Solid State NMR Studies of Biopolymers E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1460

Veröffentlichungsjahr: 2012

Beschreibung

The content of this volume has been added to eMagRes (formerly Encyclopedia of Magnetic Resonance) - the ultimate online resource for NMR and MRI.

The field of solid state NMR of biological samples [ssNMR] has blossomed in the past 5-10 years, and a cohesive overview of the technology is needed for new practitioners in industry and academia. This title provides an overview of Solid State NMR methods for studying structure dynamics and ligand-binding in biopolymers, and offers an overview of RF pulse sequences for various applications, including not only a systematic catalog but also a discussion of theoretical tools for analysis of pulse sequences. Practical examples of biochemical applications are included, along with a detailed discussion of the many aspects of sample preparation and handling that make spectroscopy on solid proteins successful.

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The Encyclopedia of Magnetic Resonance (up to 2012) and eMagRes (from 2013 onward) publish a wide range of online articles on all aspects of magnetic resonance in physics, chemistry, biology and medicine. The existence of this large number of articles, written by experts in various fields, is enabling the publication of a series of EMR Handbooks / eMagRes Handbooks on specific areas of NMR and MRI. The chapters of each of these handbooks will comprise a carefully chosen selection of articles from eMagRes. In consultation with the eMagRes Editorial Board, the EMR Handbooks / eMagRes Handbooks  are coherently planned in advance by specially-selected Editors, and new articles are written (together with updates of some already existing articles) to give appropriate complete coverage. The handbooks are intended to be of value and interest to research students, postdoctoral fellows and other researchers learning about the scientific area in question and undertaking relevant experiments, whether in academia or industry.

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Encyclopedia of Magnetic Resonance

Edited by Robin K. Harris, Roderick E. Wasylishen, Edwin D. Becker, John R. Griffiths, Vivian S. Lee, Ian R. Young, Ann E. McDermott, Tatyana Polenova, James W. Emsley, George A. Gray, Gareth A. Morris, Melinda J. Duer and Bernard C. Gerstein.

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Library of Congress Cataloging-in-Publication Data

Solid-state NMR studies of biopolymers/editors, Ann E. McDermott, Tatyana Polenova.

    p. ; cm.

Includes bibliographical references and index.

ISBN 978-0-470-72122-3 (cloth)

1. Nuclear magnetic resonance spectroscopy—Handbooks, manuals, etc. 2. Biopolymers—Spectra—Handbooks, manuals, etc. 3. Solid-phase biochemistry—Handbooks, manuals, etc. I. McDermott, Ann E. II.Polenova, Tatyana, 1970- [DNLM: 1. Magnetic Resonance Spectroscopy. 2. Biopolymers. QU 25 S686 2010]

QP519.9.N83S647 2010

616.07’548—dc22

2010020368

A catalogue record for this book is available from the British Library.

ISBN-13: 978-0-470-72122-3

Set in 9.5/11.5 pt Times by Laserwords (Private) Limited, Chennai, India Printed and bound in Singapore by Markono Print Media Pte Ltd

Encyclopedia of Magnetic Resonance

Editorial Board

Editors-in-Chief

Robin K. HarrisUniversity of DurhamDurhamUK

Roderick E. WasylishenUniversity of AlbertaEdmonton, AlbertaCanada

Section EditorsSOLID-STATE NMR & PHYSICS

Melinda J. DuerUniversity of CambridgeCambridgeUK

Bernard C. GersteinAmes, IAUSA

SOLUTION-STATE NMR & CHEMISTRY

James W. EmsleyUniversity of SouthamptonSouthamptonUK

George A. GrayVarian Inc.Palo Alto, CAUSA

Gareth A. MorrisUniversity of ManchesterManchesterUK

BIOCHEMICAL NMR

Ann E. McDermottColumbia UniversityNew York, NYUSA

Tatyana PolenovaUniversity of DelawareNewark, DEUSA

MRI &; MRS

John R. GriffithsCancer Research UK   Cambridge Research   InstituteCambridgeUK

Vivian S. LeeNYU Langone Medical   CenterNew York, NYUSA

Ian R. YoungImperial CollegeLondonUK

HISTORICAL PERSPECTIVES

Edwin D. BeckerNational Institutes of HealthBethesda, MDUSA

International Advisory Board

David M. Grant (Chairman)University of UtahSalt Lake City, UTUSA

Isao AndoTokyo Institute   of TechnologyTokyoJapan

Adriaan BaxNational Institutes of HealthBethesda, MDUSA

Chris BoeschUniversity of BernBernSwitzerland

Paul A. BottomleyJohns Hopkins UniversityBaltimore, MDUSA

William G. BradleyUCSD Medical CenterSan Diego, CAUSA

Graeme M. BydderUCSD Medical CenterSan Diego, CAUSA

Paul T. CallaghanVictoria University   of WellingtonWellingtonNew Zealand

Richard R. ErnstEidgenössische Technische   Hochschule (ETH)ZürichSwitzerland

Ray FreemanUniversity of CambridgeCambridgeUK

Lucio FrydmanWeizmann Institute   of ScienceRehovotIsrael

Maurice GoldmanVillebon sur YvetteFrance

Harald GüntherUniversität SiegenSiegenGermany

Herbert Y. KresselHarvard Medical SchoolBoston, MAUSA

C. Leon PartainVanderbilt University Medical   CenterNashville, TNUSA

Alexander PinesUniversity of California   at BerkeleyBerkeley, CAUSA

George K. RaddaUniversity of OxfordOxfordUK

Hans Wolfgang SpiessMax-Planck Institute   of Polymer ResearchMainzGermany

Charles P. SlichterUniversity of Illinois   at Urbana-ChampaignUrbana, ILUSA

John S. WaughMassachusetts Institute   of Technology (MIT)Cambridge, MAUSA

Bernd WrackmeyerUniversität BayreuthBayreuthGermany

Kurt WüthrichThe Scripps Research   InstituteLa Jolla, CAUSAandETH ZürichZürichSwitzerland

Contents

Title

Copyright

Contributors

Series Preface

Volume Preface

Part A: Fundamentals of Solid-State NMR Spectroscopy

1 Internal Spin Interactions and Rotations in Solids

1.1 Introduction

1.2 Nuclear Spin Hamiltonian Operators

1.3 NMR Spectra

1.4 Rotations

1.5 Origin Of Internal Interactions

References

2 Average Hamiltonian Theory

2.1 Introduction

2.2 Magnus Expansion

2.3 Representations and Frames of Reference: Truncation

2.4 Applications

2.5 Additional Topics

References

3 Tensors in NMR

3.1 Introduction

3.2 Cartesian to Spherical Tensors

3.3 Hamiltonians in Terms of Spherical Tensors Of Rank 0, 1, 2

3.4 Matrix Elements for Spherical Tensors

References

4 Chemical Shift Tensors

4.1 Introduction

4.2 The Chemical Shift

4.3 The Chemical Shift Tensor in a Variety of Reference Frames and Representations

4.4 Tensor Powder Patterns in Solids

4.5 Chemical Shift Tensors from Single Crystals

4.6 Molecular Origins of the Chemical Shift Tensor

4.7 Conclusions

References

5 Magic Angle Spinning

5.1 Introduction

5.2 Magic Angle Spinning and Dipolar Interactions

5.3 Magic Angle Spinning and Anisotropic Shift Interactions

5.4 Magic Angle Spinning and Aniss

5.5 Magic Angle Spinning and Indirect Spin–Spin Inter

5.6 Magic Angle Spinning and Nuclear Quadrupole Interactions

5.7 Macroscopic and Microscopic Motions

5.8 Factors Affecting Resolution

5.9 Spinners

5.10 Double Spinners

5.11 Magic Angle Spinning and Other Techniques

5.12 Magic Angle Spinning and NMR Imaging of Solids

References

6 Cross Polarization in Solids

6.1 Introduction

6.2 Strategies cor Achieving High-Resolution NMR in Solids

6.3 Theory of Cross Polarization in Solids

6.4 Cross Polarization at High Spinning Speeds

6.5 Spectral Editing and Other Tricks Using Cross Polarization

6.6 Conclusions

References

7 Quadrupolar Nuclei in Solids

7.1 Introduction

7.2 Basic Spin Properties

7.3 Interaction with Radiofrequency Fields

7.4 Experimental Methods

7.5 Theory

References

Part B: Recent Developments in Solid-State NMR Hardware and Emerging Methodologies for Structural and Dynamics Studies of Biopolymers

8 Probe Development for Biosolids NMR Spectroscopy

8.1 Introduction

8.2 General Considerations

8.3 Typical Probe Designs

8.4 Considerations For Specific Applications

References

9 High-Frequency Dynamic Nuclear Polarization

9.1 Introduction

9.2 Instrumentation And Polarizing Agents For Dnp

9.3 High-Frequency Dnp On Proteins

9.4 Dnp In Liquids

9.5 Future Developments

References

10 Homonuclear Dipolar Recoupling in Solid-State NMR

10.1 Introduction

10.2 Theoretical Background and Notation

10.3 Dipolar Recoupling by Rf Pulses Alone

10.4 Chemical-Shift-Dependent Dipolar Recoupling

10.5 Symmetry Principles In Homonuclear Dipolar Recoupling

10.6 Frequency-Selective Homonuclear Dipolar Recoupling

10.7 Other Recent Developments

References

11 Dipolar Recoupling: Heteronuclear

11.1 Introduction

11.2 Mas Hamiltonian

11.3 Heteronuclear Dipolar Recoupling in Spin Pairs

11.4 Heteronuclear Dipolar Recoupling in Multispin Systems

11.5 Conclusions

References

12 Adiabatic Polarization-Transfer Methods in MAS Spectroscopy

12.1 Introduction

12.2 Theory

12.3 Methods of Heteronuclear Polarization Transfer

12.4 Methods of Homonuclear Polarization Transfer

References

13 Symmetry-Based Pulse Sequences in Magic-Angle Spinning Solid-State NMR

13.1 Introduction

13.2 Homonuclear Sequences

13.3 Heteronuclear Sequences

13.4 Applications

13.5 Conclusions

References

14 Dipolar-Based Torsion Angle Measurements for Protein Structure Determination

14.1 Introduction

14.2 Hcch Experiment

14.3 Torsion Angle Measurements in Proteins

14.4 Other Methods for the Determination of Torsion

References

15 Deuterated Peptides and Proteins: Structure and Dynamics Studies by MAS Solid-State NMR

15.1 Introduction

15.2 Correlation Spectroscopy

15.3 Characterization Of Dynamics in the Solid State

References

16 Correlation Spectroscopy for Resonance Assignments in Solid-State Proteins Using J-couplings

16.1 Introduction

16.2 The Indirect Spin–Spin Coupling and Coherence Transfer

16.3 Scalar-Coupling-Driven Correlation Experiments in Biological Solids

16.4 Concluding Remarks

References

17 Indirect Coupling and Connectivity

17.1 Introduction

17.2 Homonuclear Through-Bond Correlation Spectroscopy

17.3 Heteronuclear Through-Bond Correlation Spectroscopy

17.4 Conclusions

References

18 Fast Magic-Angle Spinning for Protein Solid-State NMR Spectroscopy

18.1 Introduction

18.2 Fast-Mas Probes: Practical Considerations

18.3 High-Sensititivy Proton Detection

18.4 Paramagnetic Samples and Paramagnetic Doping

18.5 Conclusions

References

19 Relaxation Studies of Solid Biopolymers

19.1 Introduction

19.2 Basic Concepts

19.3 Coherent Versus Incoherent Processes: Decay is not Always Relaxation

19.4 Similarity of Dynamics in Solution and Solid State

19.5 Deuterium Relaxation

19.6 15N And 13C T1–Spin–Lattice Relaxation

19.7 Challenges for Relaxation Studies of Biopolymers

References

Part C: Computational Aspects of Solid-State NMR Spectroscopy

20 Proteins and Model Systems: Spectral Analyses

20.1 Introduction

20.2 Solution NMR

20.3 Solid-State NMR

20.4 Through-Space Interactions and Hydrogen Bonding

20.5 Metals and Metalloproteins

20.6 Conclusions and Prospects

References

21 Numerical Simulations in Solid-State NMR with SIMPSON

21.1 Introduction

21.2 Overview of Simpson

21.3 Applications of Simpson in Solid-State NMR

21.4 Conclusions

References

22 Protein Structure Calculation Using Ambiguous Restraints

22.1 Introduction

22.2 Ambiguous Data can be Translated into Structural Restraints

22.3 Noise Peaks

22.4 Symmetry

22.5 Ambiguities in Other Experimental Data

22.6 Conclusions

References

23 Protein Structure Calculation and Automated NOE Restraints

23.1 Introduction

23.2 Automated Noesy Interpretation

23.3 Automated Noesy Signal Identification

23.4 Conclusions

References

Part D: Applications of Solid-State NMR to Structural and Dynamics Studies of Biopolymers

24 Aligned Membrane Proteins: Structural Studies

24.1 Introduction

24.2 Membrane Protein Aligned Samples

24.3 Membrane Protein Spectroscopy

24.4 Further Studies

References

25 Membrane-Associated Systems: Structural Studies by MAS NMR

25.1 Introduction

25.2 Methods

25.3 Applications

25.4 Conclusions

References

26 Structural Studies of Protein Fibrils and Misfolded Proteins by Solid-State NMR

26.1 Introduction

26.2 NMR Spectra of Fibrils

26.3 Sample Preparation

26.4 Spectroscopic Aspects

26.5 Structural Aspects Specific for Fibrils

26.6 Structure Calculation

26.7 Fibrils Characterized by Solid-State NMR

26.8 Conclusions

References

27 Structural and Dynamics Studies of Lipids by Solid-State NMR

27.1 Introduction

27.2 Static Solid-State NMR Spectra of Lipid Bilayers

27.3 Magic-Angle Spinning Spectra of Lipid Bilayers

27.4 Resolution Without Spinning: Solid-State NMR Spectra of Oriented Bilayers

27.5 Applications to the Study of Peptide–Lipid Interactions

27.6 Conclusions

References

28 REDOR Applications in Biology: An Overview

28.1 Introduction

28.2 Redor Methodology

28.3 Membrane Peptides, Proteins, and Sterols

28.4 Insoluble Peptide Aggregates and Peptide-Lattice Interactions

28.5 Protein–Ligand Interactions

28.6 Nucleic Acid Interactions

28.7 Bacterial Metabolism, Cell-Walls, and Antibiotics

28.8 Plant Metabolism

References

29 Quadrupolar Metal Nuclides in Bioinorganic Chemistry: Solid-State NMR Studies

29.1 Introduction

29.2 Magic Angle-Spinning Experiments

29.3 Sensitivity Enhancement Methods for Biological Solids

29.4 Quantum Chemical Calculations for Interpretation of NMR Parameters in Terms of Molecular Structure

29.5 Conclusions

References

30 Photosynthetic Antennae and Reaction Centers

30.1 Introduction

30.2 Theoretical Background

30.3 Applications

References

31 Structure and Function Studies of Energy and Signal Transducing Proteins by Solid-State NMR

31.1 Introduction

31.2 Membrane-Bound Mastoparan-X, A Model Peptide of the G-Protein Activating Loop of G-Protein Coupled Receptor

31.3 H+-ATP Synthase Subunit C-Ring, an Energy-Conversion Rotary Motor, in the Membrane

31.4 CONCLUSION

References

32 Protein–Solvent Interactions in Solids

32.1 Introduction

32.2 Transfer Pathways

32.3 Different Water Pools

32.4 Conclusion

References

33 Unifying Solution and Solid-State NMR Studies of Nucleic Acid Dynamics

33.1 Nucleic ACID Dynamics

33.2 Theoretical Framework for Solid-State and Solution NMR

33.3 Applications to DNA and RNA Systems

33.4 Conclusions

References

Index

Contributors

Christian Ader

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

Chapter 25: Membrane-Associated Systems: Structural Studies by MAS NMR

Hideo Akutsu

Open Laboratory for Advanced Bioscience & Biotechnology, Institute for Protein Research, Osaka University, 6-2-3 Furuedai, Suita, 565-0874, Japan

Chapter 31: Structure and Function Studies of Energy and Signal Transducing Proteins by Solid-State NMR

E. Raymond Andrew

†

University of Florida, Gainesville, FL, USA

Chapter 5: Magic Angle Spinning

Michèle Auger

Department of Chemistry, Universite Laval, 1045 Avenue de la Medecine, Quebec, G1K 7P4, Canada

Chapter 27: Structural and Dynamics Studies of Lipids by Solid-State

Marc Baldus

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

Chapter 25: Membrane-Associated Systems: Structural Studies by MAS NMR

Michael F. Bardaro Jr.

Department of Chemistry, University of Washington, PO Box 351700, Seattle, WA, 98195, USA

Chapter 33: Unifying Solution and Solid-State NMR Studies of Nucleic Acid Dynamics

Benjamin Bardiaux

Institut Pasteur, Paris, France and NMR-supported Strutural Biology, Structural Biology Section, Leibniz-Institut fur Molekulare Pharmakologie, Robert-Rossle-Strasse 10, Berlin, 13125, Germany

Chapter 22: Protein Structure Calculation Using Ambiguous Restraints

Stefan Becker

Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fafiberg 11, Gottingen, D-37077, Germany

Chapter 25: Membrane-Associated Systems: Structural Studies by MAS NMR

Anja Böckmann

IBCP-CNRS UMR 5086, Universite de Lyon, 7, Passage du Vercors, Cedex 07, Lyon, 69367, France

Chapter 32: Protein-Solvent Interactions in Solids

William W. Brey

National High Magnetic Field Laboratory, Florida State University, Building 232, 1800 E. Paul Dirac Drive, Tallahassee, FL, 32310, USA

Chapter 8: Probe Development for Biosolids NMR SpectroscopyChapter 24: Aligned Membrane Proteins: Structural Studies

Douglas P. Burum

Vern Maine & Associates, 100 Main Street - Suite 2, Nashua, NH 03060, USA

Chapter 6: Cross Polarization in Solids

Lynette Cegelski

Department of Chemistry, Stanford University, Mudd Building, Room 121, 333 Campus Drive, Stanford, CA, 94305, USA

Chapter 28: REDOR Applications in Biology: An Overview

Timothy A. Cross

National High Magnetic Field Laboratory, Florida State University, Building 232, 1800 E. Paul Dirac Drive, Tallahassee, FL, 32310, USA

Chapter 24: Aligned Membrane Proteins: Structural Studies

Gary P. Drobny

Department of Chemistry, University of Washington, PO Box 351700, Seattle, WA, 98195, USA

Chapter 33: Unifying Solution and Solid-State NMR Studies of Nucleic Acid Dynamics

Dorothy C. Echodu

Department of Chemistry, University of Washington, PO Box 351700, Seattle, WA, 98195, USA

Chapter 33: Unifying Solution and Solid-State NMR Studies of Nucleic Acid Dynamics

Paul D. Ellis

Pacific Northwest National Laboratory, US Department of Energy, PO Box 999, 902 Battelle Boulevard, Richland, WA, 99352, USA

Chapter 29: Quadrupolar Metal Nuclides in Bioinorganic Chemistry: Solid-State NMR Studies

Prashant Emani

Department of Chemistry, University of Washington, PO Box 351700, Seattle, WA, 98195, USA

Chapter 33: Unifying Solution and Solid-State NMR Studies of Nucleic Acid Dynamics

Lyndon Emsley

Centre de Résonance Magnétique Nucléaire à Tres Hauts Champs, Université de Lyon/FRE 3008 CNRS/ENS-Lyon/UCB Lyon 1, 5 Rue de la Doua, Villeurbanne, 69100, France

Chapter 19: Relaxation Studies of Solid Biopolymers

Matthias Ernst

Laboratorium fur Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10, Zurich, 8093, Switzerland

Chapter 12: Adiabatic Polarization-Transfer Methods in MAS Spectroscopy

Riqiang Fu

National High Magnetic Field Laboratory, Florida State University, Building 232, 1800 E. Paul Dirac Drive, Tallahassee, FL, 32310, USA

Chapter 24: Aligned Membrane Proteins: Structural Studies

Toshimichi Fujiwara

Open Laboratory for Advanced Bioscience & Biotechnology, Institute for Protein Research, Osaka University, 6-2-3 Furuedai, Suita, 565-0874, Japan

Chapter 31: Structure and Function Studies of Energy and Signal Transducing Proteins by Solid-State NMR

Peter L. Gor’kov

National High Magnetic Field Laboratory, Florida State University, Building 232, 1800 E. Paul Dirac Drive, Tallahassee, FL, 32310, USA

Chapter 8: Probe Development for Biosolids NMR Spectroscopy

David M. Grant

University of Utah, Salt Lake City, UT, USA

Chapter 4: Chemical Shift Tensors

Robert G. Griffin

Francis Bitter Magnet Laboratory, Department of Chemistry, Massachusetts Institute of Technology, 150 Albany Street, Cambridge, MA, 2139, USA

Chapter 9: High-Frequency Dynamic Nuclear Polarization

Huub J. M. de Groot

Faculty of Science, Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands

Chapter 30: Photosynthetic Antennae and Reaction Centers

Torsten Herrmann

Centre de Résonance Magnétique Nucléaire à Tres Hauts Champs, Université de Lyon/FRE 3008 CNRS/ENS-Lyon/UCB Lyon 1, 5 Rue de la Doua, Villeurbanne, 69100, France

Chapter 23: Protein Structure Calculation and Automated NOE Restraints

Christopher P. Jaroniec

Department of Chemistry, Ohio State University, Columbus, OH, 43210, USA

Chapter 11: Dipolar Recoupling: Heteronuclear

Alexej Jerschow

Department of Chemistry, New York University, Room 1001, 100 Washington Square East, New York, NY, 10003, USA

Chapter 3: Tensors in NMR

Vladimir Ladizhansky

Department of Physics, University of Guelph, Ontario, N1G 2W1, Canada

Chapter 14: Dipolar-Based Torsion Angle Measurements for Protein Structure Determination

Anne Lesage

Laboratoire de Chimie, Institut de chimie de Lyon, University of Lyon, Ecole Normale Superieure de Lyon, Lyon Cedex 07, 69364, France

Chapter 17: Indirect Coupling and Connectivity

Malcolm H. Levitt

Chemistry Department, Southampton University, University Road, Southampton, SO17 1BJ, UK

Chapter 13: Symmetry-Based Pulse Sequences in Magic-Angle Spinning Solid-State NMR

Jόzef R. Lewandowski

Centre de Résonance Magnétique Nucléaire à Tres Hauts Champs, Université de Lyon/FRE 3008 CNRS/ENS-Lyon/UCB Lyon 1, 5 Rue de la Doua, Villeurbanne, 69100, France

Chapter 19: Relaxation Studies of Solid Biopolymers

Andrew S. Lipton

Pacific Northwest National Laboratory, US Department of Energy, PO Box 999, 902 Battelle Boulevard, Richland, WA, 99352, USA

Chapter 29: Quadrupolar Metal Nuclides in Bioinorganic Chemistry: Solid-State NMR Studies

Joanna R. Long

Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, 32611, USA

Chapter 8: Probe Development for Biosolids NMR Spectroscopy

Melody L. Mak-Jurkauskas

Francis Bitter Magnet Laboratory, Department of Chemistry, Massachusetts Institute of Technology, 150 Albany Street, Cambridge, MA, 2139, USA

Chapter 9: High-Frequency Dynamic Nuclear Polarization

Thérèse Malliavin

Unité de Bioinformatique Structurale, Institut Pasteur, 25-28 Rue du Dr Roux, Cedex 15, Paris, 75724, France

Chapter 22: Protein Structure Calculation Using Ambiguous Restraints

Michael Mehring

2 Physikalisches Institut, Universitat Stuttgart, Pfaffenwaldring 57, Stuttgart, 70569, Germany

Chapter 1: Internal Spin Interactions and Rotations in Solids

Beat H. Meier

Laboratorium fur Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10, Zurich, 8093, Switzerland

Chapter 12: Adiabatic Polarization-Transfer Methods in MAS Spectroscopy Chapter 26: Structural Studies of Protein Fibrils and Misfolded Proteins by Solid-State NMR

Gary A. Meints

Department of Chemistry, University of Washington, PO Box 351700, Seattle, WA, 98195, USA

Chapter 33: Unifying Solution and Solid-State NMR Studies of Nucleic Acid Dynamics

Paul A. Miller

Department of Chemistry, University of Washington, PO Box 351700, Seattle, WA, 98195, USA

Chapter 33: Unifying Solution and Solid-State NMR Studies of Nucleic Acid Dynamics

Leonard J. Mueller

Department of Chemistry, University of California, Riverside, CA, 92521, USA

Chapter 16: Correlation Spectroscopy for Resonance Assignments in Solid-State Proteins Using J-couplings

Niels Chr. Nielsen

Laboratory for Biomolecular NMR Spectroscopy, Department of Chemistry, University of Aarhus, Langelandsgade 140, Aarhus, DK-8000, Denmark

Chapter 21: Numerical Simulations in Solid-State NMR with SIMPSON

Michael Nilges

Unité de Bioinformatique Structurale, Institut Pasteur, 25-28 Rue du Dr Roux, Cedex 15, Paris, 75724, France

Chapter 22: Protein Structure Calculation Using Ambiguous Restraints

Eric Oldfield

A110 Chemical & Life Sciences Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA

Chapter 20: Proteins and Model Systems: Spectral Analyses

Greg L. Olsen

Department of Chemistry, University of Washington, PO Box 351700, Seattle, WA, 98195, USA

Chapter 33: Unifying Solution and Solid-State NMR Studies of Nucleic Acid Dynamics

Kari Pederson

Department of Chemistry, University of Washington, PO Box 351700, Seattle, WA, 98195, USA

Chapter 33: Unifying Solution and Solid-State NMR Studies of Nucleic Acid Dynamics

Tatyana Polenova

Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratory, Newark, DE, 19716, USA

Chapter 29: Quadrupolar Metal Nuclides in Bioinorganic Chemistry: Solid-State NMR Studies

Bernd Reif

Solid State NMR, Structural Biology Section, Leibniz-Institut fur Molekulare Pharmakologie, Robert-Rössle-Strafie 10, Berlin, 13125, Germany and Charité Universitätsmedizin, Berlin, Germany

Chapter 15: Deuterated Peptides and Proteins: Structure and Dynamics Studies by MAS Solid-State NMR

Zahra Shajani

Department of Chemistry, University of Washington, PO Box 351700, Seattle, WA, 98195, USA

Chapter 33: Unifying Solution and Solid-State NMR Studies of Nucleic Acid Dynamics

S. Chandra Shekar

Department of Chemistry, New York University, Room 1001, 100 Washington Square East, New York, NY, 10003, USA

Chapter 3: Tensors in NMR

Jeremy J. Titman

School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK

Chapter 16: Correlation Spectroscopy for Resonance Assignments in Solid-State Proteins Using J-couplings

Orsolya Toke

Chemical Research Center, Institute of Structural Chemistry, Hungarian Academy of Sciences, 59-67 Pusztaszeriut, Budapest, H-1025, Hungary

Chapter 28: REDOR Applications in Biology: An Overview

Zdenĕk Tošner

Laboratory for Biomolecular NMR Spectroscopy, Department of Chemistry, University of Aarhus, Langelandsgade 140, Aarhus, DK-8000, Denmark

Chapter 21: Numerical Simulations in Solid-State NMR with SIMPSON

Robert Tycko

Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 112, 5 Memorial Drive, Bethesda, MD, 20892, USA

Chapter 10: Homonuclear Dipolar Recoupling in Solid-State NMR

Gabriele Varani

Department of Chemistry, University of Washington, PO Box 351700, Seattle, WA, 98195, USA

Chapter 33: Unifying Solution and Solid-State NMR Studies of Nucleic Acid Dynamics

Alexander J. Vega

Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratory, Newark, DE, 19716, USA

Chapter 7: Quadrupolar Nuclei in Solids

Thomas Vosegaard

Laboratory for Biomolecular NMR Spectroscopy, Department of Chemistry, University of Aarhus, Langelandsgade 140, Aarhus, DK-8000, Denmark

Chapter 21: Numerical Simulations in Solid-State NMR with SIMPSON

John S. Waugh

Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 2139, USA

Chapter 2: Average Hamiltonian Theory

Donghua H. Zhou

Department of Physics, Oklahoma State University, 224 Physical Science, Stillwater, OK, 74078, USA

Chapter 18: Fast Magic-Angle Spinning for Protein Solid-State NMR Spectroscopy

† Deceased 2001

Series Preface

The Encyclopedia of Nuclear Magnetic Resonance was published in eight volumes in 1996, in part to celebrate the fiftieth anniversary of the first publications in NMR in January 1946. Volume 1 contains an historical overview and ca. 200 short personal articles by prominent NMR practitioners, while the remaining seven volumes comprise ca. 500 articles on a wide variety of topics in NMR (including MRI). Two “spin-off” volumes incorporating the articles on MRI and MRS (together with some new ones) were published in 2000 and a ninth volume was brought out in 2002. In 2006, the decision was taken to publish all the articles electronically (i.e. on the World Wide Web) and this was carried out in 2007. Since then, new articles have been placed on the web every three months and a number of the original articles have been updated. This process is continuing. The overall title has been changed to the Encyclopedia of Magnetic Resonance to allow for future articles on EPR and to accommodate the sensitivities of medical applications.

The existence of this large number of articles, written by experts in various fields, is enabling a new concept to be implemented, namely the publication of a series of printed handbooks on specific areas of NMR and MRI. The chapters of each of these handbooks will comprise a carefully chosen selection of Encyclopedia articles relevant to the area in question. In consultation with the Editorial Board, the handbooks are coherently planned in advance by specially selected editors. New articles are written and existing articles are updated to give appropriate complete coverage of the total area. The handbooks are intended to be of value and interest to research students, postdoctoral fellows, and other researchers learning about the topic in question and undertaking relevant experiments, whether in academia or industry.

Robin K. Harris

University of Durham, Durham, UK

Roderick E. Wasylishen

University of Alberta, Edmonton, Alberta, Canada

November 2009

Volume Preface

The purpose of this handbook is to provide a comprehensive introduction to modern biological solid-state NMR spectroscopy for students and for the general audience of scientists interested in entering the field. There has hitherto been no single volume that both covers the fundamentals in solid-state NMR theory and hardware and provides examples of contemporary applications. This handbook represents our efforts to remedy the growing need for such a treatment.

The selection of chapters is intended to give the interested reader a flavor of the richness of this rapidly developing field. The diverse nature of the experimental approaches and sample conditions, together with the high information content arising from the sensitivity of the various spin interactions to the environment and from the accumulated knowledge in the field – allowing a practising solid-state NMR spectroscopist to measure those interactions, extract the relevant physical observables and relate them to the molecular framework (i.e., geometry, electronic structure, molecular motions) through the accumulated empirical knowledge or through quantum chemical calculations – permits a wide range of biological systems to be studied at atomic-level detail.

Traditionally, solid-state NMR experiments in biological systems have focused on probing a single or a very small number of isotopically labeled sites; however, recent breakthroughs in hardware technology and pulse sequence developments have permitted high-resolution studies of uniformly and extensively labeled proteins and other biopolymers. A decade ago, the first reports emerged demonstrating that resonance assignments of uniformly isotopically enriched microcrystalline proteins are feasible using 2D and 3D magic-angle spinning spectroscopy, while subsequent investigations showed that 3D protein structures can be determined on the basis of distance and torsion angle constraints acquired in solid-state NMR experiments.

Since these initial studies, the field has experienced a spectacular growth in the number of solid-state NMR-based protein structures deposited in the Protein Data Bank, including studies of large proteins, membrane proteins, and protein assemblies that had previously been intractable using any structural biology method. Recent demonstrations that protein structures can be determined on the basis of isotropic chemical shifts alone have opened a vista of exciting opportunities for researchers entering the field.

The handbook starts with an introduction to fundamental concepts in spin physics. This is followed by a discussion of modern solid-state NMR experiments and the corresponding theoretical framework for extracting structural and dynamics information in biological systems, including recoupling and coherence transfer techniques; a review of quantum mechanical calculations of NMR spectroscopic observables follows. Computational approaches to structure calculations are presented. Discussion of the experiments for measurements of molecular motions and their interpretation is included. Modern solid-state NMR probe hardware is also described. Finally, a series of chapters on applications of contemporary solid-state NMR methods to a broad range of biological systems is presented.

We note that the field of biological solid-state NMR spectroscopy is so diverse and developing so rapidly that we have not been able to cover all topics in depth or indeed in some cases, at all. For example, some of the emerging methodologies (e.g., signal enhancement protocols through CIDNP and half-integer quadrupolar nuclei) are introduced briefly, and the interested reader is encouraged to seek additional chapters on these important topics in the Encyclopedia of Magnetic Resonance. Furthermore, technical advances in the field are unfolding even as we are preparing this handbook for press, and these will be included in future editions. It is, we feel, an exciting time for a new generation of researchers to enter the field of biological solid-state NMR spectroscopy.

We are very grateful to our colleagues—the authors of the chapters, who have contributed their time and expertise to this handbook. We hope that it will become a useful resource for a broad readership of scientists interested in solid-state NMR spectroscopy.

Ann E. McDermott

Columbia University, New York, NY, USA

Tatyana Polenova

University of Delaware, Newark, DE, USA

August 2010

Abbreviations and Acronyms

A5P

Arabinose-5-Phosphate

ac-VL

Acetyl-Val-Leu

ADR

Ambiguous Distance Restraint

AFM

Atomic Force Microscopy

AHT

Average Hamiltonian Theory

AIR

Ambiguous Interaction Restraints

APHH CP

Adiabatic-Passage Hartmann-Hahn Cross-Polarization

APRR

Adiabatic-Passage Rotational Resonance

ARIA

Ambiguous Restraints for Iterative Assignment

ATP

Adenosine Triphosphate

BABA

Back-to-Back

BChl

Bacteriochlorophyll

BDPA

α,γ -Bisdiphenylene-β-Phenylallyl

BPP

B loembergen - Purcell - Pound

BPTI

Bovine Pancreatic Trypsin Inhibitor

bR

bacteriorhodopsin

BT2E

bis-TEMPO-(Ethylene Glycol)2

bTbk

bis-TEMPO-bis-ketal

BWO

Backward Wave Oscillator

CFP

Charge Field Perturbation

CHW

Cross-Hester-Waugh

CNS

Crystallography and Nuclear Magnetic Resonance System

COSY

Correlation Spectroscopy

CP

Cross Polarization

CPMAS

Cross Polarization Magic Angle Spinning

CR

Composite Refocusing

CRAMPS

Combined Rotation and Multiple Pulse Sequence

CRDSD

Cross-Relaxation Driven Spin Diffusion

CRF

Common Reference Frame

CSA

Chemical Shift Anisotropy

CT

Central Transition

CT

Constant-Time

DAGK

Diacyl Glycerol Kinase

DARR

Dipolar-Assisted Rotational Resonance

DAS

Dynamic Angle Spinning

DCP

Double-Cross-Polarization

DDI

Dipole-Dipole Interaction