Research Report 2003 I 2004
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Amélioration De La Résolution Dans La Résonance Magnétique Nucléaire
N◦ d’ordre : 287 Annee´ 2004 N◦ attribue´ par la bibliotheque` : 04ENSL0 287 THESE` ECOLE´ NORMALE SUPERIEURE´ DE LYON Laboratoire de Chimie ECOLE NORMALE SUPERIEURE DE LYON These` de doctorat En vue d’obtenir le titre de : Docteur de l’Ecole´ Normale Superieure´ de Lyon Specialit´ e´ : Physique Present´ ee´ et soutenue publiquement le 17 septembre 2004 par : Luminita DUMA Amelioration´ de la Resolution´ dans la Resonance´ Magnetique´ Nucleaire´ Multidimensionnelle des Proteines´ Directeur de these` : Lyndon EMSLEY Apres` avis de : Monsieur Geoffrey BODENHAUSEN, Membre/Rapporteur Monsieur Hartmut OSCHKINAT, Membre/Rapporteur Devant la Commission d’examen formee´ de : Monsieur Geoffrey BODENHAUSEN, Membre/ Rapporteur Monsieur Yannick CREMILLIEUX, Membre Monsieur Lyndon EMSLEY, Membre Monsieur Alain MILON, Membre Monsieur Hartmut OSCHKINAT, Membre/Rapporteur Lyon, 2004 Order N◦: 287 Year 2004 N◦ allocated by the library: 04ENSL0 287 ECOLE´ NORMALE SUPERIEURE´ DE LYON Chemistry Laboratory ECOLE NORMALE SUPERIEURE DE LYON Doctoral Thesis For the degree of: Doctor in Physics of the Ecole´ Normale Superieure´ de Lyon Presented and defended the 17th of September 2004 by: Luminita DUMA Resolution Improvement in Multidimensional Nuclear Magnetic Resonance Spectroscopy of Proteins Supervisor: Lyndon EMSLEY After recommendation of: Mr Geoffrey BODENHAUSEN, Member/Referee Mr Hartmut OSCHKINAT, Member/Referee In front of the jury made up of: Mr Geoffrey BODENHAUSEN, Member/Referee Mr Yannick CREMILLIEUX, Member Mr Lyndon EMSLEY, Member Mr Alain MILON, Member Mr Hartmut OSCHKINAT, Member/Referee Lyon, 2004 Pa˘rint¸ilor mei. A` mes parents. To my parents. ”The principle of science, the definition, almost, is the following: The test of all knowledge is experiment. Experiment is the sole judge of sci- entific ”truth”. -
RESEARCH REPORT 2009/2010 Leibniz-Institut Für Molekulare Pharmakologie Im Forschungsverbund Berlin E.V
RESEARCH REPORT 2009/2010 Leibniz-Institut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. im Forschungsverbund Berlin e.V. Pharmakologie Leibniz-Institut für Molekulare 2009/2010 REPORT RESEARCH SCIENTIFIC CONTENT ADVISORY BOARD PREFACE What’s New at the FMP? Interview with Acting Director Hartmut Oschkinat....................................................................4 HIGHLIGHTS Propellers, Fibers, and a Magic Angle..................................................................................9 Hiding in the Membrane.......................................................................................................15 Reporters in the Labyrinth....................................................................................................21 Managing the Channels of Perception and the Chemical Workplaces of the Cell..........27 Prof. Dr. Annette G. Beck-Sickinger Leibniz Graduate School of Molecular Biophysics, Berlin...............................................32 Institut für Biochemie Interview with Bernd Reif, Coordinator Universität Leipzig RESEARCH GROUPS Prof. Dr. Bernd Bukau STRUCTURAL BIOLOGY Zentrum für Molekulare Biologie Protein Structure H. Oschkinat.............................................................................................34 Ruprecht-Karls-Universität Heidelberg* Protein Engineering C. Freund............................................................................................38 Structural Bioinformatics and Protein Design G. Krause..................................................42 -
Structure Calculation of Proteins from Solution and Solid-State NMR Data : Application to Monomers and Symmetric Aggregates
Structure calculation of proteins from solution and solid-state NMR data : Application to monomers and symmetric aggregates Inaugural-Dissertation to obtain the academic degree Doctor rerum naturalium (Dr. rer. nat.) submitted to the Department of Biology, Chemistry and Pharmacy of the Freie Universitat¨ Berlin by Benjamin Bardiaux from Nantes, France January, 2009 1st Reviewer: Prof. Dr. Michael Nilges (Institut Pasteur, Paris) 2nd Reviewer: Prof. Dr. Hartmut Oschkinat (FMP, Berlin) date of defence: 8 Sept. 2009 This work was carried out from October 2004 to September 2008 under the joint supervision of Prof. Dr. Michael Nilges (Institut Pasteur, Paris), Dr. Ther´ ese` E. Malliavin (Institut Pasteur, Paris) and Prof. Dr. Hartmut Oschkinat (Leibnizinstitut fur¨ Molekulare Pharmakologie, Berlin) at the Unite´ de Bioinformatique Structurale of the Institut Pasteur in Paris. iii Acknowledgements I would like to thank Michael Nilges for giving me the opportunity to work in an excellent scientific environment and entrusting me with all ARIA related projects during the last four years. I am deeply grateful to Ther´ ese` Malliavin for introducing me to the world of NMR and structure calculations. Her everyday support, inventiveness and cheerfulness was of great help during my thesis. I wish to thank Hartmut Oschkinat for his effective co-supervision of my thesis from Berlin. I would also like to express my gratitude to the persons across Europe without whom this work would not have been possible : Michael Habeck and Wolfgang Rieping who initiated -
CURRICULUM VITAE G. Marius Clore Bsc., MD, Phd, FRSC, C.Chem., C
1 CURRICULUM VITAE G. Marius Clore BSc., MD, PhD, FRSC, C.Chem., C.Sci., MAE NIH Distinguished Investigator Chief, Protein Nuclear Magnetic Resonance Section Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A. Tel: (301) 496 0782; Fax: (301) 496 0825 e-mail: [email protected] web: http://spin.niddk.nih.gov/clore (lab homepage) http://www.nasonline.org/member-directory/members/20033168.html (National Academy of Sciences web page) http://www.ae-info.org/ae/Member/Clore_G._Marius (Academia Europaea web page) https://en.wikipedia.org/wiki/G._Marius_Clore (Wikipedia profile) Born: 6th June 1955, London (U.K.) Citizenship: Dual US and British Education 1976: BSc. in Biochemistry (1st Class Honors), University College London. 1979: MD, University College Hospital Medical School, London. 1982: PhD in Physical Biochemistry, MRC National Institute for Medical Research, London. Positions held 2011-: Appointed NIH Distinguished Investigator 2005-: Appointed to Title 42f, Band IV, NIH, Bethesda. 1996-2005: Appointed to Senior Biomedical Research Service (SBRS), NIH, Bethesda 1991-: Chief, Protein NMR Section, NIDDK, NIH, Bethesda 1988-: Senior Investigator (Federal grade equivalent to Full Professor), Laboratory of Chemical Physics, NIDDK, NIH, Bethesda. 1984-1988: Head of the Biological NMR Group, Max-Planck Institute for Biochemistry, Martinsried, Munich, Germany. 1980-1984: Member of the Scientific Staff at the MRC National Institute for Medical Research, London. 1980: House Surgeon, St. Charles Hospital (St. Mary's Hospital Group), London. 1979: House Physician, University College Hospital, London. 1978-1980: Honorary Research Fellow, Department of Biochemistry, University College London. -
Determination of Protein Structures in the Solid State from NMR Chemical Shifts
Structure Ways & Means Determination of Protein Structures in the Solid State from NMR Chemical Shifts Paul Robustelli,1 Andrea Cavalli,1 and Michele Vendruscolo1,* 1Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK *Correspondence: [email protected] DOI 10.1016/j.str.2008.10.016 SUMMARY locations in the protein sequence. Despite these problems, much progress has been made in the use of structural information pro- Solid-state NMR spectroscopy does not require pro- vided by chemical shifts to aid the determination of native-state teins to form crystalline or soluble samples and can conformations of proteins (Williamson and Asakura, 1993; Kus- thus be applied under a variety of conditions, includ- zewski et al., 1995; Luginbuhl et al., 1995; Pearson et al., 1995; ing precipitates, gels, and microcrystals. It has re- Wilton et al., 2008). Recent approaches including CHESHIRE cently been shown that NMR chemical shifts can be (Cavalli et al., 2007; Montalvao et al., 2008), CS-Rosetta (Shen used to determine the structures of the native states et al., 2008), and CS23D (Wishart et al., 2008) have shown that backbone chemical shifts measured in solution can be used to of proteins in solution. By considering the cases of solve protein structures of up to 130 residues representative of two proteins, GB1 and SH3, we provide an initial dem- the major structural classes to a resolution of 2 A˚ or better. onstration here that this type of approach can be ex- Because there are significant and nonsystematic differences tended to the use of solid-state NMR chemical shifts between chemical shifts measured for molecular systems in to obtain protein structures in the solid state without the solid state and in solution (van Rossum et al., 2001, 2003; the need for measuring interatomic distances.