction cloning: identification of a helix-loop-helix zipper protein that interacts with c-Fos (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-05-15
    Description: A facile method for isolating genes that encode interacting proteins has been developed with a polypeptide probe that contains an amino-terminal extension with recognition sites for a monoclonal antibody, a specific endopeptidase, and a site-specific protein kinase. This probe, containing the basic region-leucine zipper dimerization motif of c-Fos, was used to screen a complementary DNA library. A complementary DNA that encoded a member of the basic-helix-loop-helix-zipper (bHLH-Zip) family of proteins was isolated. The complementary DNA-encoded polypeptide FIP (Fos interacting protein) bound to oligonucleotide probes that contained DNA binding motifs for other HLH proteins. When cotransfected with c-Fos, FIP stimulated transcription of an AP-1-responsive promoter.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blanar, M A -- Rutter, W J -- DK-21344/DK/NIDDK NIH HHS/ -- DK-41822/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 May 15;256(5059):1014-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hormone Research Institute, University of California, San Francisco 94143.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1589769" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; *Cloning, Molecular ; DNA/isolation & purification ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; *Genes, fos/genetics ; HeLa Cells ; Humans ; Leucine Zippers/*genetics ; Macromolecular Substances ; Molecular Sequence Data ; Oligonucleotide Probes/chemistry/metabolism ; Protein Conformation ; Proto-Oncogene Proteins c-fos/chemistry/metabolism ; Proto-Oncogene Proteins c-jun/chemistry/metabolism ; Sequence Homology, Nucleic Acid ; Transfection
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    Activation of transcription by IFN-gamma: tyrosine phosphorylation of a 91-kD DNA binding protein (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-12-21
    Description: Interferon-gamma (IFN-gamma) induces the transcription of the gene encoding a guanylate binding protein by activating a latent cytoplasmic factor, GAF (gamma-activated factor). GAF is translocated to the nucleus and binds a DNA element, the gamma-activated site. Through cross-linking and the use of specific antibodies GAF was found to be a 91-kilodalton DNA binding protein that was previously identified as one of four proteins in interferon-stimulated gene factor-3 (ISGF-3), a transcription complex activated by IFN-alpha. The IFN-gamma-dependent activation of the 91-kilodalton DNA binding protein required cytoplasmic phosphorylation of the protein on tyrosine. The 113-kilodalton ISGF-3 protein that is phosphorylated in response to IFN-alpha was not phosphorylated nor translocated to the nucleus in response to IFN-gamma. Thus the two different ligands result in tyrosine phosphorylation of different combinations of latent cytoplasmic transcription factors that then act at different DNA binding sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shuai, K -- Schindler, C -- Prezioso, V R -- Darnell, J E Jr -- New York, N.Y. -- Science. 1992 Dec 11;258(5089):1808-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rockefeller University, New York, NY 10021.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1281555" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Cell Line ; Cell Nucleus/metabolism ; DNA-Binding Proteins/isolation & purification/*metabolism ; Electrophoresis, Gel, Two-Dimensional ; Electrophoresis, Polyacrylamide Gel ; GTP-Binding Proteins/*genetics ; Gene Expression Regulation/drug effects ; Interferon-alpha/pharmacology ; Interferon-gamma/*pharmacology ; Models, Biological ; Molecular Sequence Data ; Molecular Weight ; Oligodeoxyribonucleotides ; Phosphorylation ; Phosphotyrosine ; Promoter Regions, Genetic ; STAT1 Transcription Factor ; Signal Transduction/drug effects ; *Trans-Activators ; *Transcription, Genetic/drug effects ; Tyrosine/analogs & derivatives/analysis
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    Human and Drosophila homeodomain proteins that enhance the DNA-binding activity of serum response factor (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-21
    Description: Cells with distinct developmental histories can respond differentially to identical signals, suggesting that signals are interpreted in a fashion that reflects a cell's identity. How this might occur is suggested by the observation that proteins of the homeodomain family, including a newly identified human protein, enhance the DNA-binding activity of serum response factor, a protein required for the induction of genes by growth and differentiation factors. Interaction with proteins of the serum response factor family may allow homeodomain proteins to specify the transcriptional response to inductive signals. Moreover, because the ability to enhance the binding of serum response factor to DNA residues within the homeodomain but is independent of homeodomain DNA-binding activity, this additional activity of the homeodomain may account for some of specificity of action of homeodomain proteins in development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grueneberg, D A -- Natesan, S -- Alexandre, C -- Gilman, M Z -- CA08968/CA/NCI NIH HHS/ -- CA45642/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Aug 21;257(5073):1089-95.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, NY 11724.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1509260" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; DNA/genetics/*metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism/*pharmacology ; Drosophila/genetics ; *Drosophila Proteins ; Fungal Proteins/chemistry/pharmacology ; *Homeodomain Proteins ; Humans ; Minichromosome Maintenance 1 Protein ; Molecular Sequence Data ; Nuclear Proteins/*metabolism ; Saccharomyces cerevisiae/genetics ; Serum Response Factor ; Transcription Factors/chemistry/*metabolism/pharmacology ; Transfection
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    Human growth hormone and extracellular domain of its receptor: crystal structure of the complex (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-01-17
    Description: Binding of human growth hormone (hGH) to its receptor is required for regulation of normal human growth and development. Examination of the 2.8 angstrom crystal structure of the complex between the hormone and the extracellular domain of its receptor (hGHbp) showed that the complex consists of one molecule of growth hormone per two molecules of receptor. The hormone is a four-helix bundle with an unusual topology. The binding protein contains two distinct domains, similar in some respects to immunoglobulin domains. The relative orientation of these domains differs from that found between constant and variable domains in immunoglobulin Fab fragments. Both hGHbp domains contribute residues that participate in hGH binding. In the complex both receptors donate essentially the same residues to interact with the hormone, even though the two binding sites on hGH have no structural similarity. Generally, the hormone-receptor interfaces match those identified by previous mutational analyses. In addition to the hormone-receptor interfaces, there is also a substantial contact surface between the carboxyl-terminal domains of the receptors. The relative extents of the contact areas support a sequential mechanism for dimerization that may be crucial for signal transduction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉de Vos, A M -- Ultsch, M -- Kossiakoff, A A -- New York, N.Y. -- Science. 1992 Jan 17;255(5042):306-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Protein Engineering, Genentech, Inc., South San Francisco, CA 94080.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1549776" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography ; Growth Hormone/*chemistry/metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Structure ; Mutation ; Receptors, Somatotropin/*chemistry/metabolism ; Signal Transduction
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    NF-kappa B subunit regulation in nontransformed CD4+ T lymphocytes (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-06-05
    Description: Regulation of interleukin-2 (IL-2) gene expression by the p50 and p65 subunits of the DNA binding protein NF-kappa B was studied in nontransformed CD4+ T lymphocyte clones. A homodimeric complex of the NF-kappa B p50 subunit was found in resting T cells. The amount of p50-p50 complex decreased after full antigenic stimulation, whereas the amount of the NF-kappa B p50-p65 heterodimer was increased. Increased expression of the IL-2 gene and activity of the IL-2 kappa B DNA binding site correlated with a decrease in the p50-p50 complex. Overexpression of p50 repressed IL-2 promoter expression. The switch from p50-p50 to p50-p65 complexes depended on a protein that caused sequestration of the p50-p50 complex in the nucleus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, S M -- Tran, A C -- Grilli, M -- Lenardo, M J -- New York, N.Y. -- Science. 1992 Jun 5;256(5062):1452-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Immunology, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1604322" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD4/*immunology ; Base Sequence ; Binding Sites ; Cell Line ; Cell Nucleus/physiology ; Chloramphenicol O-Acetyltransferase/genetics/metabolism ; Clone Cells ; Columbidae ; DNA/genetics ; *Gene Expression Regulation ; Interleukin-2/*genetics ; Macromolecular Substances ; Mice ; Molecular Sequence Data ; NF-kappa B/*metabolism ; Oligonucleotide Probes ; Promoter Regions, Genetic ; RNA, Messenger/metabolism ; Recombinant Fusion Proteins/metabolism ; T-Lymphocyte Subsets/*immunology ; Transfection ; Tumor Necrosis Factor-alpha/pharmacology
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    Allosteric effects of nucleotide cofactors on Escherichia coli Rep helicase-DNA binding (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-17
    Description: The Escherichia coli Rep helicase unwinds duplex DNA during replication. The functional helicase appears to be a dimer that forms only on binding DNA. Both protomers of the dimer can bind either single-stranded or duplex DNA. Because binding and hydrolysis of adenosine triphosphate (ATP) are essential for helicase function, the energetics of DNA binding and DNA-induced Rep dimerization were studied quantitatively in the presence of the nucleotide cofactors adenosine diphosphate (ADP) and the nonhydrolyzable ATP analog AMPP(NH)P. Large allosteric effects of nucleotide cofactors on DNA binding to Rep were observed. Binding of ADP favored Rep dimers in which both protomers bound single-stranded DNA, whereas binding of AMPP(NH)P favored simultaneous binding of both single-stranded and duplex DNA to the Rep dimer. A rolling model for the active unwinding of duplex DNA by the dimeric Rep helicase is proposed that explains vectorial unwinding and predicts that helicase translocation along DNA is coupled to ATP binding, whereas ATP hydrolysis drives unwinding of multiple DNA base pairs for each catalytic event.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wong, I -- Lohman, T M -- GM30498/GM/NIGMS NIH HHS/ -- GM45948/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Apr 17;256(5055):350-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1533057" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine Nucleotides/*pharmacology ; Adenosine Diphosphate/metabolism/pharmacology ; Adenosine Triphosphatases/*metabolism ; Adenosine Triphosphate/metabolism ; Adenylyl Imidodiphosphate/pharmacology ; Base Sequence ; Binding Sites ; Binding, Competitive ; DNA/chemistry/*metabolism ; *DNA Helicases ; DNA, Single-Stranded/metabolism ; DNA, Viral/metabolism ; Escherichia coli/*enzymology ; Escherichia coli Proteins ; Macromolecular Substances ; Magnesium/pharmacology ; Molecular Sequence Data ; Nucleic Acid Conformation
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    An unlikely sugar substrate site in the 1.65 A structure of the human aldose reductase holoenzyme implicated in diabetic complications (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-07-03
    Description: Aldose reductase, which catalyzes the reduced form of nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of a wide variety of aromatic and aliphatic carbonyl compounds, is implicated in the development of diabetic and galactosemic complications involving the lens, retina, nerves, and kidney. A 1.65 angstrom refined structure of a recombinant human placenta aldose reductase reveals that the enzyme contains a parallel beta 8/alpha 8-barrel motif and establishes a new motif for NADP-binding oxidoreductases. The substrate-binding site is located in a large, deep elliptical pocket at the COOH-terminal end of the beta barrel with a bound NADPH in an extended conformation. The highly hydrophobic nature of the active site pocket greatly favors aromatic and apolar substrates over highly polar monosaccharides. The structure should allow for the rational design of specific inhibitors that might provide molecular understanding of the catalytic mechanism, as well as possible therapeutic agents.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, D K -- Bohren, K M -- Gabbay, K H -- Quiocho, F A -- DK-39,044/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 Jul 3;257(5066):81-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1621098" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Reductase/*chemistry/metabolism ; Amino Acid Sequence ; Binding Sites ; *Diabetes Complications ; Diabetes Mellitus/*enzymology ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; X-Ray Diffraction/methods
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    Participation of non-zinc finger residues in DNA binding by two nuclear orphan receptors (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-03
    Description: Steroid-thyroid hormone receptors typically bind as dimers to DNA sequences that contain repeated elements termed half-sites. NGFI-B, an early response protein and orphan member of this receptor superfamily, binds to a DNA sequence that contains only one half-site (5'-AAAGGTCA-3'). A domain separate from the NGFI-B zinc fingers, termed the A box, was identified and is required for recognition of the two adenine-thymidine (A-T) base pairs at the 5' end of the NGFI-B DNA binding element. In addition, a domain downstream of the zinc fingers of the orphan receptor H-2 region II binding protein, termed the T box, determined binding to tandem repeats of the estrogen receptor half-site (5'-AGGTCA-3').〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, T E -- Paulsen, R E -- Padgett, K A -- Milbrandt, J -- NS01018/NS/NINDS NIH HHS/ -- P01 CA49712/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Apr 3;256(5053):107-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Washington University School of Medicine, St. Louis, MO 63110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1314418" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; CHO Cells ; Cell Nucleus/*physiology ; Cricetinae ; DNA/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Kinetics ; Mice ; Molecular Sequence Data ; Nuclear Receptor Subfamily 4, Group A, Member 1 ; Oligodeoxyribonucleotides/metabolism ; Polymerase Chain Reaction ; Receptors, Cell Surface/*metabolism ; Receptors, Cytoplasmic and Nuclear ; Receptors, Steroid ; Recombinant Fusion Proteins/metabolism ; Sequence Homology, Nucleic Acid ; Substrate Specificity ; Transcription Factors/genetics/*metabolism ; Transfection ; Zinc Fingers/genetics
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    Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-12-11
    Description: The crystal structure of a 1:1 complex between yeast cytochrome c peroxidase and yeast iso-1-cytochrome c was determined at 2.3 A resolution. This structure reveals a possible electron transfer pathway unlike any previously proposed for this extensively studied redox pair. The shortest straight line between the two hemes closely follows the peroxidase backbone chain of residues Ala194, Ala193, Gly192, and finally Trp191, the indole ring of which is perpendicular to, and in van der Waals contact with, the peroxidase heme. The crystal structure at 2.8 A of a complex between yeast cytochrome c peroxidase and horse heart cytochrome c was also determined. Although crystals of the two complexes (one with cytochrome c from yeast and the other with cytochrome c from horse) grew under very different conditions and belong to different space groups, the two complex structures are closely similar, suggesting that cytochrome c interacts with its redox partners in a highly specific manner.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pelletier, H -- Kraut, J -- DK07233/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 Dec 11;258(5089):1748-55.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, San Diego, La Jolla 92093-0317.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1334573" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Cytochrome c Group/*chemistry/metabolism ; Cytochrome-c Peroxidase/*chemistry/metabolism ; *Electron Transport ; Heme/metabolism ; Horses ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Saccharomyces cerevisiae/metabolism ; X-Ray Diffraction/methods
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    Control by asparagine residues of calcium permeability and magnesium blockade in the NMDA receptor (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-09-04
    Description: The N-methyl-D-aspartate (NMDA) receptor forms a cation-selective channel with a high calcium permeability and sensitivity to channel block by extracellular magnesium. These properties, which are believed to be important for the induction of long-term changes in synaptic strength, are imparted by asparagine residues in a putative channel-forming segment of the protein, transmembrane 2 (TM2). In the NR1 subunit, replacement of this asparagine by a glutamine residue decreases calcium permeability of the channel and slightly reduces magnesium block. The same substitution in NR2 subunits strongly reduces magnesium block and increases the magnesium permeability but barely affects calcium permeability. These asparagines are in a position homologous to the site in the TM2 region (Q/R site) of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors that is occupied by either glutamine (Q) or arginine (R) and that controls divalent cation permeability of the AMPA receptor channel. Hence AMPA and NMDA receptor channels contain common structural motifs in their TM2 segments that are responsible for some of their ion selectivity and conductance properties.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burnashev, N -- Schoepfer, R -- Monyer, H -- Ruppersberg, J P -- Gunther, W -- Seeburg, P H -- Sakmann, B -- New York, N.Y. -- Science. 1992 Sep 4;257(5075):1415-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Abteilung Zellphysiologie, Max-Planck-Institut fur Medizinische Forschung, Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1382314" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Asparagine/*chemistry ; Binding Sites ; Calcium/*metabolism/pharmacology ; Cell Line ; Electric Conductivity ; Glutamates/pharmacology ; Glutamic Acid ; Ion Channels/chemistry/*physiology ; Magnesium/metabolism/*pharmacology ; Mice ; Molecular Sequence Data ; Mutagenesis ; Oocytes/metabolism ; Permeability ; Rats ; Receptors, N-Methyl-D-Aspartate/chemistry/genetics/*physiology ; Structure-Activity Relationship ; Transfection ; Xenopus
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    Aminoacyl esterase activity of the Tetrahymena ribozyme (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-06-05
    Description: Several classes of ribozymes (catalytic RNA's) catalyze reactions at phosphorus centers, but apparently no reaction at a carbon center has been demonstrated. The active site of the Tetrahymena ribozyme was engineered to bind an oligonucleotide derived from the 3' end of N-formyl-methionyl-tRNA(fMet). This ribozyme catalyzes the hydrolysis of the aminoacyl ester bond to a modest extent, 5 to 15 times greater than the uncatalyzed rate. Catalysis involves binding of the oligonucleotide to the internal guide sequence of the ribozyme and requires Mg2+ and sequence elements of the catalytic core. The ability of RNA to catalyze reactions with aminoacyl esters expands the catalytic versatility of RNA and suggests that the first aminoacyl tRNA synthetase could have been an RNA molecule.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Piccirilli, J A -- McConnell, T S -- Zaug, A J -- Noller, H F -- Cech, T R -- New York, N.Y. -- Science. 1992 Jun 5;256(5062):1420-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1604316" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Carboxylic Ester Hydrolases/*metabolism ; Kinetics ; Models, Structural ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligoribonucleotides ; RNA, Catalytic/genetics/*metabolism ; RNA, Transfer, Amino Acyl/metabolism ; *RNA, Transfer, Met ; Substrate Specificity ; Tetrahymena/*enzymology
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    Interaction of p107 with cyclin A independent of complex formation with viral oncoproteins (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-03
    Description: The p107 protein and the retinoblastoma protein (RB) both bind specifically to two viral oncoproteins, the SV40 T antigen (T) and adenoviral protein E1A (E1A). Like RB, p107 contains a segment (the pocket) that, alone, can bind specifically to T, E1A, and multiple cellular proteins. Cyclin A bound to the p107 pocket, but not the RB pocket. Although both pockets contain two, related collinear subsegments (A and B), the unique sequence in the p107 pocket that occupies the space between A and B is required for the interaction with cyclin A.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ewen, M E -- Faha, B -- Harlow, E -- Livingston, D M -- New York, N.Y. -- Science. 1992 Jan 3;255(5040):85-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dana-Farber Cancer Institute, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1532457" target="_blank"〉PubMed〈/a〉
    Keywords: Adenovirus Early Proteins ; Amino Acid Sequence ; Antigens, Polyomavirus Transforming/*metabolism ; Base Sequence ; Binding Sites ; Cell Line ; Cloning, Molecular ; Cyclins/*metabolism ; Escherichia coli/genetics ; Eye Neoplasms ; Glutathione Transferase/genetics/metabolism ; Humans ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; *Nuclear Proteins ; Oligodeoxyribonucleotides ; Oncogene Proteins, Viral/genetics/*metabolism ; Protein Conformation ; Proteins/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Retinoblastoma ; Retinoblastoma Protein/genetics/*metabolism ; Retinoblastoma-Like Protein p107 ; Structure-Activity Relationship
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    Emerging principles for the recognition of peptide antigens by MHC class I molecules (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-14
    Description: Class I major histocompatibility complex (MHC) molecules interact with self and foreign peptides of diverse amino acid sequences yet exhibit distinct allele-specific selectivity for peptide binding. The structures of the peptide-binding specificity pockets (subsites) in the groove of murine H-2Kb as well as human histocompatibility antigen class I molecules have been analyzed. Deep but highly conserved pockets at each end of the groove bind the amino and carboxyl termini of peptide through extensive hydrogen bonding and, hence, dictate the orientation of peptide binding. A deep polymorphic pocket in the middle of the groove provides the chemical and structural complementarity for one of the peptide's anchor residues, thereby playing a major role in allele-specific peptide binding. Although one or two shallow pockets in the groove may also interact with specific peptide side chains, their role in the selection of peptide is minor. Thus, usage of a limited number of both deep and shallow pockets in multiple combinations appears to allow the binding of a broad range of peptides. This binding occurs with high affinity, primarily because of extensive interactions with the peptide backbone and the conserved hydrogen bonding network at both termini of the peptide. Interactions between the anchor residue (or residues) and the corresponding allele-specific pocket provide sufficient extra binding affinity not only to enhance specificity but also to endure the presentation of the peptide at the cell surface for recognition by T cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matsumura, M -- Fremont, D H -- Peterson, P A -- Wilson, I A -- CA-09523/CA/NCI NIH HHS/ -- CA-97489/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):927-34.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1323878" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antigens/chemistry/*metabolism ; Binding Sites ; H-2 Antigens/chemistry/*metabolism ; HLA-A2 Antigen/chemistry ; Histocompatibility Antigens Class I/chemistry/*metabolism ; Hydrogen Bonding ; Mice ; Models, Molecular ; Molecular Sequence Data ; Ovalbumin/chemistry/metabolism ; Peptide Fragments/chemistry/metabolism ; Peptides/chemistry/*metabolism ; Protein Conformation ; Solvents ; Vesicular stomatitis Indiana virus/metabolism ; Viral Proteins/chemistry/*metabolism
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    DNA sequencing by primer walking with strings of contiguous hexamers (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-12-11
    Description: When template DNA is saturated with a single-stranded DNA binding protein (SSB), strings of three or four contiguous hexanucleotides (hexamers) can cooperate through base-stacking interactions to prime DNA synthesis specifically from the 3' end of the string. Under the same conditions, priming by individual hexamers is suppressed. Strings of three of four hexamers representing more than 200 of the 4096 possible hexamers primed easily readable sequence ladders at more than 75 different sites in single-stranded or denatured double-stranded templates 6.4 kilobases to 40 kilobase pairs long, with a success rate of 60 to 90 percent. A synthesis of 1 micromole of hexamer supplies enough material for thousands of primings, so multiple libraries of all 4096 hexamers could be distributed at a reasonable cost. Such libraries would allow rapid and economical sequencing. Automating this strategy could increase the speed and efficiency of large-scale DNA sequencing by at least an order of magnitude.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kieleczawa, J -- Dunn, J J -- Studier, F W -- New York, N.Y. -- Science. 1992 Dec 11;258(5089):1787-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biology Department, Brookhaven National Laboratory, Upton, NY 11973.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1465615" target="_blank"〉PubMed〈/a〉
    Keywords: *Base Sequence ; Binding Sites ; DNA/*genetics/metabolism ; DNA, Viral/genetics ; DNA-Binding Proteins/metabolism ; Escherichia coli/metabolism ; *Genetic Techniques ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Oligodeoxyribonucleotides ; Sulfur Radioisotopes ; Templates, Genetic
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    Solution structure of the SH3 domain of Src and identification of its ligand-binding site (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-12-04
    Description: The Src homology 3 (SH3) region is a protein domain of 55 to 75 amino acids found in many cytoplasmic proteins, including those that participate in signal transduction pathways. The solution structure of the SH3 domain of the tyrosine kinase Src was determined by multidimensional nuclear magnetic resonance methods. The molecule is composed of two short three-stranded anti-parallel beta sheets packed together at approximately right angles. Studies of the SH3 domain bound to proline-rich peptide ligands revealed a hydrophobic binding site on the surface of the protein that is lined with the side chains of conserved aromatic amino acids.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, H -- Rosen, M K -- Shin, T B -- Seidel-Dugan, C -- Brugge, J S -- Schreiber, S L -- 1-S10-RR04870/RR/NCRR NIH HHS/ -- CA27951/CA/NCI NIH HHS/ -- GM44993/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Dec 4;258(5088):1665-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1280858" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Cloning, Molecular ; Escherichia coli/genetics ; Glutathione Transferase/chemistry/genetics/isolation & purification ; Ligands ; Magnetic Resonance Spectroscopy ; Molecular Sequence Data ; Neurons/physiology ; Protein Conformation ; *Protein Structure, Secondary ; Protein-Tyrosine Kinases/*genetics ; Proto-Oncogene Proteins pp60(c-src)/*chemistry ; Recombinant Fusion Proteins/chemistry/isolation & purification ; Solutions ; X-Ray Diffraction
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    A site on rod G protein alpha subunit that mediates effector activation (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-05-15
    Description: The heterotrimeric guanine nucleotide binding proteins (G proteins) are activated by sensory or hormone receptors. In turn, the G proteins activate effector proteins such as adenylyl cyclase, cyclic guanosine 3',5'-monophosphate phosphodiesterase (cGMP PDE), phospholipase C, and potassium and calcium ion channels by mechanisms that are poorly understood. A site on the alpha subunit of the G protein transducin (alpha t) has been identified that interacts with and activates cGMP phosphodiesterase, the effector enzyme in rod photoreceptors. A 22-amino acid peptide, corresponding to residues 293 to 314 from the COOH-terminal region of alpha t, fully mimicked alpha t and potently activated PDE. This region is adjacent to the receptor activation domain; thus, the alpha subunit of this G protein has a site for interaction with both its effector and receptor that maps near the COOH-terminus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rarick, H M -- Artemyev, N O -- Hamm, H E -- EY 06062/EY/NEI NIH HHS/ -- T32 HL 07692-02/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1992 May 15;256(5059):1031-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology and Biophysics, University of Illinois College of Medicine, Chicago 60680.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1317058" target="_blank"〉PubMed〈/a〉
    Keywords: 3',5'-Cyclic-GMP Phosphodiesterases/*metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Cattle ; Chromatography, High Pressure Liquid ; Enzyme Activation/drug effects ; GTP-Binding Proteins/*chemistry/*physiology ; Guanosine 5'-O-(3-Thiotriphosphate)/metabolism ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; Macromolecular Substances ; Molecular Sequence Data ; Peptide Fragments/chemistry/*pharmacology ; Protein Conformation
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    Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-06-26
    Description: A 3.5 angstrom resolution electron density map of the HIV-1 reverse transcriptase heterodimer complexed with nevirapine, a drug with potential for treatment of AIDS, reveals an asymmetric dimer. The polymerase (pol) domain of the 66-kilodalton subunit has a large cleft analogous to that of the Klenow fragment of Escherichia coli DNA polymerase I. However, the 51-kilodalton subunit of identical sequence has no such cleft because the four subdomains of the pol domain occupy completely different relative positions. Two of the four pol subdomains appear to be structurally related to subdomains of the Klenow fragment, including one containing the catalytic site. The subdomain that appears likely to bind the template strand at the pol active site has a different structure in the two polymerases. Duplex A-form RNA-DNA hybrid can be model-built into the cleft that runs between the ribonuclease H and pol active sites. Nevirapine is almost completely buried in a pocket near but not overlapping with the pol active site. Residues whose mutation results in drug resistance have been approximately located.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kohlstaedt, L A -- Wang, J -- Friedman, J M -- Rice, P A -- Steitz, T A -- GM 39546/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Jun 26;256(5065):1783-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1377403" target="_blank"〉PubMed〈/a〉
    Keywords: Azepines/pharmacology ; Binding Sites ; Crystallography ; DNA Polymerase I/chemistry ; Escherichia coli/genetics ; HIV-1/*enzymology ; Models, Molecular ; Molecular Structure ; Nevirapine ; Protein Conformation ; Pyridines/pharmacology ; RNA-Directed DNA Polymerase/*chemistry
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    Beta ribbon: a new DNA recognition motif (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-03-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, S H -- New York, N.Y. -- Science. 1992 Mar 6;255(5049):1217-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1546321" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; DNA/*chemistry/metabolism ; Models, Molecular ; Molecular Structure ; *Nucleic Acid Conformation
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    Malignant transformation by a mutant of the IFN-inducible dsRNA-dependent protein kinase (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-09-18
    Description: The double-stranded RNA-dependent protein kinase (dsRNA-PK) is thought to be a key mediator of the antiviral and antiproliferative effects of interferons (IFNs). Studies examining the physiological function of the kinase suggest that it participates in cell growth and differentiation by regulating protein synthesis. Autophosphorylation and consequent activation of dsRNA-PK in vitro and in vivo result in phosphorylation of the alpha subunit of eukaryotic initiation factor-2 (eIF-2) and inhibition of protein synthesis. Expression of a functionally defective mutant of human dsRNA-PK in NIH 3T3 cells resulted in malignant transformation, suggesting that dsRNA-PK may function as a suppressor of cell proliferation and tumorigenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koromilas, A E -- Roy, S -- Barber, G N -- Katze, M G -- Sonenberg, N -- AI22646/AI/NIAID NIH HHS/ -- RR00166/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1992 Sep 18;257(5077):1685-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1382315" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Cell Division ; Cell Line ; *Cell Transformation, Neoplastic ; Cloning, Molecular ; DNA/genetics ; Enzyme Induction ; Gene Expression ; Humans ; Immunoblotting ; Interferons/*pharmacology ; Mice ; Molecular Sequence Data ; *Mutation ; Phosphorylation ; Protein Kinases/chemistry/*genetics/physiology ; Transfection ; eIF-2 Kinase
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    Cell cycle-regulated binding of c-Abl tyrosine kinase to DNA (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-04-17
    Description: The proto-oncogene c-abl encodes a protein tyrosine kinase that is localized in the cytoplasm and the nucleus. The large carboxyl-terminal segment of c-Abl was found to contain a DNA-binding domain that was necessary for the association of c-Abl with chromatin. The DNA-binding activity of c-Abl was lost during mitosis when the carboxyl-terminal segment became phosphorylated. In vitro phosphorylation of the DNA-binding domain by cdc2 kinase abolished DNA binding. Homozygous mutant mice expressing a c-Abl tyrosine kinase without the DNA-binding domain have been reported to die of multiple defects at birth. Thus, binding of the c-Abl tyrosine kinase to DNA may be essential to its biological function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kipreos, E T -- Wang, J Y -- CA 43054/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Apr 17;256(5055):382-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of California San Diego, La Jolla 92093-0116.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1566087" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Cell Cycle/*physiology ; Chromatography, Affinity ; DNA/*metabolism ; *Genes, abl ; Mice ; Molecular Sequence Data ; Mutagenesis ; Phosphorylation ; Phosphoserine/metabolism ; Phosphothreonine/metabolism ; Protein-Tyrosine Kinases/chemistry/genetics/*metabolism ; Proto-Oncogene Proteins c-abl/chemistry/genetics/*metabolism ; Structure-Activity Relationship
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    Calcium-regulated phosphorylation within the leucine zipper of C/EBP beta (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-17
    Description: Alterations in intracellular calcium levels activate several signal transduction pathways resulting in distinct patterns of gene expression. Here, a pathway for calcium-mediated signals is demonstrated that involves C/EBP beta, a member of the bZip family of transcription factors. In pituitary cells C/EBP beta was phosphorylated in response to increased intracellular calcium concentrations as a consequence of the activation of a calcium-calmodulin-dependent protein kinase. Phosphorylation of serine at position 276 within the leucine zipper of C/EBP beta appeared to confer calcium-regulated transcriptional stimulation of a promoter that contained binding sites for C/EBP beta.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wegner, M -- Cao, Z -- Rosenfeld, M G -- New York, N.Y. -- Science. 1992 Apr 17;256(5055):370-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, San Diego, La Jolla 92093-0648.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1314426" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; CCAAT-Enhancer-Binding Proteins ; Calcimycin/pharmacology ; Calcium/*pharmacology ; Calcium-Calmodulin-Dependent Protein Kinases ; Cell Line ; DNA/chemistry/genetics/metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Enzyme Activation/drug effects ; *Leucine Zippers ; Molecular Sequence Data ; Nuclear Proteins/chemistry/*metabolism ; Phosphorylation ; Phosphoserine/metabolism ; Pituitary Gland/metabolism ; Protein Kinases/metabolism ; Signal Transduction/drug effects ; Transcription Factors/chemistry/*metabolism ; Transcription, Genetic/drug effects ; Transfection
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    Transactivation by AP-1 is a molecular target of T cell clonal anergy (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-08-21
    Description: Anergy is a mechanism of T lymphocyte tolerance induced by antigen receptor stimulation in the absence of co-stimulation. Anergic T cells were shown to have a defect in antigen-induced transcription of the interleukin-2 gene. Analysis of the promoter indicated that the transcription factor AP-1 and its corresponding cis element were specifically down-regulated. Exposure of anergic T cells to interleukin-2 restored both antigen responsiveness and activity of the AP-1 element.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, S M -- Beverly, B -- Tran, A C -- Brorson, K -- Schwartz, R H -- Lenardo, M J -- New York, N.Y. -- Science. 1992 Aug 21;257(5073):1134-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1509265" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigen-Presenting Cells/immunology ; Antigens/*immunology ; Base Sequence ; Binding Sites ; Blotting, Northern ; Cell Line ; Concanavalin A/pharmacology ; *Gene Expression Regulation ; *Immune Tolerance ; Interleukin-2/*genetics/pharmacology ; Mice ; Molecular Sequence Data ; Mutation ; Promoter Regions, Genetic/genetics ; Proto-Oncogene Proteins c-jun/*physiology ; RNA, Messenger/metabolism ; Receptors, Antigen, T-Cell/immunology ; T-Lymphocytes/*immunology ; Transcription, Genetic ; Transfection
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    Structural basis of the intrasteric regulation of myosin light chain kinases (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-10-02
    Description: The smooth muscle myosin light chain kinase (smMLCK) catalytic core was modeled by using the crystallographic coordinates of the cyclic AMP-dependent protein kinase catalytic subunit (cAPK) and a bound pseudosubstrate inhibitor peptide, PKI(5-24). Despite only 30% identity in amino acid sequence, the MLCK sequence can be readily accommodated in this structure. With the exception of the short B-helix, all major elements of secondary structure in the core are very likely conserved. The active site of the modeled MLCK complements the known requirements for peptide substrate recognition. MLCK contains a pseudosubstrate sequence that overlaps the calmodulin binding domain and has been proposed to act as an intrasteric inhibitor and occupy the substrate binding site in the absence of Ca(2+)-calmodulin. The pseudosubstrate sequence can be modeled easily into the entire backbone of PKI(5-24). The results demonstrate that the intrasteric model for regulation of MLCK by intramolecular competitive inhibition is structurally plausible.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knighton, D R -- Pearson, R B -- Sowadski, J M -- Means, A R -- Ten Eyck, L F -- Taylor, S S -- Kemp, B E -- T32CA09523/CA/NCI NIH HHS/ -- T32DK07233/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 Oct 2;258(5079):130-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California San Diego, La Jolla 92093-0654.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1439761" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chromosome Mapping ; Crystallography ; *Gene Expression Regulation, Enzymologic ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Myosin-Light-Chain Kinase/*chemistry ; Oligopeptides/genetics/metabolism ; Peptide Fragments ; Peptides/genetics/metabolism ; Protein Binding/physiology ; Protein Kinases/chemistry ; Sequence Alignment ; Sequence Homology
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    Structural models for the metal centers in the nitrogenase molybdenum-iron protein (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-09-18
    Description: Structural models for the nitrogenase FeMo-cofactor and P-clusters are proposed based on crystallographic analysis of the nitrogenase molybdenum-iron (MoFe)-protein from Azotobacter vinelandii at 2.7 angstrom resolution. Each center consists of two bridged clusters; the FeMo-cofactor has 4Fe:3S and 1Mo:3Fe:3S clusters bridged by three non-protein ligands, and the P-clusters contain two 4Fe:4S clusters bridged by two cysteine thiol ligands. Six of the seven Fe sites in the FeMo-cofactor appear to have trigonal coordination geometry, including one ligand provided by a bridging group. The remaining Fe site has tetrahedral geometry and is liganded to the side chain of Cys alpha 275. The Mo site exhibits approximate octahedral coordination geometry and is liganded by three sulfurs in the cofactor, two oxygens from homocitrate, and the imidazole side chain of His alpha 442. The P-clusters are liganded by six cysteine thiol groups, two which bridge the two clusters, alpha 88 and beta 95, and four which singly coordinate the remaining Fe sites, alpha 62, alpha 154, beta 70, and beta 153. The side chain of Ser beta 188 may also coordinate one iron. The polypeptide folds of the homologous alpha and beta subunits surrounding the P-clusters are approximately related by a twofold rotation that may be utilized in the binding interactions between the MoFe-protein and the nitrogenase Fe-protein. Neither the FeMo-cofactor nor the P-clusters are exposed to the surface, suggesting that substrate entry, electron transfer, and product release must involve a carefully regulated sequence of interactions between the MoFe-protein and Fe-protein of nitrogenase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, J -- Rees, D C -- New York, N.Y. -- Science. 1992 Sep 18;257(5077):1677-82.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1529354" target="_blank"〉PubMed〈/a〉
    Keywords: Azotobacter vinelandii/*enzymology ; Binding Sites ; Chemistry, Physical ; Crystallization ; Electron Transport ; Iron-Sulfur Proteins/chemistry ; Macromolecular Substances ; *Models, Molecular ; Molecular Structure ; Molybdoferredoxin/*chemistry ; Nitrogen/metabolism ; Nitrogenase/*chemistry ; Oxidation-Reduction ; Physicochemical Phenomena ; Spectrum Analysis ; X-Ray Diffraction
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    IL-1 beta and Escherichia coli (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-12-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, K S -- Le, J -- New York, N.Y. -- Science. 1992 Dec 4;258(5088):1562-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1455239" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Escherichia coli/*drug effects/growth & development/pathogenicity ; Humans ; Interleukin-1/*pharmacology ; Virulence
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    A transcriptional enhancer whose function imposes a requirement that proteins track along DNA (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-05-29
    Description: Transcriptional regulation of the bacteriophage T4 late genes requires the participation of three DNA polymerase accessory proteins that are encoded by T4 genes 44, 62, and 45, and that act at an enhancer-like site. Transcriptional activation by these DNA replication proteins also requires the function of an RNA polymerase-bound coactivator protein that is encoded by T4 gene 33 and a promoter recognition protein that is encoded by T4 gene 55. Transcriptional activation in DNA constructs, in which the enhancer and a T4 late promoter can be segregated on two rings of a DNA catenane, has now been analyzed. The ability of an interposed DNA-binding protein to affect communication between the enhancer and the promoter was also examined. Together, these experiments demonstrate that this transcription-activating signal is conveyed between its enhancer and a T4 late promoter by a DNA-tracking mechanism. Alternative activation mechanisms relying entirely on through-space interactions of enhancer-bound and promoter-bound proteins are excluded.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herendeen, D R -- Kassavetis, G A -- Geiduschek, E P -- New York, N.Y. -- Science. 1992 May 29;256(5061):1298-303.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of California, San Diego, La Jolla 92093-0634.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1598572" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; DNA Replication ; DNA, Viral/*genetics/metabolism ; DNA-Directed DNA Polymerase/metabolism ; Deoxyribonuclease EcoRI/genetics/metabolism ; *Enhancer Elements, Genetic ; Escherichia coli/*genetics ; Gene Expression Regulation, Viral ; *Genes, Viral ; Models, Genetic ; Plasmids ; Restriction Mapping ; T-Phages/*genetics ; *Trans-Activators ; *Transcription, Genetic ; Transcriptional Activation ; Viral Proteins/genetics/*metabolism
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    Alternative forms of Max as enhancers or suppressors of Myc-ras cotransformation (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-04-17
    Description: Max is a basic-helix-loop-helix-leucine zipper protein capable of forming sequence-specific DNA binding complexes with Myc proteins. An alternatively spliced messenger RNA has been identified that encodes a form of Max truncated at the COOH-terminus. This delta Max protein retained the ability to bind to the CACGTG motif in a complex with c-Myc but lacks the nuclear localization signal and the putative regulatory domain of Max. When tested in a myc-ras cotransformation assay in rat embryo fibroblasts, Max suppressed, whereas delta Max enhanced, transformation. Thus, the max gene may encode both a negative and a positive regulator of c-Myc function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Makela, T P -- Koskinen, P J -- Vastrik, I -- Alitalo, K -- New York, N.Y. -- Science. 1992 Apr 17;256(5055):373-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Virology, University of Helsinki, Finland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1566084" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; Basic-Leucine Zipper Transcription Factors ; Binding Sites ; Cell Nucleus/metabolism ; Cell Transformation, Neoplastic/*drug effects/genetics ; DNA/chemistry/metabolism ; DNA-Binding Proteins/genetics/metabolism/*pharmacology ; Fibroblasts ; *Genes, myc ; *Genes, ras ; Humans ; Immunosorbent Techniques ; Molecular Sequence Data ; Polymerase Chain Reaction ; Proto-Oncogene Proteins c-myc/genetics/metabolism ; RNA Splicing ; RNA, Messenger/genetics ; Rats ; Structure-Activity Relationship ; *Transcription Factors ; Transfection
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  • 76
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    Invariant chain peptides in most HLA-DR molecules of an antigen-processing mutant (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-12-11
    Description: Class II major histocompatibility complexes bind peptides in an endosome-like compartment. When the class II null cell line 721.174 was transfected with class II DR3 genes, DR molecules were produced in normal amounts. However, the DR molecules were abnormally conformed and unstable because deletion of an antigen-processing gene had impaired intracellular formation of most class II-peptide complexes. Yet, 70 percent of the DR molecules still bore peptides, 80 percent of which were 21- to 24-amino acid fragments of the class II-associated invariant chain. These peptides were rare on DR3 from control cells. Thus, a defect in the main antigen-processing pathway revealed a process in which DR molecules bind long peptides derived from proteins present in the same compartment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sette, A -- Ceman, S -- Kubo, R T -- Sakaguchi, K -- Appella, E -- Hunt, D F -- Davis, T A -- Michel, H -- Shabanowitz, J -- Rudersdorf, R -- AI15486/AI/NIAID NIH HHS/ -- AI18634/AI/NIAID NIH HHS/ -- GM37537/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1992 Dec 11;258(5089):1801-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Genetics, University of Wisconsin, Madison 53706.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1465617" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Cell Line ; Gene Deletion ; *Genes, MHC Class II ; HLA-DR Antigens/*genetics/*metabolism ; HLA-DR3 Antigen/*genetics/metabolism ; Humans ; Kinetics ; Macromolecular Substances ; Molecular Sequence Data ; Peptides/*metabolism ; Transfection
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  • 77
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    Acquisition of myogenic specificity by replacement of three amino acid residues from MyoD into E12 (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-05-15
    Description: The basic helix-loop-helix (bHLH) protein MyoD is a transcription factor that is important for the induction of the myogenic phenotype. The DNA binding basic region (13 amino acids) is necessary for recognition of the consensus MyoD binding site, for transcriptional activation, and for conversion of fibroblasts to muscle. In contrast, the non-tissue-specific bHLH protein E12 can bind to the MyoD binding site but does not induce myogenesis. Here, it is shown that only two amino acids in the MyoD basic region and a single amino acid from the junction, which separates the basic region and helix 1, are sufficient for myogenic specificity when substituted into the corresponding region of E12. These findings suggest that the recognition of particular determinants in the basic region is required for conversion of fibroblasts to muscle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davis, R L -- Weintraub, H -- New York, N.Y. -- Science. 1992 May 15;256(5059):1027-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute Laboratory, Fred Hutchinson Cancer Research Center, Seattle, WA 98104.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1317057" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Cell Differentiation ; Cell Line ; DNA/metabolism ; DNA Probes ; DNA-Binding Proteins/chemistry/metabolism/pharmacology ; Fibroblasts/cytology ; Fluorescent Antibody Technique ; Molecular Sequence Data ; Muscle Proteins/chemistry/genetics/*physiology ; Muscles/*cytology ; MyoD Protein ; Protein Conformation ; Structure-Activity Relationship ; Transcription Factors/chemistry/metabolism/pharmacology ; Transfection
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  • 78
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    Interaction of U6 snRNA with a sequence required for function of the nematode SL RNA in trans-splicing (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-12-11
    Description: Nematode trans-spliced leader (SL) RNAs are composed of two domains, an exon [the 22-nucleotide spliced leader] and a small nuclear RNA (snRNA)-like sequence. Participation in vitro of the spliced leader RNA in trans-splicing reactions is independent of the exon sequence or size and instead depends on features contained in the snRNA-like domain of the molecule. Chemical modification interference analysis has revealed that two short sequence elements in the snRNA-like domain are necessary for SL RNA activity. These elements are sufficient for such activity because when added to a 72-nucleotide fragment of a nematode U1 snRNA, this hybrid RNA could participate in trans-splicing reactions in vitro. One of the critical sequence elements may function by base-pairing with U6 snRNA, an essential U snRNA for both cis- and trans-splicing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hannon, G J -- Maroney, P A -- Yu, Y T -- Hannon, G E -- Nilsen, T W -- AI28799/AI/NIAID NIH HHS/ -- GM31528/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Dec 11;258(5089):1775-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1465612" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ascaris/*genetics ; Base Sequence ; Binding Sites ; Exons ; Models, Structural ; Molecular Sequence Data ; Nucleic Acid Conformation ; *RNA Splicing ; RNA, Messenger/genetics/*metabolism ; RNA, Small Nuclear/chemistry/genetics/*metabolism
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    Conformation of the TAR RNA-arginine complex by NMR spectroscopy (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-07-03
    Description: The messenger RNAs of human immunodeficiency virus-1 (HIV-1) have an RNA hairpin structure, TAR, at their 5' ends that contains a six-nucleotide loop and a three-nucleotide bulge. The conformations of TAR RNA and of TAR with an arginine analog specifically bound at the binding site for the viral protein, Tat, were characterized by nuclear magnetic resonance (NMR) spectroscopy. Upon arginine binding, the bulge changes conformation, and essential nucleotides for binding, U23 and A27.U38, form a base-triple interaction that stabilizes arginine hydrogen bonding to G26 and phosphates. Specificity in the arginine-TAR interaction appears to be derived largely from the structure of the RNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Puglisi, J D -- Tan, R -- Calnan, B J -- Frankel, A D -- Williamson, J R -- AI29135/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1992 Jul 3;257(5066):76-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1621097" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/*metabolism ; Base Sequence ; Binding Sites ; Gene Products, tat/metabolism ; HIV-1/*genetics ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Messenger/*chemistry/metabolism ; RNA, Viral/*chemistry/metabolism ; RNA-Binding Proteins/*chemistry/metabolism ; tat Gene Products, Human Immunodeficiency Virus
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  • 80
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    Molecular characterization of helix-loop-helix peptides (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-02-21
    Description: A class of regulators of eukaryotic gene expression contains a conserved amino acid sequence responsible for protein oligomerization and binding to DNA. This structure consists of an arginine- and lysine-rich basic region followed by a helix-loop-helix motif, which together mediate specific binding to DNA. Peptides were prepared that span this motif in the MyoD protein; in solution, they formed alpha-helical dimers and tetramers. They bound to DNA as dimers and their alpha-helical content increased on binding. Parallel and antiparallel four-helix models of the DNA-bound dimer were constructed. Peptides containing disulfide bonds were engineered to test the correctness of the two models. A disulfide that is compatible with the parallel model promotes specific interaction with DNA, whereas a disulfide compatible with the antiparallel model abolishes specific binding. Electron paramagnetic resonance (EPR) measurements of nitroxide-labeled peptides provided intersubunit distance measurements that also supported the parallel model.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anthony-Cahill, S J -- Benfield, P A -- Fairman, R -- Wasserman, Z R -- Brenner, S L -- Stafford, W F 3rd -- Altenbach, C -- Hubbell, W L -- DeGrado, W F -- GM13731/GM/NIGMS NIH HHS/ -- GM14321/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Feb 21;255(5047):979-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biotechnology Department, DuPont Merck Pharmaceutical Co., Wilmington, DE 19880-0328.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1312255" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Circular Dichroism ; DNA-Binding Proteins/*chemistry ; Disulfides ; Electron Spin Resonance Spectroscopy ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Regulatory Sequences, Nucleic Acid ; Sequence Alignment ; Transcription Factors/*chemistry
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  • 81
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    A mutation in the POU-homeodomain of Pit-1 responsible for combined pituitary hormone deficiency (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-08-21
    Description: Pit-1 is a pituitary-specific transcription factor responsible for pituitary development and hormone expression in mammals. Mutations in the gene encoding Pit-1 have been found in two dwarf mouse strains displaying hypoplasia of growth hormone, prolactin, and thyroid-stimulating, hormone-secreting cell types in the anterior pituitary. A point mutation in this gene was identified on one allele in a patient with combined pituitary hormone deficiency. Mutant Pit-1 binds DNA normally but acts as a dominant inhibitor of Pit-1 action in the pituitary.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Radovick, S -- Nations, M -- Du, Y -- Berg, L A -- Weintraub, B D -- Wondisford, F E -- New York, N.Y. -- Science. 1992 Aug 21;257(5073):1115-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pediatrics, Rainbow Babies and Childrens Hospital, Cleveland, OH.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1509262" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; DNA/chemistry/genetics/metabolism ; DNA-Binding Proteins/chemistry/*genetics ; Growth Hormone/deficiency/genetics ; Humans ; Molecular Sequence Data ; *Mutation ; Pituitary Gland, Anterior/metabolism/pathology ; Pituitary Hormones/*deficiency ; Polymerase Chain Reaction ; Prolactin/deficiency/genetics ; Promoter Regions, Genetic ; Thyrotropin/deficiency/genetics ; Transcription Factor Pit-1 ; Transcription Factors/chemistry/*genetics ; Transfection
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    Isolation of a complementary DNA that encodes the mammalian splicing factor SC35 (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-24
    Description: The mammalian splicing factor SC35 is required for the first step in the splicing reaction and for spliceosome assembly. The cloning and characterization of a complementary DNA encoding this protein revealed that it is a member of a family of splicing factors that includes mammalian SF2/ASF. This family of proteins is characterized by the presence of a ribonucleoprotein (RNP)-type RNA binding motif and a carboxyl-terminal serine-arginine-rich (SR) domain. A search of the DNA sequence database revealed that the thymus-specific exon (ET) of the c-myb proto-oncogene is encoded on the antisense strand of the SC35 gene.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fu, X D -- Maniatis, T -- GM42231/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Apr 24;256(5056):535-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1373910" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Baculoviridae/genetics ; Base Sequence ; Binding Sites ; Blotting, Northern ; Cell Line ; Cloning, Molecular ; Codon ; DNA/chemistry/*isolation & purification ; Exons ; Humans ; Molecular Sequence Data ; *Nuclear Proteins ; Proteins/chemistry/*genetics ; Proto-Oncogene Proteins/genetics ; Proto-Oncogene Proteins c-myb ; RNA/metabolism ; *RNA Splicing ; *Ribonucleoproteins ; Sequence Homology, Nucleic Acid ; Transfection
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  • 83
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    Participation of the intron in the reaction catalyzed by the Xenopus tRNA splicing endonuclease (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-03-13
    Description: Introns have generally been assumed to be passive in the transfer RNA splicing reaction. Experiments have now been done showing that the endonuclease is able to cut a precursor provided that a base in the single-stranded loop of the intron can pair with the base of the 5' exon situated at the position that immediately follows the anticodon stem (position 33 in the yeast tRNA isoacceptor pre-tRNA(Leu)3, position 32 in yeast pre-tRNA(Phe)). The elucidation of the role of the intron reveals that in addition to the conserved bases, there are positions in the mature domain which, although not necessarily occupied by the same base in all pre-tRNA's, nevertheless have a fundamental role in the splicing reaction. These positions are termed cardinal positions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baldi, M I -- Mattoccia, E -- Bufardeci, E -- Fabbri, S -- Tocchini-Valentini, G P -- New York, N.Y. -- Science. 1992 Mar 13;255(5050):1404-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Cell Biology, Consiglio Nazionale delle Ricerche, Roma, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1542788" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Endoribonucleases/*metabolism ; Exons/physiology ; Introns/*physiology ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; RNA Precursors/chemistry/*metabolism ; RNA Splicing/*physiology ; RNA, Transfer/chemistry/*metabolism ; RNA, Transfer, Leu/metabolism ; RNA, Transfer, Phe/metabolism ; Xenopus laevis
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    Crystal structures of two viral peptides in complex with murine MHC class I H-2Kb (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-08-14
    Description: The x-ray structures of a murine MHC class I molecule (H-2Kb) were determined in complex with two different viral peptides, derived from the vesicular stomatitis virus nucleoprotein (52-59), VSV-8, and the Sendai virus nucleoprotein (324-332), SEV-9. The H-2Kb complexes were refined at 2.3 A for VSV-8 and 2.5 A for SEV-9. The structure of H-2Kb exhibits a high degree of similarity with human HLA class I, although the individual domains can have slightly altered dispositions. Both peptides bind in extended conformations with most of their surfaces buried in the H-2Kb binding groove. The nonamer peptide maintains the same amino- and carboxyl-terminal interactions as the octamer primarily by the insertion of a bulge in the center of an otherwise beta conformation. Most of the specific interactions are between side-chain atoms of H-2Kb and main-chain atoms of peptide. This binding scheme accounts in large part for the enormous diversity of peptide sequences that bind with high affinity to class I molecules. Small but significant conformational changes in H-2Kb are associated with peptide binding, and these synergistic movements may be an integral part of the T cell receptor recognition process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fremont, D H -- Matsumura, M -- Stura, E A -- Peterson, P A -- Wilson, I A -- CA-09523/CA/NCI NIH HHS/ -- CA-97489/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):919-27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1323877" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; H-2 Antigens/*chemistry/metabolism ; Mice ; Models, Molecular ; Molecular Sequence Data ; Parainfluenza Virus 1, Human/metabolism ; Protein Binding ; Protein Conformation ; Solvents ; Vesicular stomatitis Indiana virus/metabolism ; Viral Proteins/*chemistry/metabolism ; X-Ray Diffraction
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    Getting a handle on Ras activity (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoffman, M -- New York, N.Y. -- Science. 1992 Jan 10;255(5041):159.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1553541" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; GTP Phosphohydrolases/*metabolism ; GTPase-Activating Proteins ; Proteins/*metabolism ; Signal Transduction ; ras GTPase-Activating Proteins
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    A critical role for conserved residues in the cleft of HLA-A2 in presentation of a nonapeptide to T cells (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-14
    Description: The peptide binding cleft of the class I human histocompatibility antigen, HLA-A2, contains conserved amino acid residues clustered in the two ends of the cleft in pockets A and F as well as polymorphic residues. The function of two conserved tyrosines in the A pocket was investigated by mutating them to phenylalanines and of a conserved tyrosine and threonine in the F pocket by mutating them to phenylalanine and valine, respectively. Presentation of influenza virus peptides and of intact virus to cytolytic T lymphocytes (CTLs) was then examined. The magnitude of the reduction seen by the mutation of the two tyrosines in the A pocket suggests that hydrogen bonds involving them have a critical function in the binding of the NH2-terminal NH3+ of the peptide nonamer and possibly of all bound peptide nonamers. In contrast, the mutations in the F pocket had no effect on CTL recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Latron, F -- Pazmany, L -- Morrison, J -- Moots, R -- Saper, M A -- McMichael, A -- Strominger, J L -- AI 20182/AI/NIAID NIH HHS/ -- CA 47554/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):964-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1380181" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; B-Lymphocytes/immunology ; Binding Sites ; Cell Line ; Cloning, Molecular ; Epitopes/immunology/metabolism ; HLA-A2 Antigen/chemistry/genetics/*metabolism ; Influenza A virus ; Kinetics ; Models, Molecular ; Mutagenesis, Site-Directed ; Oligopeptides/immunology/*metabolism ; Protein Conformation ; Recombinant Proteins/chemistry/metabolism ; T-Lymphocytes, Cytotoxic/*immunology ; Transfection ; Viral Proteins/metabolism
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  • 87
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    Positive control of pre-mRNA splicing in vitro (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-04-10
    Description: Positive control of the sex-specific alternative splicing of doublesex (dsx) precursor messenger RNA (pre-mRNA) in Drosophila melanogaster involves the activation of a female-specific 3' splice site by the products of the transformer (tra) and transformer-2 (tra-2) genes. The mechanisms of this process were investigated in an in vitro system in which the female-specific 3' splice site could be activated by recombinant Tra or Tra-2 (or both). An exon sequence essential for regulation in vivo was shown to be both necessary and sufficient for activation in vitro. Nuclear proteins in addition to Tra and Tra-2 were found to bind specifically to this exon sequence. Therefore, Tra and Tra-2 may act by promoting the assembly of a multiprotein complex on the exon sequence. This complex may facilitate recognition of the adjacent 3' splice site by the splicing machinery.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tian, M -- Maniatis, T -- GM42231/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Apr 10;256(5054):237-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1566072" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Baculoviridae/genetics ; Binding Sites ; Cell Nucleus/metabolism ; Cloning, Molecular ; *Drosophila Proteins ; Drosophila melanogaster/*genetics ; Exons ; Female ; Globins/genetics ; HeLa Cells ; Humans ; Male ; Nuclear Proteins/genetics/*metabolism ; RNA Precursors/*genetics ; *RNA Splicing ; Recombinant Proteins/metabolism ; Ribonucleoproteins/genetics/*metabolism ; Sex Characteristics ; Transcription, Genetic
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  • 88
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    Site-specific modification of pre-mRNA: the 2'-hydroxyl groups at the splice sites (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-05-15
    Description: A simple and efficient method for synthesizing long, site-specifically modified RNA molecules was developed whereby segments of RNA were joined with the use of bacteriophage T4 DNA ligase. A single hydrogen or O-methyl group was substituted for the 2'-hydroxyl group at either splice site of a nuclear pre-messenger RNA substrate. Splicing of the modified pre-messenger RNA's in vitro revealed that, although a 2'-hydroxyl is not absolutely required at either splice site, the 2'-hydroxyl at the 3' splice site is important for the second step of splicing. These results are compared to previous studies of analogous 2'-hydroxyl groups in the self-splicing Tetrahymena group I intron.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moore, M J -- Sharp, P A -- P30-CA14051/CA/NCI NIH HHS/ -- R01 GM34277/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 May 15;256(5059):992-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Cancer Research, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1589782" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; DNA Ligases/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Exons ; Introns ; Kinetics ; Molecular Sequence Data ; RNA Precursors/*chemistry/metabolism ; *RNA Splicing ; RNA, Messenger/*chemistry/metabolism ; Structure-Activity Relationship ; Tetrahymena/genetics ; Viral Proteins
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  • 89
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    Threshold phenomena and long-distance activation of transcription by RNA polymerase II (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-09-18
    Description: To explore the underlying mechanisms by which genes are regulated in eukaryotes, long-distance transcriptional activation and threshold effects were reconstituted in vitro. Long-range activation of transcription by GAL4-VP16 protein located 1300 base pairs upstream of the RNA start site was dependent on packaging of the template into histone H1-containing chromatin. A transcriptional threshold effect by GAL4-VP16 was observed with repressed chromatin templates but not naked DNA templates. The experimental data with the chromatin templates were similar to the theoretical activation profile that is predicted if the action of each DNA bound protomer of GAL4-VP16 were independent and additive in terms of free energy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laybourn, P J -- Kadonaga, J T -- New York, N.Y. -- Science. 1992 Sep 18;257(5077):1682-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of California, San Diego, La Jolla 92093.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1388287" target="_blank"〉PubMed〈/a〉
    Keywords: Adenovirus Early Proteins ; Binding Sites ; Chromatin/metabolism ; DNA/metabolism ; Fungal Proteins/metabolism/pharmacology ; Oncogene Proteins, Viral/genetics ; Promoter Regions, Genetic/genetics ; RNA Polymerase II/*metabolism ; Sp1 Transcription Factor/pharmacology ; Templates, Genetic ; Trans-Activators/metabolism/pharmacology ; Transcription Factors/metabolism/pharmacology ; *Transcription, Genetic/drug effects
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  • 90
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    Cytochrome b558: the flavin-binding component of the phagocyte NADPH oxidase (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-06-05
    Description: The phagocyte respiratory burst oxidase is a flavin-adenine dinucleotide (FAD)-dependent dehydrogenase and an electron transferase that reduces molecular oxygen to superoxide anion, a precursor of microbicidal oxidants. Several proteins required for assembly of the oxidase have been characterized, but the identity of its flavin-binding component has been unclear. Oxidase activity was reconstituted in vitro with only the purified oxidase proteins p47phox, p67phox, Rac-related guanine nucleotide (GTP)-binding proteins, and membrane-bound cytochrome b558. The reconstituted oxidase required added FAD, and FAD binding was localized to cytochrome b558. Alignment of the amino acid sequence of the beta subunit of cytochrome b558 (gp91phox) with other flavoproteins revealed similarities to the nicotinamide adenine dinucleotide phosphate (reduced) (NADPH)-binding domains. Thus flavocytochrome b558 is the only obligate electron transporting component of the NADPH oxidase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rotrosen, D -- Yeung, C L -- Leto, T L -- Malech, H L -- Kwong, C H -- New York, N.Y. -- Science. 1992 Jun 5;256(5062):1459-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1318579" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Cell Line ; Cell-Free System ; Cytochrome b Group/*blood/genetics/isolation & purification ; Ferredoxin-NADP Reductase/genetics/metabolism ; Humans ; Insects ; Molecular Sequence Data ; NADH, NADPH Oxidoreductases/*blood/genetics/isolation & purification ; NADP/metabolism ; NADPH Oxidase ; Neutrophils/*enzymology ; Phagocytes/*enzymology ; Plants/enzymology ; Recombinant Proteins/chemistry/metabolism ; Sequence Homology, Nucleic Acid ; Superoxides/blood ; Transfection
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  • 91
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    The location of bound lipid in the lipovitellin complex (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-07-31
    Description: The location of the bound lipid in the soluble lipoprotein lipovitellin has been determined by neutron crystallographic techniques. With the use of the contrast variation method, whereby the crystals are soaked in different H2O-D2O mixtures, the lipid has been found to occupy a large cavity in the protein whose structure had previously been determined by x-ray crystallography. The lipid appears to be bound in the form of a bilayer with the major protein-lipid interactions being hydrophobic and with the lipid headgroups projecting into the bulk solvent and into a solvent-filled space in the cavity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Timmins, P A -- Poliks, B -- Banaszak, L -- New York, N.Y. -- Science. 1992 Jul 31;257(5070):652-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Laue-Langevin, Grenoble, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1496377" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chemistry, Physical ; Crystallography ; Deuterium ; Egg Proteins ; Egg Proteins, Dietary/*chemistry/metabolism ; *Lipid Metabolism ; Lipids/analysis ; Macromolecular Substances ; Molecular Structure ; Neutrons ; Physicochemical Phenomena ; Protein Conformation ; Water ; X-Ray Diffraction
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  • 92
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    Phthalate dioxygenase reductase: a modular structure for electron transfer from pyridine nucleotides to [2Fe-2S] (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-12-04
    Description: Phthalate dioxygenase reductase (PDR) is a prototypical iron-sulfur flavoprotein (36 kilodaltons) that utilizes flavin mononucleotide (FMN) to mediate electron transfer from the two-electron donor, reduced nicotinamide adenine nucleotide (NADH), to the one-electron acceptor, [2Fe-2S]. The crystal structure of oxidized PDR from Pseudomonas cepacia has been analyzed at 2.0 angstrom resolution resolution; reduced PDR and pyridine nucleotide complexes have been analyzed at 2.7 angstrom resolution. NADH, FMN, and the [2Fe-2S] cluster, bound to distinct domains, are brought together near a central cleft in the molecule, with only 4.9 angstroms separating the flavin 8-methyl and a cysteine sulfur ligated to iron. The domains that bind FMN and [2Fe-2S] are packed so that the flavin ring and the plane of the [2Fe-2S] core are approximately perpendicular. The [2Fe-2S] group is bound by four cysteines in a site resembling that in plant ferredoxins, but its redox potential (-174 millivolts at pH 7.0) is much higher than the potentials of plant ferredoxins. Structural and sequence similarities assign PDR to a distinct family of flavoprotein reductases, all related to ferredoxin NADP(+)-reductase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Correll, C C -- Batie, C J -- Ballou, D P -- Ludwig, M L -- GM 16429/GM/NIGMS NIH HHS/ -- GM 20877/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Dec 4;258(5088):1604-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Biophysics, University of Michigan, Ann Arbor 48109.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1280857" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Burkholderia cepacia/enzymology ; Electron Transport ; Flavin Mononucleotide/*metabolism ; Iron-Sulfur Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; NAD/*metabolism ; Oxidoreductases/*chemistry/metabolism ; *Protein Conformation ; *Protein Structure, Secondary ; Sequence Homology, Amino Acid
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  • 93
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    Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-09-18
    Description: The nitrogenase enzyme system catalyzes the ATP (adenosine triphosphate)-dependent reduction of dinitrogen to ammonia during the process of nitrogen fixation. Nitrogenase consists of two proteins: the iron (Fe)-protein, which couples hydrolysis of ATP to electron transfer, and the molybdenum-iron (MoFe)-protein, which contains the dinitrogen binding site. In order to address the role of ATP in nitrogen fixation, the crystal structure of the nitrogenase Fe-protein from Azotobacter vinelandii has been determined at 2.9 angstrom (A) resolution. Fe-protein is a dimer of two identical subunits that coordinate a single 4Fe:4S cluster. Each subunit folds as a single alpha/beta type domain, which together symmetrically ligate the surface exposed 4Fe:4S cluster through two cysteines from each subunit. A single bound ADP (adenosine diphosphate) molecule is located in the interface region between the two subunits. Because the phosphate groups of this nucleotide are approximately 20 A from the 4Fe:4S cluster, it is unlikely that ATP hydrolysis and electron transfer are directly coupled. Instead, it appears that interactions between the nucleotide and cluster sites must be indirectly coupled by allosteric changes occurring at the subunit interface. The coupling between protein conformation and nucleotide hydrolysis in Fe-protein exhibits general similarities to the H-Ras p21 and recA proteins that have been recently characterized structurally. The Fe-protein structure may be relevant to the functioning of other biochemical energy-transducing systems containing two nucleotide-binding sites, including membrane transport proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Georgiadis, M M -- Komiya, H -- Chakrabarti, P -- Woo, D -- Kornuc, J J -- Rees, D C -- GM45162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Sep 18;257(5077):1653-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Columbia University, New York, NY 10032.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1529353" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism/pharmacology ; Amino Acid Sequence ; Azotobacter vinelandii/*enzymology ; Binding Sites ; Chemistry, Physical ; Crystallization ; Electron Transport ; Hydrolysis ; Iron-Sulfur Proteins/*chemistry ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Molybdoferredoxin/chemistry ; Nitrogenase/*chemistry/metabolism ; Physicochemical Phenomena ; Protein Conformation ; X-Ray Diffraction
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  • 94
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    Getting some "backbone": how MHC binds peptides (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barinaga, M -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):880-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1502554" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Histocompatibility Antigens Class I/*chemistry/metabolism ; Humans ; Hydrogen Bonding ; Major Histocompatibility Complex ; Models, Molecular ; Protein Binding ; Protein Conformation ; Proteins/chemistry/metabolism ; T-Lymphocytes/immunology
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  • 95
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    Identification of a naturally occurring transforming variant of the p65 subunit of NF-kappa B (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-04-17
    Description: Transcription factor NF-kappa B comprises two proteins, p50 and p65, that have sequence similarity to the v-rel oncogene. In primary hematopoietic cell populations an alternatively spliced form of NF-kappa B p65 mRNA was observed that encoded a protein designated p65 delta. Expression of the p65 delta cDNA in Rat-1 fibroblasts resulted in focus formation, anchorage-independent growth in soft agar, and tumor formation in athymic nude mice, effects not obtained with expression of p65 or a p65 delta mutant that contains a disruption within the transcriptional activation domain. Thus, p65 delta, which associated weakly and interfered with DNA binding by p65, may sequester an essential limiting regulatory factor or factors required for NF-kappa B function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Narayanan, R -- Klement, J F -- Ruben, S M -- Higgins, K A -- Rosen, C A -- New York, N.Y. -- Science. 1992 Apr 17;256(5055):367-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, Hoffmann-LaRoche, Inc., Nutley, NJ 07110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1566083" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Cell Transformation, Neoplastic/*genetics ; DNA/genetics/metabolism ; Fibroblasts/metabolism ; *Genetic Variation ; Hematopoietic Stem Cells/chemistry ; Humans ; Mice ; Mice, Nude ; Molecular Sequence Data ; NF-kappa B/*genetics ; Neoplasm Transplantation ; Oncogene Proteins v-rel ; Polymerase Chain Reaction ; RNA Splicing ; RNA, Messenger/analysis/genetics ; Rats ; Retroviridae Proteins, Oncogenic/genetics ; Transfection
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  • 96
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    E2F: a link between the Rb tumor suppressor protein and viral oncoproteins (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-10-16
    Description: The cellular transcription factor E2F, previously identified as a component of early adenovirus transcription, has now been shown to be important in cell proliferation control. E2F appears to be a functional target for the action of the tumor suppressor protein Rb that is encoded by the retinoblastoma susceptibility gene. The disruption of this E2F-Rb interaction, as well as a complex involving E2F in association with the cell cycle-regulated cyclin A-cdk2 kinase complex, may be a common mechanism of action for the oncoproteins encoded by the DNA tumor viruses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nevins, J R -- New York, N.Y. -- Science. 1992 Oct 16;258(5081):424-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Section of Genetics, Duke University Medical Center, Durham, NC 27710.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1411535" target="_blank"〉PubMed〈/a〉
    Keywords: Adenovirus E1A Proteins/metabolism ; Adenoviruses, Human/genetics ; Binding Sites ; *Carrier Proteins ; Cell Cycle ; *Cell Cycle Proteins ; *Cell Transformation, Viral ; Cloning, Molecular ; DNA-Binding Proteins/metabolism ; E2F Transcription Factors ; *Gene Expression Regulation, Viral ; Genes, Tumor Suppressor ; Humans ; Oncogene Proteins, Viral/*metabolism ; Protein Binding ; Regulatory Sequences, Nucleic Acid ; Retinoblastoma Protein/*metabolism ; Retinoblastoma-Binding Protein 1 ; Transcription Factor DP1 ; Transcription Factors/*metabolism
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  • 97
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    Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-14
    Description: Effective methods are needed to identify and isolate those genes that are differentially expressed in various cells or under altered conditions. This report describes a method to separate and clone individual messenger RNAs (mRNAs) by means of the polymerase chain reaction. The key element is to use a set of oligonucleotide primers, one being anchored to the polyadenylate tail of a subset of mRNAs, the other being short and arbitrary in sequence so that it anneals at different positions relative to the first primer. The mRNA subpopulations defined by these primer pairs were amplified after reverse transcription and resolved on a DNA sequencing gel. When multiple primer sets were used, reproducible patterns of amplified complementary DNA fragments were obtained that showed strong dependence on sequence specificity of either primer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liang, P -- Pardee, A B -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):967-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1354393" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Breast Neoplasms/genetics ; Cloning, Molecular/methods ; DNA/genetics ; Humans ; Molecular Sequence Data ; Neoplasm Metastasis ; Nucleoside-Phosphate Kinase/genetics ; Oligodeoxyribonucleotides ; Poly A/genetics ; Polymerase Chain Reaction/*methods ; RNA, Messenger/biosynthesis/*genetics ; Templates, Genetic
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  • 98
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    Solution structure of a calmodulin-target peptide complex by multidimensional NMR (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-05-01
    Description: The three-dimensional solution structure of the complex between calcium-bound calmodulin (Ca(2+)-CaM) and a 26-residue synthetic peptide comprising the CaM binding domain (residues 577 to 602) of skeletal muscle myosin light chain kinase, has been determined using multidimensional heteronuclear filtered and separated nuclear magnetic resonance spectroscopy. The two domains of CaM (residues 6 to 73 and 83 to 146) remain essentially unchanged upon complexation. The long central helix (residues 65 to 93), however, which connects the two domains in the crystal structure of Ca(2+)-CaM, is disrupted into two helices connected by a long flexible loop (residues 74 to 82), thereby enabling the two domains to clamp residues 3 to 21 of the bound peptide, which adopt a helical conformation. The overall structure of the complex is globular, approximating an ellipsoid of dimensions 47 by 32 by 30 angstroms. The helical peptide is located in a hydrophobic channel that passes through the center of the ellipsoid at an angle of approximately 45 degrees with its long axis. The complex is mainly stabilized by hydrophobic interactions which, from the CaM side, involve an unusually large number of methionines. Key residues of the peptide are Trp4 and Phe17, which serve to anchor the amino- and carboxyl-terminal halves of the peptide to the carboxyl- and amino-terminal domains of CaM, respectively. Sequence comparisons indicate that a number of peptides that bind CaM with high affinity share this common feature containing either aromatic residues or long-chain hydrophobic ones separated by a stretch of 12 residues, suggesting that they interact with CaM in a similar manner.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ikura, M -- Clore, G M -- Gronenborn, A M -- Zhu, G -- Klee, C B -- Bax, A -- New York, N.Y. -- Science. 1992 May 1;256(5057):632-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1585175" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Calcium/metabolism ; Calmodulin/*chemistry/metabolism ; Drosophila melanogaster ; Hydrogen Bonding ; *Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Muscles/enzymology ; Myosin-Light-Chain Kinase/chemistry/metabolism ; Peptide Fragments/*chemistry/metabolism ; Protein Conformation ; Rabbits
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