ESR Spectroscopy in Membrane Biophysics
Volume 27
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Marcus A. Hemminga and Lawrence J. Berliner
ESR Spectroscopy in Membrane Biophysics
Volume 27
Library of Congress Control Number: 2006936900 ISBN-10: 0-387-25066-2 e-ISBN-10: 0-387-38880-X ISBN-13: 978-0-387-25066-3 e-ISBN-13: 978-0-387-49367-1 Printed on acid-free paper.
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Marcus A. Hemminga Laboratory of Biophysics Wageningen University Dreijenlaan 3
6703 HA Wageningen The Netherlands
email: marcus.hemminga@wur.nl
Lawrence J. Berliner
Department of Chemistry &
Biochemistry University of Denver 2190 E. lliff Avenue F. W. Olin Hall, Room 202 Denver, CO 80208 USA
email: berliner@du.edu
v
R. Linn Belford (app. 2) Department of Chemistry University of Illinois 600 South Mathews Avenue Urbana, IL 61801, USA (217) 333-2553 rbelford@uiuc.edu
Enrica Bordignon (chap. 5) Experimental Physics —
Macromolecular Structure Universität Osnabrück Barbarastrasse 7
Osnabrück D-49076, Germany +49 541 969 2664
enrica.bordignon@uos.de
Louise Brown (chap. 4) Department of Chemistry and
Biomolecular Sciences Division of Environmental and
Life Sciences
F7B 335, Macquarie University Sydney NSW 2109, Australia +61-2-9850-8294
lbrown@alchemist.chem.mq.edu.au
Mikolai I. Fajer (app. 1)
National High Magnetic Fields Laboratory Kasha Laboratory of Molecular Biophysics Florida State University
1800 Paul Dirac Drive Tallahassee, FL 32310, USA (850) 645-1335
mfajer@gmail.com
Piotr G. Fajer (chap. 4, app. 1)
National High Magnetic Fields Laboratory Kasha Laboratory of Molecular Biophysics Department of Biology, Florida State
University
1800 East Paul Dirac Drive Tallahassee, FL 32310, USA (850) 644-2600
fajer@magnet.fsu.edu
Jack H. Freed (app. 3) ACERT, Cornell University B52 Baker Laboratory Ithaca, NY 14853, USA (607) 255-3647 jhf@ccmr.cornell.edu
Marcus A. Hemminga (chap. 1) Laboratory of Biophysics Wageningen University Dreijenlaan 3
Wageningen 6703 HA, The Netherlands +31 317 482044
marcus.hemminga@wur.nl
Gunnar Jeschke (chap. 2, app. 4) EPR Group
Max Planck Institute for Polymer Research Ackermannweg 10
Mainz D-55128, Germany +49 6131 379 247
jeschke@mpip-mainz.mpg.de
Karen Mattson (app. 2) Bayer Material Science LLC 100 Bayer Road
Pittsburgh, PA 15205-9741, USA
CONTRIBUTORS
vi
Mark J. Nilges (app. 2) Illinois EPR Research Center University of Illinois 506 South Matthews Avenue Urbana, IL 61801, USA (217) 333-3969 mjnilges@uiuc.edu
Kenneth L. Sale (app. 1) Biosystems Research Department Sandia National Laboratories 7011 East Avenue
Livermore, CA 94551, USA (925) 294-2143
klsale@sandia.gov
Arthur Schweiger (app. 6) Laboratory of Physical Chemistry ETH Zürich, HCI F 225
Wolfgang-Pauli-Strasse 10 Zürich CH-8093, Switzerland [deceased 4 January 2006]
Alex I. Smirnov (chap. 6, app. 5) Department of Chemistry North Carolina State University 614F Cox
Raleigh, NC 27695-8204, USA (919) 513-4377
Alex_Smirnov@ncsu.edu
Tatyana I. Smirnova (chap. 6) Department of Chemistry North Carolina State University 612B Cox
Raleigh, NC 27695-8204, USA (919) 513-4375
Tatyana_Smirnova@ncsu.edu
Likai Song
National High Magnetic Fields Laboratory Department of Biology, Florida State
University 1800 Paul Dirac Drive Tallahassee, FL 32310, USA (850) 645-1335
song@magnet.fsu.edu
Heinz-Jürgen Steinhoff (chap. 5) Experimental Physics —
Macromolecular Structure Universität Osnabrück Barbarastrasse 7
Osnabrück D-49076, Germany +49 541 969 2675
heinz-juergen.steinhoff@uos.de
Stefan Stoll (app. 6)
Laboratory of Physical Chemistry ETH Zürich, HCI F 225
Wolfgang-Pauli-Strasse 10 Zürich CH-8093, Switzerland +41 44 6334259
stefan.stoll@ethz.ch
Janez Štrancar (chap. 3, app. 7) Laboratory of Biophysics, EPR Center Jožef Stefan Institute
Jamova 39
Ljubljana SI-1000, Slovenia +386 1 4773226
janez.strancar@ijs.si
vii
FOREWORD
This book flows from the “Graduate Course: Advanced ESR Spectroscopy in Membrane Biophysics” held in Wageningen (The Netherlands) during March–
April 2004, which was coordinated by one of the editors, Marcus A. Hemminga (Wageningen), Janez Štrancar (Ljubljana), and Heinz-Jürgen Steinhoff (Os- nabrück). The course was organized under the auspices of the Graduate School of
“Experimental Plant Sciences” (EPS). It was a phenomenal success and fitted well the needs of students who desired a thorough understanding of the theory as well as the applications of spin-label ESR in biophysics.
In the spirit of the graduate course, this volume is strongly enhanced by the enlistment of an international group of experts. We are confident that it will receive the same enthusiastic reception that was given by the students and research scien- tists who participated in the first graduate course and should serve as an excellent pedagogical tool.
Lawrence J. Berliner Denver, Colorado
ix
PREFACE
Membrane proteins comprise almost a third of all the proteins in an organism or cell. However, progress in determining their structure has been slow. Compared to soluble proteins, only a handful of membrane protein structures have been solved. Therefore, membrane proteins offer the greatest challenge in struc- tural biology, and there is an urgent need to develop and apply new biophysical methodologies that are able to generate detailed structural information. Among modern biophysical techniques, site-directed spin-labeling electron spin resonance (SDSL-ESR) appears to show the highest potential to further develop the field. The objective of this book is to provide in-depth information about new advances of SDSL-ESR in membrane biophysics, emphasizing recent developments in the ap- plication to membrane proteins. Of course, the methodology is applicable to other protein systems as well, such as water-soluble proteins, proteins assemblies, and protein–nuclei acid complexes.
The contributions in this volume illustrate the current state of the art of SDSL- ESR and highlight new advances in high-field ESR and pulsed ESR, especially aimed at providing highly resolved structural information about proteins. In addi- tion, background information is presented concerning the analysis of ESR spectra in complex situations.
Together with this book, a CD-ROM is bundled that contains background ma- terial not suitable for inclusion within the book and software to simulate and ana- lyze ESR spectra. In this way, the CD-ROM covers the most recent innovations and advances in the field of ESR spectroscopy, and will also be helpful in training new students in the field.
We are very much indebted to the contributors to this book, who are experts in the field, and who spent a great deal of time and effort in producing the materials for the book as well as reviewing other chapter contributions.
Marcus A. Hemminga Wageningen, The Netherlands
Lawrence J. Berliner Denver, Colorado, USA
xi
CONTENTS
Foreword... vii
Preface... ix
Chapter 1 Introduction and Future of Site-Directed Spin Labeling of Membrane Proteins Marcus A. Hemminga 1. Structural Biology and Proteomics... 1
2. Membrane Proteins: Production and Reconstitution Challenges... 2
3. SDSL-ESR ... 2
4. Cysteine Modification ... 3
5. Structure and Dynamics Information from SDSL-ESR ... 4
6. Pulsed ESR Spectroscopy ... 6
7. High-Field ESR Spectroscopy... 8
8. Molecular Dynamics Simulations ... 9
9. Spectral Simulation and Analysis... 11
10. Comparison with Site-Directed Fluorescence Labeling ... 11
11. Future ... 13
Chapter 2 Instrumentation and Experimental Setup Gunnar Jeschke 1. Continuous-Wave ESR ... 18
2. Basics of Pulsed ESR ... 25
3. Pulsed ENDOR ... 31
4. Pulsed ELDOR (DEER)... 39
5. Acknowledgments ... 43
6. Problems... 44
7. Answers... 44
xii
Chapter 3
Advanced ESR Spectroscopy in Membrane Biophysics Janez Štrancar
1. Introduction ... 49
2. Motional Averaging in a Spin-Labeled Biomembrane... 55
3. Strategies for Calculating Powder Spectra ... 66
4. Solving an Inverse Problem and Condensation of Results ... 77
5. Appendix... 89
Chapter 4 Practical Pulsed Dipolar ESR (DEER) Piotr G. Fajer, Louise Brown, and Likai Song 1. DEER Signal ... 95
2. Practical DEER ... 104
3. Applications ... 113
Chapter 5 Membrane Protein Structure and Dynamics Studied by Site-Directed Spin-Labeling ESR Enrica Bordignon and Heinz-Jürgen Steinhoff 1. Introduction ... 129
2. Spin Labeling ... 130
3. Structural Information Derived from ESR Spectra Analysis... 133
4. Detection of Conformational Changes ... 155
Chapter 6 High-Field ESR Spectroscopy in Membrane and Protein Biophysics Tatyana I. Smirnova and Alex I. Smirnov 1. Introduction ... 165
2. Analysis of High-Field ESR Spectra of Spin Labels... 166
3. High-Field ESR of Spin-Labeled Aqueous Samples: Experimental Considerations ... 193
4. High-field ESR in Studies of Molecular Dynamics ... 204
5. High-field ESR in Studies of Molecular Structure ... 215
6. Characterization of the Nitroxide Microenvironment by High-Field ESR ... 223
7. Perspectives... 234
xiii Appendices: Software Descriptions
Appendix 1
Molecular Modeling of Spin Labels
Mikolai I. Fajer, Kenneth L. Sale, and Piotr G. Fajer
1. System Requirements ... 254
2. Preparation of Structures ... 254
3. Simulations... 255
4. Analysis of Nitroxide Trajectories ... 256
5. Force Fields ... 256
6. Spin Label Topologies ... 257
Appendix 2 SIMPOW6: A Software Package for the Simulation of ESR Powder-Type Spectra Mark J. Nilges, Karen Mattson, and R. Linn Belford 1. Introduction ... 261
2. Spin Hamiltonian for SIMPOW6 ... 262
3. Calculation of Resonance Fields ... 263
4. Lineshapes... 264
5. Intensity (Transition Moment) ... 266
6. Generation (Integration) of a Powder Spectrum... 266
7. Spectral Optimization... 267
8. Summary of Input Parameters ... 268
9. Running the Program ... 268
10. Examples ... 270
11. Appendix A: Format of the Input Files: Spin Hamiltonian Parameters ... 276
12. Appendix B: Format of the Input Files: Optimization Parameters and Control ... 279
13. Appendix C: Format of the Output Simulation Files... 280
Appendix 3
ACERT Software: Simulation and Analysis of ESR Spectra Jack H. Freed
xiv
Appendix 4
DeerAnalysis 2006: Distance Measurements on Nanoscopic Length Scales by Pulse ESR
Gunnar Jeschke
Appendix 5
EWVoigt and EWVoigtn: Inhomogeneous Line Shape Simulation and Fitting Programs
Alex I. Smirnov
1. Introduction ... 289
2. Convolution-Based Fitting of Continuous Wave EPR Spectra ... 289
3. Brief Description of EWVOIGT Capabilities ... 292
4. Convolution Algorithm with Levenberg-Marquardt Optimization for Fitting Inhomogeneous EPR Spectra ... 293
Appendix 6 EasySpin: Simulating cw ESR Spectra Stefan Stoll and Arthur Schweiger 1. Introduction ... 299
2. Four Dynamic Regimes in cw ESR... 300
3. Simulation of cw ESR Spectra ... 302
4. Other EasySpin functions... 316
Appendix 7 EPRSIM-C: A Spectral Analysis Package Janez Štrancar 1. Introduction ... 323
2. Main Characteristics... 325
3. EPRSIM-C Library ... 326
4. EPRSIM-C Programs ... 338
Contents of Previous Volumes ... 343
Index... 369
