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  • 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems
  • 04. Solid Earth::04.04. Geology::04.04.08. Sediments: dating, processes, transport
  • 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy
  • 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology
  • Acoustics
  • Binding Sites
  • Data analysis / ~ processing
  • Fluids
  • Schussler
  • Textbook of geophysics
  • American Association for the Advancement of Science (AAAS)  (32)
  • Elsevier  (9)
  • Springer  (3)
  • Cambridge U. Press
  • Cambridge Univ. Press
  • Soc. of Exploration Geophys.
  • W.H. Freeman
  • 2020-2023
  • 2010-2014  (44)
  • 2000-2004
  • 1980-1984
  • 2011  (44)
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  • 2020-2023
  • 2010-2014  (44)
  • 2000-2004
  • 1980-1984
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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
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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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
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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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
    Electronic ISSN: 1095-9203
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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
    Electronic ISSN: 1095-9203
    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
    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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  • 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
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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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
    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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  • 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
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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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
    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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    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
    Print ISSN: 0036-8075
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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
    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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    Tracing thermal aquifers of El Chichón volcano-hydrothermal system (México) with 87Sr/86Sr, Ca/Sr and REE (2011)
    Elsevier
    Details
    Publication Date: 2020-11-26
    Description: The volcano–hydrothermal system of El Chichón volcano, Chiapas, Mexico, is characterized by numerous thermal manifestations including an acid lake, steam vents and boiling springs in the crater and acid and neutral hot springs and steaming ground on the flanks. Previous research on major element chemistry reveals that thermal waters of El Chichón can be divided in two groups: (1) neutral waters discharging in the crater and southern slopes of the volcano with chloride content ranging from 1500 to 2200 mg/l and (2) acid-toneutral waters with Cl up to 12,000 mg/l discharging at the western slopes. Our work supports the concept that each group of waters is derived from a separate aquifer (Aq. 1 and Aq. 2). In this study we apply Sr isotopes, Ca/Sr ratios and REE abundances along with the major and trace element water chemistry in order to discriminate and characterize these two aquifers. Waters derived from Aq. 1 are characterized by 87Sr/86Sr ratios ranging from 0.70407 to 0.70419, while Sr concentrations range from 0.1 to 4 mg/l and Ca/Sr weight ratios from 90 to 180, close to average values for the erupted rocks. Waters derived from Aq. 2 have 87Sr/86Sr between 0.70531 and 0.70542, high Sr concentrations up to 80 mg/l, and Ca/Sr ratio of 17–28. Aquifer 1 is most probably shallow, composed of volcanic rocks and situated beneath the crater, within the volcano edifice. Aquifer 2 may be situated at greater depth in sedimentary rocks and by some way connected to the regional oil-gas field brines. The relative water output (l/s) from both aquifers can be estimated as Aq. 1/Aq. 2– 30. Both aquifers are not distinguishable by their REE patterns. The total concentration of REE, however, strongly depends on the acidity. All neutral waters including high-salinity waters from Aq. 2 have very low total REE concentrations (b0.6 μg/l) and are characterized by a depletion in LREE relative to El Chichón volcanic rock, while acid waters from the crater lake (Aq. 1) and acid AS springs (Aq. 2) have parallel profile with total REE concentration from 9 to 98 μg/l. The highest REE concentration (207 μg/l) is observed in slightly acid shallow cold Ca-SO4 ground waters draining fresh and old pyroclastic deposits rich in magmatic anhydrite. It is suggested that the main mechanism controlling the concentration of REE in waters of El Chichón is the acidity. As low pH results from the shallow oxidation of H2S contained in hydrothermal vapors, REE distribution in thermal waters reflects the dissolution of volcanic rocks close to the surface or lake sediments as is the case for the crater lake.
    Description: -
    Description: Published
    Description: 55-66
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: JCR Journal
    Description: reserved
    Keywords: hydrogeochemistry ; geothermal systems ; Sr isotopes ; REE ; El Chichón Volcano ; 03. Hydrosphere::03.02. Hydrology::03.02.03. Groundwater processes ; 03. Hydrosphere::03.04. Chemical and biological::03.04.03. Chemistry of waters ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Chronology of the Lower-Middle Pleistocene succession of the south-western part of the Crotone Basin (Calabria, Southern Italy) (2011)
    Elsevier
    Details
    Publication Date: 2021-05-17
    Description: Biostratigraphy based on calcareous nannofossils, integrated by magnetostratigraphic, geochronological and isotopic data, allowed establishing a precise chronological framework for the Pleistocene succession within the south-western sector of the Crotone Basin (Calabria, Southern Italy), where the Pliocenee Pleistocene global stratotype section and point is defined, thus demonstrating that sedimentation was quasi-continuous during most of the Lower and Middle Pleistocene. At a large scale, the Pleistocene succession in this sector of the Crotone Basin is characterized by an evident shallowing-upwards trend, showing facies changes from bathyal to shelfal to littoral/continental. However, comparison between adjacent sectors within the investigated area demonstrates that stratigraphic architectures change vastly on very short distances. Our chronological constraints indicate that such changes in sedimentation styles probably occurred in response to differential subsidence rates, which originated tectonically-controlled synsedimentary structures where accommodation space and sediment yield were allotted unevenly. This articulated physiography led to striking differences in the overall thicknesses and organization of Pleistocene stratigraphies and, eventually, to a distinct diachroneity in the first appearance of shallow-marine deposits. In addition, superimposed are complex interplays between regional and local tectonics, eustasy and orbitally-forced climate changes. These interactions have been highlighted by the oxygen isotope stratigraphy established for a part of the studied succession, which is likely to document almost continuously the interval from Marine Isotope Stage (MIS) 26 to MIS 17. In its younger part (post-MIS 17), chronological ties are poor, as the succession is dominated by shallow-water to continental deposits showing a prominent organization into cyclothems. Nevertheless, based on the chronology of the underlying units, it is feasible that basin infill ended during MIS 15-MIS 14 times.
    Description: Published
    Description: 1185-1200
    Description: 2.2. Laboratorio di paleomagnetismo
    Description: JCR Journal
    Description: restricted
    Keywords: Pleistocene ; Chronostratigraphy ; Southern Italy ; 04. Solid Earth::04.04. Geology::04.04.08. Sediments: dating, processes, transport ; 04. Solid Earth::04.05. Geomagnetism::04.05.06. Paleomagnetism
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Sedimentary processes on the Wilkes Land continental rise reflect changes in glacial dynamic and bottom water flow (2011)
    Springer
    Details
    Publication Date: 2020-12-15
    Description: Four sediment cores were analysed in order to determine the sedimentary processes associated with the channel-ridge depositional system that characterise the George V Land continental margin on the Wilkes Land. The sedimentary record indicates that the WEGA channel was a dynamic turbiditic system up to M.I.S. 11. After this time, the channel became a lower-energy environment with sediments delivered to the channel through high-density bottom waters that we identify to be the high salinity shelf waters (HSSW) forming on the shelf area. The HSSW entrains the fine-grained sediments of the shelf area and deliver them to the continental rise. The biostratigraphy and facies of the sediments within the WEGA channel indicate that the HSSW down flow was active also during last glacial. The change from a turbiditic system to a lowenergy bottom current system within the WEGA channel likely reflects a different ice-flow pattern, with ice-sheet reaching the continental shelf edge only within the ice trough (ice stream).
    Description: Published
    Description: 909 - 926
    Description: 2.2. Laboratorio di paleomagnetismo
    Description: JCR Journal
    Description: restricted
    Keywords: High salinity shelf water ; Turbidity currents ; Glacio-marine depositional processes ; Marine isotopic stage 11 ; Glacial dynamic changes ; 02. Cryosphere::02.02. Glaciers::02.02.05. Ice dynamics ; 04. Solid Earth::04.04. Geology::04.04.08. Sediments: dating, processes, transport ; 04. Solid Earth::04.05. Geomagnetism::04.05.06. Paleomagnetism
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 36
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    A model for seismicity rates observed during the 1982–1984 unrest at Campi Flegrei caldera (Italy) (2011)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: We consider the space–time distribution of seismicity during the 1982–1984 unrest at Campi Flegrei caldera (Italy) where a correlation between seismicity and rate of ground uplift was suggested. In order to investigate this effect, we present a model based on stress transfer from the deformation source responsible for the unrest to potential faults. We compute static stress changes caused by an inflating source in a layered half-space. Stress changes are evaluated on optimally oriented planes for shear failure, assuming a regional stress with horizontal extensional axis trending NNE-SSW. The inflating source is modeled as inferred by previous studies from inversion of geodetic data with the same crustal model here assumed. The magnitude of the regional stress is constrained by imposing an initial condition of “close to failure” to potential faults. The resulting spatial distribution of stress changes is in agreement with observations. We assume that the temporal evolution of ground displacement, observed by a tide-gauge at Pozzuoli, was due mainly to time dependent processes occurring at the inflating source. We approximate this time dependence in piecewise-linear way and we attribute it to each component of average stress-change in the region interested by the observed seismicity. Then we evaluate the effect of a time dependent stressing rate on seismicity, by following the approach indicated by Dieterich (1994) on the basis of the rate- and state-dependent rheology of faults. The seismicity rate history resulting from our model is in general agreement with data during the period 1982– 1984 for reasonable values of unconstrained model-parameters, the initial value of the direct effect of friction and the reference shear stressing rate. In particular, this application shows that a decreasing stressing-rate is effective in damping the seismicity rate.
    Description: Published
    Description: 287-298
    Description: 3.6. Fisica del vulcanismo
    Description: JCR Journal
    Description: reserved
    Keywords: Triggered seismicity ; Volcanic tremor ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 37
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    Societal need for improved understanding of climate change, anthropogenic impacts, and geo-hazard warning drive development of ocean observatories in European Seas (2011)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Society’s needs for a network of in situ ocean observing systems cross many areas of earth and marine science. Here we review the science themes that benefit from data supplied from ocean observatories. Understanding from existing studies is fragmented to the extent that it lacks the coherent long-term monitoring needed to address questions at the scales essential to understand climate change and improve geo-hazard early warning. Data sets from the deep sea are particularly rare with long-term data available from only a few locations worldwide. These science areas have impacts on societal health and well-being and our awareness of ocean function in a shifting climate. Substantial efforts are underway to realise a network of open-ocean observatories around European Seas that will operate over multiple decades. Some systems are already collecting high-resolution data from surface, water column, seafloor, and sub-seafloor sensors linked to shore by satellite or cable connection in real or near-real time, along with samples and other data collected in a delayed mode. We expect that such observatories will contribute to answering major ocean science questions including: How can monitoring of factors such as seismic activity, pore fluid chemistry and pressure, and gas hydrate stability improve seismic, slope failure, and tsunami warning? What aspects of physical oceanography, biogeochemical cycling, and ecosystems will be most sensitive to climatic and anthropogenic change? What are natural versus anthropogenic changes? Most fundamentally, how are marine processes that occur at differing scales related? The development of ocean observatories provides a substantial opportunity for ocean science to evolve in Europe. Here we also describe some basic attributes of network design. Observatory networks provide the means to coordinate and integrate the collection of standardised data capable of bridging measurement scales across a dispersed area in European Seas adding needed certainty to estimates of future oceanic conditions. Observatory data can be analysed along with other data such as those from satellites, drifting floats, autonomous underwater vehicles, model analysis, and the known distribution and abundances of marine fauna in order to address some of the questions posed above. Standardised methods for information management are also becoming established to ensure better accessibility and traceability of these data sets and ultimately to increase their use for societal benefit. The connection of ocean observatory effort into larger frameworks including the Global Earth Observation System of Systems (GEOSS) and the Global Monitoring of Environment and Security (GMES) is integral to its success. It is in a greater integrated framework that the full potential of the component systems will be realised.
    Description: Published
    Description: 1-33
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: Seafloor and water columnobservatories ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate ; 01. Atmosphere::01.01. Atmosphere::01.01.04. Processes and Dynamics ; 01. Atmosphere::01.01. Atmosphere::01.01.08. Instruments and techniques ; 03. Hydrosphere::03.01. General::03.01.03. Global climate models ; 03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactions ; 03. Hydrosphere::03.01. General::03.01.08. Instruments and techniques ; 03. Hydrosphere::03.03. Physical::03.03.01. Air/water/earth interactions ; 03. Hydrosphere::03.03. Physical::03.03.02. General circulation ; 03. Hydrosphere::03.03. Physical::03.03.03. Interannual-to-decadal ocean variability ; 03. Hydrosphere::03.03. Physical::03.03.05. Instruments and techniques ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.02. Carbon cycling ; 03. Hydrosphere::03.04. Chemical and biological::03.04.03. Chemistry of waters ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems ; 03. Hydrosphere::03.04. Chemical and biological::03.04.08. Instruments and techniques ; 04. Solid Earth::04.01. Earth Interior::04.01.02. Geological and geophysical evidences of deep processes ; 04. Solid Earth::04.04. Geology::04.04.04. Marine geology ; 04. Solid Earth::04.04. Geology::04.04.11. Instruments and techniques ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.05. Geomagnetism::04.05.05. Main geomagnetic field ; 04. Solid Earth::04.05. Geomagnetism::04.05.08. Instruments and techniques ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring ; 04. Solid Earth::04.06. Seismology::04.06.07. Tomography and anisotropy ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.06. Seismology::04.06.10. Instruments and techniques ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics ; 04. Solid Earth::04.07. Tectonophysics::04.07.03. Heat generation and transport ; 04. Solid Earth::04.07. Tectonophysics::04.07.04. Plate boundaries, motion, and tectonics ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.02. Experimental volcanism ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques ; 05. General::05.01. Computational geophysics::05.01.01. Data processing ; 05. General::05.02. Data dissemination::05.02.99. General or miscellaneous ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data ; 05. General::05.02. Data dissemination::05.02.02. Seismological data ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions ; 05. General::05.02. Data dissemination::05.02.04. Hydrogeological data ; 05. General::05.08. Risk::05.08.01. Environmental risk ; 05. General::05.08. Risk::05.08.02. Hydrogeological risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 38
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    Acoustic Emission spectra classification from rock samples of Etna basalt in deformation-decompression laboratory experiments (2011)
    Springer
    Details
    Publication Date: 2020-02-24
    Description: Recent laboratory experiments on Etna basalt have permitted the generation of an extensive catalogue of acoustic emissions (AE) during two key experimental phases. Firstly, AE have been generated during triaxial compressional tests and formation of a complex fracture/damage zone. Secondly, rapid fluid decompression through the damage/shear zone after failure. We report new results from an advanced analysis method using AE spectrograms, allowing us to qualitatively identify high and low frequency events; essentially comparable to seismicity in volcanic areas. Our analysis, for the first time, quantitatively classifies ‘families’ of AE events belonging to the same experimental stage without prior knowledge. We then test the method using the AE catalogue for verification, which is not possible with field data. FFT spectra, obtained from AE, are subdivided into equal log intervals for which a local slope is calculated. Factor analysis has been then applied, in which we use a data matrix of columns representing the variables considered (frequency data averaged in bins) vs. rows indicating each AE data set. Factor analysis shows that the method is very effective and suitable for reducing data complexity, allowing distinct factors to be obtained. We conclude that most of the data variance (information content) can be well represented by three factors only, each one representing a well defined frequency range. Through the factor scores it is possible to represent data in a lower dimension factor space. Classification is then possible by identifying clusters of AE belonging to the same experimental stage. This allows us to propose a deformation/decompression interpretation based solely on the AE frequency analysis and to identify a third type of AE related to fluid movements in the deformation stage.
    Description: Published
    Description: 201-211
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: open
    Keywords: acoustic emissions ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 05. General::05.01. Computational geophysics::05.01.04. Statistical analysis
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 39
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    Source location of long period seismicity at Volcàn de Colima, México (2011)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: This paper presents an analysis of seismicity associated with the volcanic activity of Volcàn de Colima (México) and recorded in the period November 2005–April 2006 during a field survey by the Istituto Nazionale di Geofisica e Vulcanologia (INGV)–Osservatorio Vesuviano, the Observatorio Vulcanologico de Colima of Colima University and the Instituto Andaluz de Geofisica, University of Granada. Three different types of volcanic earthquakes have been identified on the basis of their spectral properties: Type A (0.3–1 Hz), Type B (1–5 Hz) and Type C (3–4 Hz). Results of polarization analysis applied to Type A events show a predominance of radial motion, indicating that the wavefield comprises compressional waves (P) and shear waves polarized in the vertical plane (SV), while the signal always begins with a negative polarity. Type A, B and C earthquakes have been located using both a flat layered model and a 3D model including topography. Hypocentre distributions indicate that the source of Type A signals is very shallow and confined to a small volume lying about 1 km below the crater. In contrast, the source of Type B and C events is significantly deeper, with most hypocentres located in a volume of about 1 km3 centred at 2.5–3 km depth. A cluster analysis based on the crosscorrelation among the waveforms of different events recorded at the same station was applied to Type A earthquakes. Only two clusters, which include only a small percentage of events were found, indicating that earthquake families were uncommon during the period of our survey.
    Description: Published
    Description: 887-898
    Description: 3.1. Fisica dei terremoti
    Description: JCR Journal
    Description: reserved
    Keywords: Colima Volcano ; Long Period Events ; Earthquake location ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 40
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    The magmatic feeding system of the Campi Flegrei caldera: Architecture and temporal evolution (2011)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: To develop a model of both the structure and evolution of the Campi Flegrei caldera (CFc) magmatic feeding system, geochronological, geochemical and Sr, Nd, Pb and B isotopic data of representative volcanic products of the past 15 ka have been combined with geophysical and melt inclusion literature data, structural setting and dynamics of the resurgent caldera. According to previous petrological data, the CFc magmatic feeding system consists of a deep reservoir, in which mantle-derived K-basaltic parental magmas differentiate to shoshonite, latite and trachyte, through combined crustal contamination and fractional crystallization processes, and shallowreservoirswhere the evolvedmagmas further differentiate andmingle/mix before eruptions. The Sr,Nd, Pb, and B isotope data allowrecognition of three distinctmagmatic components.One component is believedto be residualmagmafromtheNeapolitanYellowTuff (NYT) caldera forming eruption. The NYT component (87Sr/86Sr of 0.70750–53, 143Nd/144Nd ratio of ca. 0.51246, 206Pb/204Pb of ca. 19.04 and δ11B of ca. –7.9‰), has been the most prevalent component over the past 15 ka being mixed, in most cases, with the other two components. One of these other components is best recognized in the Minopoli 2 magma, first erupted 10 ka ago. Minopoli 2 magma is shoshonitic in composition and is the most enriched in radiogenic Sr (87Sr/86Sr of ca. 0.70860) and unradiogenic Nd and Pb (143Nd/144Nd ratio of ca. 0.51236, 206Pb/204Pb of ca. 18.90), and is characterised by δ11B value of ca. –7.32‰. The third component is trachytic in composition and has higher 206Pb/204Pb (ca. 19.08), lower 87Sr/86Sr (ca. 0.70726) and δ11B (−9.8‰) and higher 143Nd/144Nd (ca. 0.51250), with respect to the NYT component. This third component is best recognized in the Astroni 6 magma and did not appear until ca. 4 ka. The identified isotopically distinct magmatic components were erupted in different sectors of the CFc. During both I (b14.9–9.5 ka) and II (8.6–8.2 ka) epochs of volcanic activity,magmas similar to the NYT component, and those resulting from mixing between Minopoli 2 and NYT components were erupted from vents located mostly on the marginal faults of the NYT caldera. During the III epoch (4.8–3.8 ka) magmas either similar to NYT, or resulting from mixing between Astroni 6 and NYT components were erupted from vents located along faults bordering the La Starza resurgent block and, subordinately, the NYT caldera. Moreover, magmas resulting from mixing betweenMinopoli 2 and NYT components were erupted fromvents located along NE–SW regional faults activated during caldera resurgence. The inferred present structure of the feeding system is characterised by a deep reservoir, whose top is at about 8 kmdepth, that hosts shoshonitic–trachyticmagmas. Remnants of the NYT magma reside at shallower depth in different sectors of the crust underlying CFc, and were sometimes intercepted by volatile-rich magmas of deep provenance during the three epochs of CFc volcanic activity.
    Description: Published
    Description: 227-241
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 3.5. Geologia e storia dei vulcani ed evoluzione dei magmi
    Description: JCR Journal
    Description: reserved
    Keywords: Campi Flegrei caldera ; Magmatic system ; Caldera structure ; Geochemistry ; Isotopes ; 04. Solid Earth::04.04. Geology::04.04.07. Rock geochemistry ; 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks
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  • 41
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    Insights into explosive activity at closely-spaced eruptive vents using infrasound signals: Example of Mt. Etna 2008 eruption (2011)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: On 13 May 2008 an eruptive fissure opened on Mount Etna's eastern flank feeding both explosive activity and lava effusion from multiple vents for about 14 months. During the investigated May-September 2008 eruptive period, infrasound recordings from a 4 station-sparse network allowed tracking of the explosive activity in terms of location and dynamics. In order to focus on activity from the eruptive fissure, the infrasonic events generated by the summit craters were selected by using both spectral features and time delays between pairs of stations and excluded from our analysis. Then, to accurately locate events from the fissure, we used a composite method, based on the semblance and brightness functions. This enabled the study of the co-existence of more than one infrasound source and/or its migration along the eruptive fissure. Hence, results permitted us to discriminate the number of active vents and their location along the fissure even when, due to poor weather conditions, it was not possible to access the vents or carry out direct observations. The eruptive activity was characterised by variations in the number of active vents according to the overall intensity of the eruptive event. Variability of the infrasound waveforms highlighted either that distinct vents produced signals with different waveforms, or that single vents generated different events during distinct periods of time, or finally both the previous phenomena. We applied the strombolian bubble vibration model to model waveform differences and attributed the signal variations to bubble radius changes.
    Description: Published
    Description: 1-11
    Description: 1.4. TTC - Sorveglianza sismologica delle aree vulcaniche attive
    Description: JCR Journal
    Description: reserved
    Keywords: Etna ; Infrasound ; Infrasonic source location ; explosive activity ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology
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  • 42
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    Spatio-temporal evolution of volcano seismicity: A laboratory study (2011)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: We report a laboratory and microstructural study of a suite of deformation experiments in which basalt from Mount Etna volcano is deformed and fractured at an effective confining pressure representative of conditions under a volcanic edifice (40 MPa). Particular attention was paid to the formation of a fracture and damage zone with which to stimulate coupled hydro-mechanical interactions that create the various types of seismicity recorded on volcanic edifices, and which usually precede eruption. Location of AE events through time shows the formation of a fault plane during which waveforms exhibit the typical high frequency characteristics of volcano-tectonic (VT) earthquakes. We found that these VT earthquakes were particularly pronounced when generated using dry samples, compared to samples saturated with a pore fluid (water). VT events generated during deformation of water saturated sample are characterised by a distinctive high frequency onset and a longer, low frequency coda exhibiting properties often seen in the field as hybrid events. We present evidence that hybrid events are, in fact, the common type of volcanic seismic event with either VT or low frequency (LF) events representing end members, and whose proportion depend on pore fluid being present in the rock type being deformed, as well as how close the rock is to failure. We find a notable trend of reducing instances of hybrid events leading up to the failure stage in our experiments, suggesting that during this stage, the pore fluid present in the rock moves sufficiently quickly to provide a resonance, seen as a LF coda. Our data supports recent modeling and field studies that postulate that hybrid events generated in volcanic areas are likely to be generated through the interaction of hydrothermal fluids moving through a combination of pre-existing microcrack networks and larger faults, such as those we observe in forensic (post-test) examination.
    Description: Published
    Description: 315-323
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: JCR Journal
    Description: reserved
    Keywords: volcano-tectonics, acoustic emission, rock physics, seismology, hazard ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.02. Seismological data
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  • 43
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    Short residence times for alkaline Vesuvius magmas in a multi-depth supply system: Evidence from geochemical and textural studies (2011)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: It is crucial to understand magma chamber chemico-physical conditions and residence times for high-risk volcanoes because these factors control the occurrence and size of future eruptions. In order to define magmatic pressure–temperature conditions and residence times at the Somma–Vesuvius volcano, we studied the geochemistry and texture of selected past eruptions that are representative of the entire volcanic history. Our petrological model indicates a multi-depth magma chamber composed of a deeper tephritic (350– 400 Mpa) magma layer, which fed Strombolian and effusive eruptions during open-conduit activity, and an upper (200–250 Mpa) phonolitic level, which supplied the high explosive events that followed closedconduit repose time. This upper reservoir matches the inferred transition between sedimentary sequences and metamorphic basement. At this level, the presence of a structural and lithological discontinuity favors magma storage during closed-conduit periods. The prevalent differentiation process was fractional crystallization during the magma cooling associated with upward migration of less dense, evolved liquids. Our results indicate that major steam exolution occurred during the late crystallization stage of phonolites, which accounts for the high Volcanic Explosivity Index (VEI) of eruptions supplied by these melts. Moreover, our phenocryst CSD data reveal the rapid crystallization and differentiation (decades to centuries) of alkaline Somma–Vesuvius magmas. This implies that the 400 km2 partial melting zone detected by tomography studies at 8–10 km depth beneath Vesuvius should consist of differentiated magma that is already capable of generating a large-scale (plinian) explosive event if renewed activity develops out of the present closed-conduit state. Additionally, because our microlite CSD data indicate rapid magma migration from the chamber toward the surface, precursory activity could appear only short time before a major eruption.
    Description: Published
    Description: 133–143
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 3.5. Geologia e storia dei vulcani ed evoluzione dei magmi
    Description: 3.6. Fisica del vulcanismo
    Description: JCR Journal
    Description: reserved
    Keywords: residence time ; phonolite ; Vesuvius ; 04. Solid Earth::04.01. Earth Interior::04.01.04. Mineral physics and properties of rocks ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology ; 04. Solid Earth::04.04. Geology::04.04.07. Rock geochemistry ; 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy
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  • 44
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    Fluid geochemistry and geothermometry in the western sector of the Sabatini Volcanic District and the Tolfa Mountains (Central Italy) (2011)
    Elsevier
    Details
    Publication Date: 2024-05-09
    Description: A geochemical survey of 197 fluid discharges (cold and thermal waters and bubbling pools) and 15 gas emissions from the western sector of the Sabatini Volcanic District and the Tolfa Mountains (Latium, Central Italy) was carried out in 2007–2008. The chemical and isotopic compositions of the fluid discharges indicate the occurrence of two main sources: 1) relatively shallow aquifers with Ca(Na,K)–HCO3 and Ca(Mg)–HCO3 compositions when trapped in volcanic and sedimentary formations, respectively; and 2) a deep reservoir, which is hosted in the Mesozoic carbonate sequence, rich in CO2 and having a Ca–SO4(HCO3) composition. Dissolution of a CO2-rich gas phase into the shallow aquifers produces high-TDS and high-pCO2 cold waters, while oxidation of deep-derived H2S to SO4 2− generates low-pH (b4) sulfate waters. The δ13C–CO2 values for gas emissions (from−2.8 to+2.7‰vs. VPDB) suggest that the origin of CO2 associated with the deep fluids ismainly related to thermo-metamorphic reactions within the carbonate reservoir, although significant mantle contribution may also occur. However, R/Ra values (0.37–0.62) indicate that He is mainly produced by a crustal source, with a minor component from a crust-contaminated mantle. On the basis of the δ13C–CH4 and δD–CH4 values (from −25.7 to −19.5‰ vs. VPDB and from −152 to −93.4‰ vs. VSMOW, respectively) CH4 production is associated with thermogenic processes, possibly related to abiogenic CO2 reduction within the carbonate reservoir. The δ34S–H2S values (from+9.3 to +10.4‰ vs. VCDT) are consistent with the hypothesis of a sedimentary source of sulfur from thermogenic reduction of Triassic sulfates. Geothermometric evaluations based on chemical equilibria CO2–CH4 and, separately, H2S suggest that the reservoir equilibriumtemperature is up to ~300 °C. The δDand δ18O data indicate thatwater recharging both the shallow and deep aquifers has a meteoric origin. Fluid geochemistry, coupled with gravimetric data and tectonic lineaments, supports the idea that significant contributions from a deep-seated geothermal brine are present in the Stigliano thermal fluid discharges. Exploration surveys investigated this area during 70's–90's for geothermal purposes. Nevertheless, presently the area is still under-exploited. The presence of thermal waters and anomalous heat flow together with the demographic growth of the last years,makes this site a suitable location for direct applications of the geothermal resource.
    Description: Published
    Description: 160-181
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: reserved
    Keywords: Geochemistry Water Gas Stable isotope Geothermometry Central Italy ; 03. Hydrosphere::03.04. Chemical and biological::03.04.03. Chemistry of waters ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems
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