NMR of biomolecules : towards mechanistic systems biology /

Preface XXI List of Contributors XXIII List of Abbreviations XXIX Part One Introduction 1 1 NMR and its Place in Mechanistic Systems Biology 3 Ivano Bertini, Kathleen S. McGreevy, and Giacomo Parigi 2 Structure of Biomolecules: Fundamentals 7 2.1 Structural Features of Proteins 7 Lucia Banci and Francesca Cantini 2.2 Nucleic Acids 21 Mirko Cevec, Hendrik R.A. Jonker, Senada Nozinovic, Christian Richter, and Harald Schwalbe 3 What Can be Learned About the Structure and Dynamics of Biomolecules from NMR 33 3.1 Proteins Studied by NMR 33 Lucio Ferella, Antonio Rosato, and Paola Turano 3.2 Nucleic Acids Studied by NMR 47 Janez Plavec Part Two Role of NMR in the Study of the Structure and Dynamics of Biomolecules 51 4 Determination of Protein Structure and Dynamics 53 Lucio Ferella, Antonio Rosato, and Paola Turano 5 DNA 97 Janez Plavec 6 RNA 119 Richard Stefl and Vladimir Sklenar 7 Intrinsically Disordered Proteins 137 Isabella C. Felli, Roberta Pierattelli, and Peter Tompa 8 Paramagnetic Molecules 155 Ivano Bertini, Claudio Luchinat, and Giacomo Parigi Part Three Role of NMR in the Study of the Structure and Dynamics of Biomolecular Interactions 173 9 NMR Methodologies for the Analysis of Protein-Protein Interactions 175 Tobias Madl and Michael Sattler 10 Metal-Mediated Interactions 197 Simone Ciofi-Baffoni 11 Protein-Paramagnetic Protein Interactions 205 Peter H.J. Keizers, Yoshitaka Hiruma, and Marcellus Ubbink 12 Protein-RNA Interactions 219 Vijayalaxmi Manoharan, Jose Manuel Perez-Ca~nadillas, and Andres Ramos 13 Protein-DNA Interactions 239 Lidija Kovacic and Rolf Boelens Part Four NMR in Drug Discovery 253 14 High-Throughput Screening and Fragment-Based Design: General Considerations for Lead Discovery and Optimization 255 Maurizio Pellecchia 15 Ligand-Observed NMR in Fragment-Based Approaches 265 Pawe /l Sledz, Chris Abell, and Alessio Ciulli 16 Interactions of Metallodrugs with DNA 283 Hong-Ke Liu and Peter J. Sadler 17 RNA as a Drug Target 299 Jan-Peter Ferner, Elke Duchardt Ferner, JEUROorg Rinnenthal, Janina Buck, Jens WEUROohnert, and Harald Schwalbe 18 Fluorine NMR Spectroscopy for Biochemical Screening in Drug Discovery 315 Claudio Dalvit 19 NMR of Peptides 329 Johannes G. Beck, Andreas O. Frank, and Horst Kessler Part Five Solid-State NMR 345 20 Biomolecular Solid-State NMR/Basics 347 Emeline Barbet-Massin and Guido Pintacuda 21 Protein Dynamics in the Solid State 367 Jozef R. Lewandowski and Lyndon Emsley 22 Microcrystalline Proteins - An Ideal Benchmark for Methodology Development 377 W. Trent Franks, Barth-Jan van Rossum, Benjamin Bardiaux, Enrico Ravera, Giacomo Parigi, Claudio Luchinat, and Hartmut Oschkinat 23 Structural Studies of Protein Fibrils by Solid-State NMR 395 Anja BEUROockmann and Beat H. Meier 24 Solid-State NMR on Membrane Proteins: Methods and Applications 407 A.A. Cukkemane, M. Renault, and M. Baldus Part Six Frontiers in NMR Spectroscopy 419 25 Dynamic Nuclear Polarization 421 Thomas F. Prisner 26 13C Direct Detection NMR 433 Isabella C. Felli and Roberta Pierattelli 27 Speeding Up Multidimensional NMR Data Acquisition 445 Bernhard Brutscher, Dominique Marion, and Lucio Frydman 28 Metabolomics 467 Leonardo Tenori 29 In-Cell Protein NMR Spectroscopy 479 David S. Burz, David Cowburn, Kaushik Dutta, and Alexander Shekhtman 30 Structural Investigation of Cell-Free Expressed Membrane Proteins 497 Solmaz Sobhanifar, Sina Reckel, Frank LEUROohr, Frank Bernhard, and VolkerDEUROotsch Part Seven Computational Aspects 509 31 Grid Computing 511 Antonio Rosato 32 Protein-Protein Docking with HADDOCK 521 Christophe Schmitz, Adrien S.J. Melquiond, Sjoerd J. de Vries, Ezgi Karaca, Marc van Dijk, Panagiotis L. Kastritis, and Alexandre M.J.J. Bonvin 33 Automated Protein Structure Determination Methods 537 Paul Guerry and Torsten Herrmann 34 NMR Structure Determination of Protein-Ligand Complexes 549 Ulrich Schieborr, Sridhar Sreeramulu, and Harald Schwalbe 35 Small Angle X-Ray Scattering/Small Angle Neutron Scattering as Methods Complementary to NMR 563 M.V. Petoukhov and D.I. Svergun Further Reading 574 References 575 Index 609