NMR of Biomolecules E-Book

• Herausgeber: Wiley-VCH
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1670

Veröffentlichungsjahr: 2012

Beschreibung

NMR is one of the most powerful methods for imaging of biomolecules. This book is the ultimate NMR guide for researchers in the biomedical community and gives not only background and practical tips but also a forward looking view on the future of NMR in systems biology.

Leseprobe

Contents

Cover

Related Titles

Title Page

Copyright

Preface

List of Contributors

List of Abbreviations

Part One: Introduction

Chapter 1: NMR and its Place in Mechanistic Systems Biology

Chapter 2: Structure of Biomolecules: Fundamentals

2.1 Structural Features of Proteins

2.2 Nucleic Acids

Chapter 3: What Can be Learned About the Structure and Dynamics of Biomolecules from NMR

3.1 Proteins Studied by NMR

3.2 Nucleic Acids Studied by NMR

Part Two: Role of NMR in the Study of the Structure and Dynamics of Biomolecules

Chapter 4: Determination of Protein Structure and Dynamics

4.1 Determination of Protein Structures

4.2 NMR Restraints

4.3 Structure Calculations

4.5 Protein Dynamics and NMR Observables

4.6 Protocols

4.7 Troubleshooting

Further Reading

Chapter 5: DNA

5.1 NMR studies of DNA

5.2 Assessment of the Folding Topology

5.3 Resonance Assignment through Sequential and Interstrand Interactions

5.4 Pseudorotation of Deoxyribofuranose Rings

5.5 Backbone Conformation

5.6 Natural Abundance Nucleobase Substitutions

5.7 Natural Abundance Heteronuclear Experiments

5.8 Site-Specific Low Isotopic Enrichment

5.9 Translational Diffusion Coefficients

5.10 Determination of Three-Dimensional Structure

5.11 Search for Transient Structures

5.12 Protocols

5.13 Example Experiments and Troubleshooting

Acknowledgments

Further Reading

Chapter 6: RNA

6.1 NMR Spectroscopy of RNA

6.2 Preparation of RNA Samples for NMR

6.3 Probing of the RNA Fold

6.4 Assessment of the Spectral Resolution

6.5 Strategy for the Resonance Assignment

6.6 Collection of Structural Information

6.7 Structural Calculation of RNA

6.8 Assessment of Quality of NMR Structures

6.9 Protocols

6.10 Troubleshooting

Acknowledgments

Further Reading

Chapter 7: Intrinsically Disordered Proteins

7.1 Intrinsically Disordered Proteins

7.2 Importance of NMR to Study IDPs

7.3 Structural and Dynamic Information on IDPs – NMR Observables

7.4 Protocols

7.5 Troubleshooting

Further Reading

Chapter 8: Paramagnetic Molecules

8.1 Paramagnetism-Assisted NMR

8.2 Scalar and Dipolar Electron Spin–Nuclear Spin Interactions: Hyperfine Shift

8.3 Scalar and Dipolar Electron Spin–Nuclear Spin Interactions: PRE

8.4 Indirect Electron Spin–Nuclear Spin Effects: Paramagnetism-Induced RDCs

8.5 Cross-Correlation Between Curie and Dipolar Relaxation

8.6 “Good” Metal Ions and “Bad” Metal Ions

8.7 Paramagnetism-Based Drug Discovery

8.8 Protocols

8.9 Troubleshooting

Further Reading

Part Three: Role of NMR in the Study of the Structure and Dynamicsof Biomolecular Interactions

Chapter 9: NMR Methodologies for the Analysis of Protein–Protein Interactions

9.1 Introduction

9.2 Dynamics and Ligand Binding

9.3 General Strategy

9.4 Overview of Methods

9.5 Outlook

9.6 Protocols for the Analysis of Protein Complexes

9.7 Troubleshooting

Further Reading

Chapter 10: Metal-Mediated Interactions

10.1 Theoretical Background

10.2 Protocol for the Structural Determination of a Metal-Mediated Complex

10.3 Example Experiment

10.4 Troubleshooting

Further Reading

Chapter 11: Protein–Paramagnetic Protein Interactions

11.1 Paramagnetic Sources in Protein Complexes

11.2 Types of NMR Restraints Obtained from Paramagnetic Centers

11.4 Protocols

11.5 Example Experiment

11.6 Troubleshooting

Acknowledgments

Further Reading

Chapter 12: Protein–RNA Interactions

12.1 Introduction

12.2 NMR Methodology

12.5 Protocols and Troubleshooting

Acknowledgments

Further Reading

Chapter 13: Protein–DNA Interactions

13.1 State of the Art

13.2 Conclusions and Perspectives

13.3 Protocols

13.4 Troubleshooting

Further Reading

Part Four: NMR in Drug Discovery

Chapter 14: High-Throughput Screening and Fragment-Based Design: General Considerations for Lead Discovery and Optimization

14.1 High-Throughput Screening and Fragment-Based Design

14.2 General Aspects of NMR Spectroscopy in Hit Identification and Optimization Processes

14.3 Chemical Shift Perturbation as a Screening Method

Acknowledgments

Further Reading

Chapter 15: Ligand-Observed NMR in Fragment-Based Approaches

15.1 Ligand-Observed NMR Spectroscopy

15.2 On the Transient Binding of Small Molecules to the Protein

15.3 Questions Asked by Ligand-Based Fragment Screening

15.4 Summary

15.5 Protocols

15.6 Example Experiments

15.7 Troubleshooting

Further Readings

Chapter 16: Interactions of Metallodrugs with DNA

16.1 Metallodrugs and DNA Interactions

16.2 Coordinative Binding

16.3 Groove Binding

16.4 Intercalation and Insertion

16.5 Dual Binding (Coordination and Intercalation)

16.6 Protocols

16.7 Tricks and Troubleshooting

Further Reading

Chapter 17: RNA as a Drug Target

17.1 RNA as a Target for Small Molecules

17.2 Chemical Shift Perturbation and Paramagnetic Relaxation Enhancement

17.3 Nuclear Overhauser Effect-Based Methods

17.4 Fluorine Labeling of RNA

17.5 Ligand-Based Methods

17.6 Protocols

Further Reading

Chapter 18: Fluorine NMR Spectroscopy for Biochemical Screening in Drug Discovery

18.1 Enzymatic Inhibition Mechanisms

18.2 n-FABS

18.3 Comparison of n-FABS with Other Biophysical Techniques

18.4 Outlook

18.5 Protocols

18.6 Troubleshooting

Acknowledgments

Further Reading

Chapter 19: NMR of Peptides

19.1 Introduction

19.2 Resonance Assignment

19.3 Stereostructure and Conformational Restraints

19.4 Structure Calculation

19.5 Importance of Peptide Conformations for Biological Activity

19.6 Protocols

19.7 Troubleshooting

Further Reading

Part Five: Solid-State NMR

Chapter 20: Biomolecular Solid-State NMR/Basics

20.1 Introduction

20.2 NMR Hamiltonian

20.3 Magic Angle Spinning

20.4 Cross-Polarization

20.5 Heteronuclear 1H Decoupling

20.6 Dipolar Recoupling

20.7 Recent Progress: New Probes – Ultrafast MAS – High Magnetic Fields

20.8 Protocols

20.9 Troubleshooting

Acknowledgments

Further Reading

Chapter 21: Protein Dynamics in the Solid State

21.1 Introduction

21.2 Basic Concepts

21.3 Coherent versus Incoherent Processes: Decay is not Always Relaxation

21.4 Deuterium as a Probe of Dynamics

21.5 15N and 13C T1 – Spin-Lattice Relaxation

21.6 Protocols

Acknowledgments

Further Reading

Chapter 22: Microcrystalline Proteins – An Ideal Benchmark for Methodology Development

22.1 Microcrystalline Protein Sample Preparation

22.2 Sequential Assignment of Proteins

22.3 Structural Restraints

22.4 Paramagnetic Systems

22.5 Benchmarking of the Solid-State NMR Structure Determination Methodology: Comparison of Structure Calculation Protocols and Accuracy of Structures

22.6 Protocols

22.7 Troubleshooting

Further Reading

Chapter 23: Structural Studies of Protein Fibrils by Solid-State NMR

23.1 Background

23.2 NMR Spectra of Fibrils

23.3 Outlook

23.4 Protocols and Examples

23.5 Troubleshooting

Further Reading

Chapter 24: Solid-State NMR on Membrane Proteins: Methods and Applications

24.1 Solid-State NMR of Membrane Proteins

24.2 MAS Applied to Ion Channels and Retinal Proteins

24.3 Protocols

24.4 Troubleshooting

Acknowledgments

Further Reading

Part Six: Frontiers in NMR Spectroscopy

Chapter 25: Dynamic Nuclear Polarization

25.1 Dynamic Nuclear Polarization at High Magnetic Fields

25.2 Theoretical Background

25.3 Protocols

25.4 Example Experiment

25.5 Perspectives

Further Reading

Chapter 26: 13C Direct Detection NMR

26.1 13C Direct Detection NMR for Biomolecular Applications

26.2 Protocols for Experimental Setup

26.3 Troubleshooting

Further Reading

Chapter 27: Speeding Up Multidimensional NMR Data Acquisition

27.1 Multidimensional NMR: Basic Concepts and Features

27.2 Fast Methods in N-Dimensional NMR

27.3 Protocols for Fast N-Dimensional NMR and Troubleshooting

Further Reading

Chapter 28: Metabolomics

28.1 Metabolomics in Systems Biology

28.2 NMR and Metabolomics

28.3 Data Analysis

28.4 Success in the Application of Metabolomics

28.5 Protocols

28.6 Troubleshooting

Further Reading

Chapter 29: In-Cell Protein NMR Spectroscopy

29.1 Background

29.2 Specific Applications

29.3 Conclusions and Future Directions

29.4 Protocols and Example Experiments

29.5 Troubleshooting

Acknowledgments

Further Reading

Chapter 30: Structural Investigation of Cell-Free Expressed Membrane Proteins

30.1 Introduction

30.2 Cell-Free Expression of Membrane Proteins

30.3 Cell-Free Expression in Membrane-Mimetic Environments

30.4 Strategies for Functional Protein Expression

30.5 Cell-Free Approaches for Structural Studies

30.6 Cell-Free Labeling Strategies for Backbone Assignment

30.7 Structure Determination with Limited Nuclear Overhauser Effect Long-Distance Restraints

30.8 Protocols

30.9 Troubleshooting

Further Reading

Part Seven: Computational Aspects

Chapter 31: Grid Computing

31.1 Grid Infrastructure

31.2 e-NMR Web Platform

31.3 Protocols

31.4 Troubleshooting

Acknowledgments

Further Reading

Chapter 32: Protein–Protein Docking with HADDOCK

32.1 Protein–Protein Docking: General Concepts

32.2 Gathering Experimental Information for Data-Driven Docking

32.3 How Does HADDOCK Use the Information?

32.4 Protocol: A Guided Tour of the HADDOCK Web Interface

32.5 Troubleshooting

Further Reading

Chapter 33: Automated Protein Structure Determination Methods

33.1 NMR Experiment-Driven Protein Modeling

33.2 NOE-Based Structure Determination

33.3 Sequence-Specific Resonance Assignment

33.4 NMR Signal Identification

33.5 Perspectives

33.6 Protocols

33.7 Example Structure Determination and Troubleshooting

Further Reading

Chapter 34: NMR Structure Determination of Protein–Ligand Complexes

34.1 Protein–Ligand Complex Structure Determination by NMR

34.2 Methods for High-Affinity Binders

34.3 Methods for Low-Affinity Binders

34.4 Protocols and Troubleshooting

Further Reading

Chapter 35: Small Angle X-Ray Scattering/Small Angle Neutron Scattering as Methods Complementary to NMR

35.1 Introduction

35.2 Invariants

35.3 Ab Initio Shape Determination

35.4 Validation of Atomic Models

35.5 Rigid-Body Modeling of Quaternary Structure

35.6 Equilibrium Mixtures and Flexible Systems

35.7 Protocols

35.8 Troubleshooting

Further Reading

References

Index

Related Titles

Keeler, J.Understanding NMR Spectroscopy 2010 ISBN: 978-0-470-74608-0

de Graaf, R.In Vivo NMR Spectroscopy Principles and Techniques 2007 ISBN: 978-0-470-02670-0

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Preface

The use of NMR to solve protein structures has a tradition that dates back to 1984 (M.P. Williamson, T.F. Havel, and K. Wüthrich (1985) J. Mol. Biol. 182, 295). Since that time, the role of NMR in structural biology has constantly increased in terms of the number of researchers involved and the scientific relevance of the results. Spectrometers are becoming more and more powerful, with magnetic fields that currently reach 22 T, and high-temperature superconducting materials raise the possibility that this value can be surpassed. The investment required for a magnet of the above intensity is currently around 10 million (US$14.3 million) and an estimate of 18 million (US$25.7 million) is reasonable for new-generation magnets. It is clear that NMR is a technology that deserves a special place in research infrastructures, as individual schools may find it difficult to have a battery of machines, all at the forefront of the technology, dedicated to various types of experiments. In 1994, the European Commission (EC) began financing transnational access to NMR instrumentation at some research infrastructures, which have continued and grown in number until the present with the EC-funded Bio-NMR1 project. In Europe, the recent European Strategy Forum for Research Infrastructures (ESFRI) Roadmap identifies NMR as a fundamental node in the Integrated Structural Biology Infrastructure (INSTRUCT),2 while it also plays a role in the EU-OPENSCREEN (European Infrastructure of Open Screening Platforms for Chemical Biology)3 infrastructure, Euro-BioImaging,4 and Biobanking and Biomolecular Resources Research Infrastructure (BBMRI).5

The EC-funded electronic infrastructures (e-NMR6 and WeNMR7) provide nonspecialists with tools for automatic data handling, structure calculations, molecular dynamics simulations, and the creation of interaction models in such a way that the potential of the NMR technology can blossom in favor of the progress of science.

Much of this reasoning was debated during the FP6-funded Coordination Action NMR-Life8 and resulted in a booklet entitled NMR in Mechanistic Systems Biology,9 which ultimately served as the spark for this volume. We were pleased when Gregor Cicchetti from Wiley-VCH noticed this booklet and proposed that we edit a book on the very same subject, and we gathered a number of outstanding contributors to fulfill the task.

Our intention, which we hope pervades the book, was to provide a text for graduate students, junior post-docs, and other newcomers that would serve as an introduction to the field, addressing classical NMR approaches from solution to the solid state, providing some tips and tricks not available in journal articles, and providing perspectives on future developments. It is our hope that the Protocols and Troubleshooting sections will be of assistance and guidance when choosing experiments and overcoming difficulties.

However, everyone who has experience in editing books knows how difficult a task it is – obtaining the manuscripts on time, convincing everyone to adhere to a template and write for students and not for their fellow professors, and even drawing the line on what content to include and when to call an end to the editorial process, including substitution of recalcitrant contributors. We editors have tried our best to overcome these difficulties, but we are aware that much more could have been done. For example, the development of isotopic labeling has been fundamental for the development of NMR, but we decided not to address it here. The reader should therefore be aware that the field of NMR is even broader and more exciting than it appears from our efforts!

Part I of the book (Introduction) explains NMR's role in Mechanistic Systems Biology and provides a broad overview of biomolecular structure before identifying what NMR can teach us about the structure and dynamics of biomolecules. Parts II–VII address a series of relevant topics in NMR-driven biological research: the role of NMR in the study of the structure and dynamics of biomolecules, its role in the study of the structure and dynamics of biomolecular interactions, NMR in drug discovery, solid-state NMR, frontiers in NMR spectroscopy, and computational aspects.

We would like to take the opportunity to thank, in addition to Gregor, Dr. Marco Fragai of the Center for Magnetic Resonance (CERM) at the University of Florence for his assistance in editing some chapters of the book, and Professor Claudio Luchinat, who consistently demonstrates his friendship and his willingness to support any initiative of CERM, and the scientific personnel of CERM who have contributed to discussions and sustained the work.

It is our sincere hope that this book will find a home not only in NMR facilities, but also in biomedical laboratories around the world, where it can be of use to the broader scientific community and help diffuse NMR as a technique for the study of biological systems.

Ivano BertiniKathleen S. McGreevyGiacomo Parigi

Florence, January 2012

Notes

1.http://www.bio-nmr.net.

2.http://www.structuralbiology.eu.

3.http://www.eu-openscreen.eu.

4.http://www.eurobioimaging.eu.

5.http://www.bbmri.eu.

6.http://www.enmr.eu.

7.http://www.wenmr.eu.

8.http://www.postgenomicnmr.net.

9.http://www.postgenomicnmr.net/NMRLife/docs/NMR_in_MSB.pdf.

List of Contributors

Chris Abell University of Cambridge University Chemical Laboratory Lensfield Road Cambridge CB2 1EW UK

Marc Baldus Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht The Netherlands

Lucia Banci University of Florence Department of Chemistry and Magnetic Resonance Center (CERM) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Emeline Barbet-Massin Université de Lyon Institut de Sciences Analitiques Centre de RMN à Très Hauts Champs 5 rue de la Doua 69100 Villeurbanne France

Benjamin Bardiaux Leibniz-Institut für Molekulare Pharmakologie NMR-Supported Structural Biology Robert-Rössle-Strasse 10 13125 Berlin Germany

Johannes G. Beck Technische Universität München Department Chemie Lichtenbergstrasse 4 85747 Garching Germany

Frank Bernhard Goethe University Frankfurt Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ) Max-von-Laue-Strasse 9 60438 Frankfurt am Main Germany

Ivano Bertini University of Florence Department of Chemistry and Magnetic Resonance Center (CERM) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Anja Böckmann Université de Lyon IBCP UMR 5086 CNRS 7 passage du Vercors 69367 Lyon France

Rolf Boelens Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht The Netherlands

Alexandre M.J.J. Bonvin Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht The Netherlands

Bernhard Brutscher Institut de Biologie Structurale – Jean-Pierre Ebel UMR5075 CNRS-CEA-UJF 41 rue Jules Horowitz 38027 Grenoble Cedex France

Janina Buck Goethe University Frankfurt Center for Biomolecular Magnetic Resonance (BMRZ) and Institute of Organic Chemistry and Chemical Biology Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany

David S. Burz University at Albany Department of Chemistry 1400 Washington Avenue Albany, NY 12222 USA

Francesca Cantini University of Florence Department of Chemistry and Magnetic Resonance Center (CERM) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Mirko Cevec Goethe University Frankfurt Center for Biomolecular Magnetic Resonance (BMRZ) and Institute of Organic Chemistry and Chemical Biology Max-von-Laue-Straße 7 60438 Frankfurt Germany

Simone Ciofi-Baffoni University of Florence Department of Chemistry and Magnetic Resonance Center (CERM) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Alessio Ciulli University of Cambridge University Chemical Laboratory Lensfield Road Cambridge CB2 1EW UK

David Cowburn Yeshiva University Albert Einstein College of Medicine 1300 Morris Park Avenue Bronx, NY 10461 USA

Abhishek A. Cukkemane Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht The Netherlands

Claudio Dalvit University of Neuchâtel Department of Chemistry Avenue de Bellevaux 51 2000 Neuchâtel Switzerland

Marc van Dijk Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht The Netherlands

Volker Dötsch Goethe University Frankfurt Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ) Max-von-Laue-Strasse 9 60438 Frankfurt am Main Germany

Elke Duchardt-Ferner Goethe University Frankfurt Center for Biomolecular Magnetic Resonance (BMRZ) and Institute of Molecular Biosciences Max-von-Laue-Straße 9 60438 Frankfurt am Main Germany

Kaushik Dutta New York Structural Biology Center New York, NY 10027 USA

Lyndon Emsley Université de Lyon CNRS/ENS Lyon/UCB-Lyon 1 Centre de RMN à Très Hauts Champs 5 rue de la Doua 69100 Villeurbanne France

Isabella C. Felli University of Florence Department of Chemistry and Magnetic Resonance Center (CERM) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Lucio Ferella University of Florence Magnetic Resonance Center (CERM) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Jan-Peter Ferner Goethe University Frankfurt Center for Biomolecular Magnetic Resonance (BMRZ) and Institute of Organic Chemistry and Chemical Biology Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany

Andreas O. Frank Vanderbilt University School of Medicine Department of Biochemistry 802 Robinson Research Building Nashville, TN 37232-0146 USA

W. Trent Franks Leibniz-Institut für Molekulare Pharmakologie NMR-Supported Structural Biology Robert-Rössle-Strasse 10 13125 Berlin Germany

Lucio Frydman Weizmann Institute of Science Department of Chemical Physics Chemical Science Building Rehovot 76100 Israel

Paul Guerry Université de Lyon CNRS/ENS Lyon/UCB-Lyon 1 Centre de RMN à Très Hauts Champs 5 rue de la Doua 69100 Villeurbanne France

Torsten Herrmann Université de Lyon CNRS/ENS Lyon/UCB-Lyon 1 Centre de RMN à Très Hauts Champs 5 rue de la Doua 69100 Villeurbanne France

Yoshitaka Hiruma Leiden University Leiden Institute of Chemistry Gorlaeus Laboratories Einsteinweg 55 2333 CC Leiden The Netherlands

Hendrik R.A. Jonker Goethe University Frankfurt Johann Wolfgang Goethe-University Center for Biomolecular Magnetic Resonance (BMRZ) and Institute of Organic Chemistry and Chemical Biology Max-von-Laue-Straße 7 60438 Frankfurt Germany

Ezgi Karaca Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht The Netherlands

Panagiotis L. Kastritis Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht The Netherlands

Peter H.J. Keizers Leiden University Leiden Institute of Chemistry Gorlaeus Laboratories Einsteinweg 55 2333 CC Leiden The Netherlands

Horst Kessler Technische Universität München Department Chemie Lichtenbergstrasse 4 85747 Garching Germany

Lidija Kovai University of Utrecht Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht The Netherlands

and

Jožef Stefan Institute Department of Molecular and Biomedical Sciences Jamova cesta 39 1000 Ljubljana Slovenia

Józef R. Lewandowski Université de Lyon CNRS/ENS Lyon/UCB-Lyon 1 Centre de RMN à Très Hauts Champs 5 rue de la Doua 69100 Villeurbanne France

Hong-Ke Liu Nanjing Normal University College of Chemistry and Materials Science Jiangsu Key Laboratory of Biofunctional Materials Wenyuan Road 1, Nanjing 210046 China

Frank Löhr Goethe University Frankfurt Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ) Max-von-Laue-Strasse 9 60438 Frankfurt am Main Germany

Claudio Luchinat University of Florence Department of Chemistry and Magnetic Resonance Center (CERM) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Tobias Madl Helmholtz Zentrum München Institute of Structural Biology Ingolstädter Landstrasse 1 85764 Neuherberg Germany

and

Technische Universität München Biomolecular NMR and Munich Center for Integrated Protein Science Department Chemie Lichtenbergstrasse 4 85747 Garching Germany

Vijayalaxmi Manoharan Medical Research Council National Institute for Medical Research Molecular Structure Division The Ridgeway Mill Hill London NW7 1AA UK

Dominique Marion Institut de Biologie Structurale – Jean-Pierre Ebel UMR5075 CNRS-CEA-UJF 41 rue Jules Horowitz 38027 Grenoble Cedex France

Kathleen S. McGreevy University of Florence Department of Chemistry and Magnetic Resonance Center (CERM) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Beat H. Meier ETH Zurich Laboratory of Physical Chemistry Wolfgang-Pauli-Strasse 10 8093 Zurich Switzerland

Adrien S.J. Melquiond Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht The Netherlands

Senada Nozinovic Goethe University Frankfurt Center for Biomolecular Magnetic Resonance (BMRZ) and Institute of Organic Chemistry and Chemical Biology Max-von-Laue-Straße 7 60438 Frankfurt Germany

Hartmut Oschkinat Leibniz-Institut für Molekulare Pharmakologie NMR-Supported Structural Biology Robert-Rössle-Strasse 10 13125 Berlin Germany

Giacomo Parigi University of Florence Department of Chemistry and Magnetic Resonance Center (CERM) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Maurizio Pellecchia Sanford-Burnham Medical Research Institute 10901 North Torrey Pines Road La Jolla, CA 92037 USA

Jose Manuel Perez-Canadillas Consejo Superior de Investigaciones Científicas (CSIC) Instituto de Quimica Fisica “Rocasolano” Serrano 119 28006 Madrid Spain

Maxim V. Petoukhov European Molecular Biology Laboratory Hamburg Outstation Notkestrasse 85 22607 Hamburg Germany

Roberta Pierattelli University of Florence Department of Chemistry and Magnetic Resonance Center (CERM) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Guido Pintacuda Université de Lyon Institut de Sciences Analitiques Centre de RMN à Très Hauts Champs 5 rue de la Doua 69100 Villeurbanne France

Janez Plavec National Institute of Chemistry Slovenian NMR Center Hajdrihova 19 1000 Ljubljana Slovenia

and

EN-FIST Center of Excellence Dunajska 156 1000 Ljubljana Slovenia

and

University of Ljubljana Faculty of Chemistry and Chemical Technology Askerceva cesta 5 1000 Ljubljana Slovenia

Thomas F. Prisner Goethe University Frankfurt Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ) Max-von-Laue-Strasse 7 60438 Frankfurt Germany

Andres Ramos Medical Research Council National Institute for Medical Research Molecular Structure Division The Ridgeway Mill Hill London NW7 1AA UK

Enrico Ravera University of Florence Department of Chemistry and Magnetic Resonance Center (CERM) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Sina Reckel Goethe University Frankfurt Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ) Max-von-Laue-Strasse 9 60438 Frankfurt am Main Germany

Marie Renault Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht The Netherlands

Christian Richter Johann Wolfgang Goethe-University Center for Biomolecular Magnetic Resonance (BMRZ) and Institute of Organic Chemistry and Chemical Biology Max-von-Laue-Straße 7 60438 Frankfurt Germany

Jörg Rinnenthal Goethe University Frankfurt Center for Biomolecular Magnetic Resonance (BMRZ) and Institute of Organic Chemistry and Chemical Biology Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany

Antonio Rosato University of Florence Department of Chemistry and Magnetic Resonance Center (CERM) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Barth-Jan van Rossum Leibniz-Institut für Molekulare Pharmakologie NMR-Supported Structural Biology Robert-Rössle-Strasse 10 13125 Berlin Germany

Peter J. Sadler University of Warwick Department of Chemistry Gibbet Hill Road Coventry CV4 7AL UK

Michael Sattler Helmholtz Zentrum München Institute of Structural Biology Ingolstädter Landstrasse 1 85764 Neuherberg Germany

and

Technische Universität München Biomolecular NMR and Munich Center for Integrated Protein Science Department Chemie Lichtenbergstrasse 4 85747 Garching Germany

Ulrich Schieborr Goethe University Frankfurt Center for Biomolecular Magnetic Resonance (BMRZ) and Institute of Organic Chemistry and Chemical Biology Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany

Christophe Schmitz Utrecht University Bijvoet Center for Biomolecular Research Science Faculty Padualaan 8 3584 CH Utrecht The Netherlands

Harald Schwalbe Goethe University Frankfurt Center for Biomolecular Magnetic Resonance (BMRZ) and Institute of Organic Chemistry and Chemical Biology Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany

Alexander Shekhtman University at Albany Department of Chemistry 1400 Washington Avenue Albany, NY 12222 USA

Vladimír Sklená Masaryk University National Center for Biomolecular Research Faculty of Science and Central European Institute of Technology (CEITEC) Kamenice 5 625 00 Brno Czech Republic

Pawel led University of Cambridge University Chemical Laboratory Lensfield Road Cambridge CB2 1EW UK

Solmaz Sobhanifar Goethe University Frankfurt Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ) Max-von-Laue-Strasse 9 60438 Frankfurt am Main Germany

Sridhar Sreeramulu Goethe University Frankfurt Center for Biomolecular Magnetic Resonance (BMRZ) and Institute of Organic Chemistry and Chemical Biology Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany

Richard Štefl Masaryk University National Center for Biomolecular Research Faculty of Science and Central European Institute of Technology (CEITEC) Kamenice 5 625 00 Brno Czech Republic

Dimitri I. Svergun European Molecular Biology Laboratory Hamburg Outstation Notkestrasse 85 22607 Hamburg Germany

Leonardo Tenori University of Florence Magnetic Resonance Center (CERM) and FiorGen Foundation Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Peter Tompa VIB Department of Structural Biology Vrije Universiteit Brussel Pleinlaan 2 1050 Brussels Belgium

and

Hungarian Academy of Sciences Institute of Enzymology Biological Research Center Karolina út 29 1113 Budapest Hungary

Paola Turano University of Florence Department of Chemistry and Magnetic Resonance Center (CERM) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Marcellus Ubbink Leiden University Leiden Institute of Chemistry Gorlaeus Laboratories Einsteinweg 55 2333 CC Leiden The Netherlands

Sjoerd J. de Vries Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht The Netherlands

and

Technische Universität München Physik-Department T38 James Franck Straße 1 85748 Garching Germany

Jens Wöhnert Goethe University Frankfurt Center for Biomolecular Magnetic Resonance (BMRZ) and Institute of Molecular Biosciences Max-von-Laue-Straße 9 60438 Frankfurt am Main Germany

List of Abbreviations

Aβamyloid beta9-AA9-aminoacridineABCATP-binding cassetteAcPacetyl phosphateACRAMTUacridinylthioureaACSautomatic sample changerADME-Tadsorption, distribution, metabolism, excretion, and toxicityA-Ealanine-glutamic acidAFMatomic force microscopyahaz3-aminohexahydroazepineAIRambiguous interaction restraintAKTserine/threonine protein kinaseAmpampicillinAOacridine orangeAPHHadiabatic passage through the Hartman-Hahn conditionAPSYautomated projection spectroscopyATPadenosine triphosphateAtx1antioxidant protein 1AUIMataxin 3 ubiquitin interacting motifbenbenzeneBESTband-selective excitation short-transientbipbiphenylBMRBbiological magnetic resonance data bankBPback-projectionBPTIbovine pancreatic trypsin inhibitorbpybipyridinebRbacteriorhodopsinBRCTbreast cancer 1 C-terminalBSAburied surface areaBSAbovine serum albuminBSEbovine spongiform encephalopathyBURPband-selective uniform-response pure-phaseBUSIproteinase inhibitor from bull seminal plasma1C31-[(3-aminopropyl)amino]-anthracene-9,10-dioneCAcertification authorityCA150coactivator of 150 kDaCamchloramphenicolcAMPcyclic adenosine monophosphateCAPcatabolite activator proteinCAPcAMP-binding proteinCASDcritical assessment of automatic structure determinationCATHclass, architecture, topology, homologous superfamilyCBPCREB-binding proteinCcc2adomain a of Ca2+-sensitive cross-complementer2CCPNcollaborative computing project for NMRCCRcross correlation rateCdk2cyclin-dependent kinase 2CEcomputing elementCECFcontinuous exchange cell-free