ESR Spectroscopy in Membrane Biophysics. Volume 27

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

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 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. 2007 Springer Science+Business Media, LLC All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. 987654321 springer.com

v CONTRIBUTORS 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

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 (Osnabrück). 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 scientists 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 structural 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 application 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 addition, 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 material not suitable for inclusion within the book and software to simulate and analyze 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