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3 results on '"Departments of biochemistry and chemistry [Nashville]"'

1. Data publication with the structural biology data grid supports live analysis

Author

Emil F. Pai, Qing R. Fan, Yousif Shamoo, Kevin D. Corbett, Dominika Borek, Tom Kirchhausen, James S. Fraser, Elizabeth Ransey, Stephanie M. Socias, Peter A. Meyer, Enrico Di Cera, Oleg V. Tsodikov, Jason S. McLellan, C. S. Raman, James Withrow, Mercè Crosas, Karen S. Anderson, Carlo Petosa, Filipe R. N. C. Maia, Gabrielle Rudenko, Yorgo Modis, Peng Gong, Walter J. Chazin, Zongchao Jia, Zbyszek Otwinowski, Adrian R. Ferré-D'Amaré, Yunsun Nam, Stephen C. Harrison, Sirano Dhe-Paganon, Joseph Schlessinger, Catherine L. Drennan, Kenneth D. Westover, Holger Sondermann, Richard H. G. Baxter, Marc Kvansakul, Ekaterina E. Heldwein, J. Christopher Fromme, Sean Crosson, Michael K. Rosen, Antonina Roll-Mecak, Robert J. Keenan, Tamir Gonen, Andrew C. Kruse, Ian Foster, Kanagalaghatta R. Rajashankar, Titus J. Boggon, Ming Lei, K. Christopher Garcia, Alexandre M. J. J. Bonvin, Michael S. Cosgrove, Amedeo Caflisch, Michael J. Eck, Brandt F. Eichman, Thomas U. Schwartz, Chung-I Chang, Rachelle Gaudet, Yizhi Jane Tao, Emily C. Tjon, Pedro Pereira, Jason Key, David B. Neau, Stephen C. Blacklow, Kay Diederichs, Hao Wu, Tom A. Rapoport, Alejandro Buschiazzo, Tom J. Brett, Piotr Sliz, Chris Botka, Niraj H. Tolia, Department of Biological Chemistry and Molecular Pharmacology [Boston] (DBCMP), Harvard Medical School [Boston] (HMS), Laboratory of molecular and structural microbiology, Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Shanghai Institutes for Biological Sciences (Institute of Biochemistry and Cell Biology), Chinese Academy of Sciences [Beijing] (CAS), NE-CAT and department of chemistry and chemical biology [Argonne], Cornell University, Departments of pharmacology and molecular biophysics and biochemistry [New Haven], Yale University School of Medicine, Department of Chemistry and Molecular Biophysics & Biochemistry [New Haven], Yale University [New Haven], Bijovet center [Utrecht], Utrecht University [Utrecht], Department of Biophysics and Biochemistry [Dallas], University of Texas Southwestern Medical Center [Dallas], Department of Internal Medicine [St Louis], Washington University School of Medicine, Department of Biochemistry [Zurich], University of Zürich [Zürich] (UZH), Institute of Biological Chemistry (IBC Sinica), Academia Sinica, Departments of biochemistry and chemistry [Nashville], Vanderbilt University [Nashville], Ludwig Institute for Cancer Research, University of California [San Diego] (UC San Diego), University of California, SUNY Upstate Medical University, State University of New York (SUNY), University of Chicago, Dana-Farber Cancer Institute [Boston], Saint Louis University School of Medicine [St Louis], Massachusetts Institute of Technology (MIT), Department of Biological Chemistry and Molecular Pharmacology (DBCMP), Columbia University [New York], National Heart, Lung, and Blood Institute [Bethesda] (NHLBI), Weill Institute for Cell and Molecular Biology, Howard Hughes Medical Institute [Stanford], Stanford University School of Medicine [CA, USA], Harvard University [Cambridge], Wuhan Institute of Virology, Howard Hughes Medical Institute [Boston], Tufts University School of Medicine [Boston], Queen's University [Kingston], La Trobe University [Melbourne], Geisel School of Medicine at Dartmouth, University of Cambridge [UK] (CAM), University of Texas at Dallas [Richardson] (UT Dallas), Campbell Family Institute for Breast Cancer Research, University Health Network, University of Toronto, Instituto de Biologia Molecular e Celular (IBMC), Institut de biologie structurale (IBS - UMR 5075), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), University of Maryland [Baltimore County] (UMBC), University of Maryland System, National Institute of Neurological Disorders and Stroke [Bethesda] (NINDS), National Institutes of Health [Bethesda] (NIH), Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch (UTMB), Rice University [Houston], University of Washington School of Medicine, University of Kentucky, Boston Children's Hospital, Department of Computer Science, University of Chicago, University of California [San Francisco] (UCSF), Uppsala University, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Howard Hughes Medical Institute [Ashburn], Fachbereich Biologie, University of Konstanz, Institute for Quantitative Social Sciences, Development of the Structural Biology Data Grid is funded by The Leona M. and Harry B. Helmsley Charitable Trust 2016PG-BRI002 to PS and MC. Development of citation workflows is supported NSF 1448069 (to PS). DAA is being developed as a pilot project of the National Data Service, with additional funds to support storage and technology development, including NIH P41 GM103403 (NE-CAT) and 1S10RR028832 (HMS) and DOE DE-AC02-06CH11357, NIH 1U54EB020406-01, Big Data for Discovery Science Center, and NIST 60NANB15D077 (Globus Project), Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Department of Chemistry, Drennan, Catherine L., Schwartz, Thomas, Sub NMR Spectroscopy, NMR Spectroscopy, Instituto de Investigação e Inovação em Saúde, Molecular and structural microbiology / Microbiología Molecular y Estructural [Montevideo], Cornell University [New York], Universität Zürich [Zürich] = University of Zurich (UZH), Howard Hughes Medical Institute (HHMI), Queen's University [Kingston, Canada], Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), University of Zurich, Sliz, Piotr, Yale School of Medicine [New Haven, Connecticut] (YSM), University of California (UC), Harvard University, Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Kentucky (UK), University of California [San Francisco] (UC San Francisco), Harrison, Seamus Conor [0000-0003-1480-1143], Modis, Yorgo [0000-0002-6084-0429], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Chemistry(all), Experiences, General Physics and Astronomy, computer.software_genre, Crystallography, X-Ray, Biochemistry, Software, Structural Biology, Databases, Genetic, Structure models, Macromolecular crystallography, media_common, Strukturbiologi, Uncategorized, Multidisciplinary, Crystallography, Data grid, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Publications, X-ray scattering, 1.5 Resources and infrastructure (underpinning), 3100 General Physics and Astronomy, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Networking and Information Technology R&D, Networking and Information Technology R&D (NITRD), The Internet, Data mining, Macromolecular Substances, media_common.quotation_subject, Science, 610 Medicine & health, 1600 General Chemistry, Biology, Physics and Astronomy(all), General Biochemistry, Genetics and Molecular Biology, Article, Synchrotron, 03 medical and health sciences, Databases, Genetic, Underpinning research, 1300 General Biochemistry, Genetics and Molecular Biology, ddc:570, 10019 Department of Biochemistry, Quality (business), Internet, business.industry, Biochemistry, Genetics and Molecular Biology(all), Data quality, Experimental data, General Chemistry, Data science, 030104 developmental biology, Data access, Protein data-bank, Paradigm shift, X-Ray, 570 Life sciences, biology, Resolution, business, computer, Department of Biochemistry, Genetics and Molecular Biology(all)
Abstract

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis., The validation and analysis of X-ray crystallographic data is essential for reproducibility and the development of crystallographic methods. Here, the authors describe a repository for crystallographic datasets and demonstrate some of the ways it could serve the crystallographic community.

Published
2016
Full Text
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2. Data publication with the structural biology data grid supports live analysis

Author

Pa, Meyer, Socias S, Key J, Ransey E, Ec, Tjon, Alejandro Buschiazzo, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Ks, Anderson, Rh, Baxter, Sc, Blacklow, Tj, Boggon, Am, Bonvin, Borek D, Tj, Brett, Caflisch A, Ci, Chang, Department of Biological Chemistry and Molecular Pharmacology [Boston] (DBCMP), Harvard Medical School [Boston] (HMS), Molecular and structural microbiology = Microbiología Molecular y Estructural [Montevideo], Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Shanghai Institutes for Biological Sciences (Institute of Biochemistry and Cell Biology), Chinese Academy of Sciences [Beijing] (CAS), NE-CAT and department of chemistry and chemical biology [Argonne], Cornell University, Departments of pharmacology and molecular biophysics and biochemistry [New Haven], Yale University School of Medicine, Department of Chemistry and Molecular Biophysics & Biochemistry [New Haven], Yale University [New Haven], Bijovet center [Utrecht], Utrecht University [Utrecht], Department of Biophysics and Biochemistry [Dallas], University of Texas Southwestern Medical Center [Dallas], Department of Internal Medicine [St Louis], Washington University School of Medicine, Department of Biochemistry [Zurich], University of Zürich [Zürich] (UZH), Institute of Biological Chemistry (IBC Sinica), Academia Sinica, Departments of biochemistry and chemistry [Nashville], Vanderbilt University [Nashville], Ludwig Institute for Cancer Research, University of California [San Diego] (UC San Diego), University of California, SUNY Upstate Medical University, State University of New York (SUNY), University of Chicago, Dana-Farber Cancer Institute [Boston], Saint Louis University School of Medicine [St Louis], Massachusetts Institute of Technology (MIT), Department of Biological Chemistry and Molecular Pharmacology (DBCMP), Columbia University [New York], National Heart, Lung, and Blood Institute [Bethesda] (NHLBI), Weill Institute for Cell and Molecular Biology, Howard Hughes Medical Institute [Stanford], Stanford University School of Medicine [CA, USA], Harvard University [Cambridge], Wuhan Institute of Virology, Howard Hughes Medical Institute [Boston], Tufts University School of Medicine [Boston], Queen's University [Kingston], La Trobe University [Melbourne], Geisel School of Medicine at Dartmouth, University of Cambridge [UK] (CAM), University of Texas at Dallas [Richardson] (UT Dallas), Campbell Family Institute for Breast Cancer Research, University Health Network, University of Toronto, Instituto de Biologia Molecular e Celular (IBMC), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), University of Maryland [Baltimore County] (UMBC), University of Maryland System, National Institute of Neurological Disorders and Stroke [Bethesda] (NINDS), National Institutes of Health [Bethesda] (NIH), Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch (UTMB), Rice University [Houston], University of Washington School of Medicine, University of Kentucky, Boston Children's Hospital, Department of Computer Science, University of Chicago, University of California [San Francisco] (UCSF), Uppsala University, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Howard Hughes Medical Institute [Ashburn], Fachbereich Biologie, University of Konstanz, Institute for Quantitative Social Sciences, Development of the Structural Biology Data Grid is funded by The Leona M. and Harry B. Helmsley Charitable Trust 2016PG-BRI002 to PS and MC. Development of citation workflows is supported NSF 1448069 (to PS). DAA is being developed as a pilot project of the National Data Service, with additional funds to support storage and technology development, including NIH P41 GM103403 (NE-CAT) and 1S10RR028832 (HMS) and DOE DE-AC02-06CH11357, NIH 1U54EB020406-01, Big Data for Discovery Science Center, and NIST 60NANB15D077 (Globus Project), Department of Biological Chemistry and Molecular Pharmacology [Boston] ( DBCMP ), Harvard Medical School [Boston] ( HMS ), Laboratory of molecular and structural microbiology, Institut Pasteur Montevideo-Réseau International des Instituts Pasteur ( RIIP ), Shanghai Institutes for Biological Sciences ( Institute of Biochemistry and Cell Biology ), Chinese Academy of Sciences [Beijing] ( CAS ), Yale University, Faculty of Science, Utrecht University, University of Zürich [Zürich] ( UZH ), Institute of Biological Chemistry ( IBC Sinica ), Vanderbilt University of Nashville, University of California [San Diego] ( UC San Diego ), Massachusetts Institute of Technology ( MIT ), Department of Biological Chemistry and Molecular Pharmacology ( DBCMP ), National Heart, Lung, and Blood Institute [Bethesda] ( NHLBI ), Stanford University School of Medicine, Havard Medical School, University of Cambridge [UK] ( CAM ), University of Texas at Dallas [Richardson] ( UT Dallas ), Instituto de Biologia Molecular e Celular ( IBMC ), Institut de biologie structurale ( IBS - UMR 5075 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), University of Maryland Baltimore County [Baltimore] ( UMBC ), National Institute of Neurological Disorders and Stroke [Bethesda] ( NINDS ), National Institutes of Health [Bethesda] ( NIH ), The University of Texas Medical Branch ( UTMB ), Yale School of Medicine, University of California [San Francisco] ( UCSF ), Lawrence Berkeley National Laboratory [Berkeley] ( LBNL ), Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Department of Chemistry, Drennan, Catherine L., Schwartz, Thomas, Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), and Instituto de Investigação e Inovação em Saúde

Subjects
Data set, Data quality, General Physics and Astronomy, Experimental data, General Chemistry, Data grid, General Biochemistry, Genetics and Molecular Biology, Data science, Genetics, Paradigm shift, Data access, Data mining, Biology, The Internet
Abstract

The validation and analysis of X-ray crystallographic data is essential for reproducibility and the development of crystallographic methods. Here, the authors describe a repository for crystallographic datasets and demonstrate some of the ways it could serve the crystallographic community., Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

Published
2016
Full Text
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3. Solution NMR Structure of Apo-Calmodulin in Complex with the IQ Motif of Human Cardiac Sodium Channel NaV1.5

Author

Walter J. Chazin, Benjamin Chagot, Departments of biochemistry and chemistry [Nashville], Vanderbilt University [Nashville], and Center for Structural Biology

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, Calmodulin, Protein Conformation, Molecular Sequence Data, Protein Data Bank (RCSB PDB), Muscle Proteins, NAV1.5 Voltage-Gated Sodium Channel, calcium signaling, Protein Structure, Secondary, Sodium Channels, Article, Protein–protein interaction, hydrophobic anchors, protein-protein interaction, 03 medical and health sciences, 0302 clinical medicine, Protein structure, Structural Biology, Humans, Protein Interaction Domains and Motifs, Amino Acid Sequence, Structural motif, Molecular Biology, Nuclear Magnetic Resonance, Biomolecular, 030304 developmental biology, 0303 health sciences, Voltage-dependent calcium channel, biology, Sequence Homology, Amino Acid, Chemistry, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Biochemistry, Mutation, Biophysics, biology.protein, Calcium, Calcium Channels, calcium sensor, Long QT syndrome, Sequence Alignment, 030217 neurology & neurosurgery, Heteronuclear single quantum coherence spectroscopy
Abstract

International audience; The function of the human voltage-gated sodium channel Na V 1.5 is regulated in part by intracellular calcium signals. The ubiquitous calcium sensor protein calmodulin (CaM) is an important part of the complex calcium-sensing apparatus in Na V 1.5. CaM interacts with an IQ motif in the large intracellular C-terminal domain of the channel. Using co-expression and co-purification, we have been able to isolate a CaM-IQ motif complex and to determine its high-resolution structure in absence of calcium using multi-dimensional solution NMR. Under these conditions, the Na V 1.5 IQ motif interacts with the C-terminal domain (C-lobe) of CaM, with the N-terminal domain remaining free in solution. The structure reveals that the C-lobe adopts a semi-open conformation with the IQ motif bound in a narrow hydrophobic groove. Sequence similarities between voltage-gated sodium channels and voltage-gated calcium channels suggest that the structure of the CaM-Na V 1.5 IQ motif complex can serve as a general model for the interaction between CaM and ion channels IQ motifs under conditions of low calcium. The structure also provides insight into the biochemical basis for disease-associated mutations that map to the IQ motif in Na V 1.5.

Published
2011
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