Biological Magnetic Resonance Volume 19. Distance Measurements in Biological Systems by EPR

Transcription

1 Biological Magnetic Resonance Volume 19 Distance Measurements in Biological Systems by EPR

2 A Continuation Order Plan is available for this series. A continuation order will bring delivery of each new volume immediately upon publication. Volumes are billed only upon actual shipment. For further information please contact the publisher.

3 Biological Magnetic Resonance Volume 19 Distance Measurements in Biological Systems by EPR Edited by Lawrence J. Berliner Ohio State University Columbus, Ohio Gareth R. Eaton and Sandra S. Eaton University of Denver Denver, Colorado KLUWER ACADEMIC/PLENUM PUBLISHERS NEW YORK, BOSTON, DORDRECHT, LONDON, MOSCOW

4 ISBN ISBN (ebook) DO I / Kluwer Academic/Plenum Publishers, New York Softcover reprint of the hardcover 1 st edition Spring Street, New York, New York ill A c.i.p. record for this book is available from the Library of Congress All rights reserved No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher

5 To Pier Luigi Nordio

6 CONTRIBUTORS Albert H. Beth. Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee Petr P. Borbat. Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York Gary W. Brudvig. Department of Chemistry, Yale University, P.O. Box , New Haven, Connecticut Sergei A. Dzuba Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk, Russia Gareth R. Eaton. Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado Sandra S. Eaton. Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado Jack H. Freed. Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York Arnold J. Hoff. Department of Biophysics, Leiden University, Leiden, the Netherlands Eric J. Hustedt Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee Gunnar Jeschke. Max-Planck-Institute for Polymer Research, Postfach 3148, D Mainz, Germany K. V. Lakshmi. Department of Chemistry, Yale University, P.O. Box , New Haven, Connecticut Gertz I. Likhtenshtein Department of Chemistry, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel vii

7 viii Contributors Hassane S. Mchaourab Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee Joseph C. McNulty. Department of Chemistry and Biochemistry, University of California, Santa Cruz, California Glenn L. Millhauser Department of Chemistry and Biochemistry, University of California, Santa Cruz, California Eduardo Perozo. Department of Molecular Physiology and Biological Physics, University of Virginia Health Science Center, Charlottesville, VA Martin Pannier. Max-Planck-Institute for Polymer Research, Postfach 3148, D Mainz, Germany Arnold Raitsimring. Department of Chemistry, University of Arizona, Tucson, Arizona Yeon-Kyun Shin. Department of Biochemistry and Biophysics, Iowa State University, Ames, Iowa Hans W. Spiess. Max-Planck-Institute for Polymer Research, Postfach 3148, D Mainz, Germany Wenzhong Xiao. Department of Chemistry, University of California, Berkeley, California 94270

8 Preface Distance measurements in biological systems by EPR The foundation for understanding function and dynamics of biological systems is knowledge of their structure. Many experimental methodologies are used for determination of structure, each with special utility. Volumes in this series on Biological Magnetic Resonance emphasize the methods that involve magnetic resonance. This volume seeks to provide a critical evaluation of EPR methods for determining the distances between two unpaired electrons. The editors invited the authors to make this a very practical book, with specific numerical examples of how experimental data is worked up to produce a distance estimate, and realistic assessments of uncertainties and of the range of applicability, along with examples of the power of the technique to answer biological problems. The first chapter is an overview, by two of the editors, of EPR methods to determine distances, with a focus on the range of applicability. The next chapter, also by the Eatons, reviews what is known about electron spin relaxation times that are needed in estimating distances between spins or in selecting appropriate temperatures for particular experiments. Albert Beth and Eric Hustedt describe the information about spin-spin interaction that one can obtain by simulating CW EPR line shapes of nitroxyl radicals. The information in fluid solution CW EPR spectra of dual-spin labeled proteins is illustrated by Hassane Mchaourab and Eduardo Perozo. Wenzhoug Xiao and Yeon-Kyun Shin show a way to determine dipolar interactions by Fourier deconvolution of nitroxyl CW EPR spectra. Glenn Millhauser describes the use of the rigid spin label abbreviated TOAC. The broadening of CW EPR of spin labels caused by paramagnetic metals reveals depth of the radical beneath the surface and the electrostatic environment, as described by Gertz Likhtenshtein. The use of T I and T m effects to determine distances is described by the Eatons. Arnold Raitsimring shows how to apply the "2+ 1" pulse sequence for distance and spatial distribution measurements of paramagnetic centers. Double-Quantum ESR is applied to distance measurements by Petr Borbat and Jack Freed. Pulsed double ix

9 x Preface electron-electron methods, sometimes called PELDOR or DEER are described by Gunnar Jeschke, Martin Pannier and Hans Spiess. K. V. Lakshmi and Gary Brudvig discuss spin-spin interactions in the photosynthetic reaction center revealed by CW EPR spectra. The distance information that is obtainable from out-of-phase electron spin echoes of photo-induced radical pairs is explained by Sergei Dzuba and Arnold Hoff. Some related topics have been discussed in other volumes of Biological Magnetic Resonance and consequently are not included in the present volume. In particular, we call the reader's attention to the Mims and Peisach review of ESEEM in Volume 3, the review of biological applications of time domain EPR by Thomann, Dalton, and Dalton in Volume 6, the four reviews of ENDOR by Hoffman and coworkers, Hiittermann, Mobius, and Thomann and Bernardo in Volume 13, progressive saturation and saturation transfer EPR by Marsh, Pali, and Horvath in Volume 14, and of ENDOR by Makinen, Mustafi and Kasa in Volume 14. Other reviews are cited in the appropriate chapters. Site-directed spin labeling and time-domain EPR are enabling technologies for using spin-spin interactions to estimate distances. Now that commercial pulsed EPR spectrometers are available, both the CW and pulsed EPR the techniques that are described in this volume can be applied by many researchers. We hope that this volume guides users to the technique(s) most suitable for the problem to be solved. Sandra S. Eaton Gareth R. Eaton Denver, Colorado Lawrence J. Berliner Columbus, Ohio

10 Contents Section I. Introduction Chapter 1 Distance Measure,ments by CW and Pulsed EPR Sandra S. Eaton and Gareth R. Eaton 1. Structural Studies of Biomolecules...,..., Structure and Dynamics...,...,...,..., Rationale for Distance Measurements by EPR..., Dipolar Interactions Exchange Interaction Determination of Electron-Electron Distances from Dipolar Interaction Measured by EPR Pairwise Interaction Between Two Slowly-Relaxing Spins in an Immobilized Sample Pairwise Interaction Between Two Slowly-Relaxing Spins in a Siowly- Tumbling Macromolecule in Fluid Solution Pairwise Interaction Between a Slowly-Relaxing Spin and a More Rapidly-Relaxing Spin in an Immobilized Sample Out-of-Phase Echo for Spin-Polarized Radical Pairs..., Collisions Between Slowly-Relaxing Label and More Rapidly- Relaxing Spin in Fluid Solution..., Distributions of Distances...,..., Accuracy and Precision of Distances Measured..., References...,...,.., Chapter 2 Relaxation Times of Organic Radicals and Transition Metal Ions Sandra S. Eaton and Gareth R. Eaton 1. Introduction..., Scope of this Chapter..., , Why You Should Care about Relaxation Times Terminology...,..., Experimental Measurements of Relaxation Times xi

11 xii Contents 3.1. Which Spins are Observed? Spin-Lattice Relaxation, T j Spin Echo Dephasing, Tm Spin-Spin Relaxation, T Processes that Contribute to T j in Immobilized Samples Debye Temperature Direct Process Raman Process Orbach Process Local Modes Spectral Density Functions Fitting Experimental T j Data Modulation of Spin-orbit Coupling Tunnelling Fractal Relaxation Field/frequency Dependence of Relaxation Effect of Pairs and Clusters Processes that Contribute to T m in Immobilized Samples The Shape of the Echo Decay Curve Instantaneous Diffusion Nuclear Spin Diffusion Dephasing by Methyl Groups in the Solvent/Surroundings Averaging of Electron-nuclear Couplings due to Rotation of Methyl Groups Within the Radical or Transition Metal Complex Collapse of Electron-Electron Spin-Spin Coupling to a More Rapidly Relaxing Partner Librational Motion Molecular Tumbling Oxygen Processes that Contribute to T j and T2 in Fluid Solution Small Molecules Macromolecules Oxygen The Ultimate Limit on Relaxation Experimental Data Nitroxyls Other Organic Radicals Radicals Produced by Irradiation Radicals in Polymers Triplets Transition metals with S = h Transition metals with S > h Lanthanides and Actinides Frequency Dependence of Relaxation Implications for Recording CW spectra of Nitroxyls at -100 K Summary of Trends in T m and T j from Experimental Data

12 Contents xiii 9.l. Spin Echo Dephasing and T2 for S = Yl Spin-lattice Relaxation for S = Yl Spin-lattice Relaxation for S > Yl Summary of Relaxation Mechanisms Estimating Relaxation Times of Species or Environments for Which Experimental Values are Not Available References Section II. CW Measurements Chapter 3 Structural Information from CW-EPR Spectra of Dipolar Coupled Nitroxide Spin Labels Eric J. Hustedt and Albert H. Beth l. Overview of Site Directed Spin Labeling The Three Cases l. Distinguishing Between the Three Cases Theoretical Basis Analysis of Experimental Data for Case l. Factors Influencing the Precision of the Determined Parameters Analysis of Experimental Data for Case Analysis of Experimental Data for Case Conclusions Availability of Computer Programs References Chapter 4 Determination of Protein Folds and Conformational Dynamics using Spin Labeling EPR Spectroscopy Hassane S. Mchaourab and Eduardo Peraza 1. Introduction Spatial Restraints and Protein Conformational Space Experimental Strategies in Protein Fold Determination Structural Information Derived from EPR Analysis of Spin Labeled Proteins Methods for Secondary Structure Assignment Methods for the Analysis of Inter-Nitroxide Proximities

13 xiv Contents 3.4. Quaternary Structure Packing and Symmetry from Inter-Subunit Spin Coupling Determination of Protein Folding Patterns and Quaternary Structure Packing a-crystallin as an Example of Water Soluble Proteins Membrane Proteins Detection of Conformational Dynamics in Spin-Labeled Proteins Conformation Dynamics in Proteins Triggered Structural Transitions Critical Perspective... '" References Chapter 5 EPR Spectroscopic Ruler: the Deconvolution Method and its Applications Wenzhong Xiao and Yeon-Kyun Shin 1. Introduction Review of the Theory for Dipolar Interactions Between Two Nitroxides Fourier Deconvolution Spectral Analysis Model Systems: a Spectroscopic Ruler Monoradical Impurities Structural Modeling Using EPR-Determined Distances Investigating Membrane Protein Dynamics using Dipolar and Time-Resolved EPR References Chapter 6 TOAC: The Rigid Nitroxide Side Chain Joseph C. McNulty and Glenn L. Millhauser 1. Introduction: Incorporating TOAC into Polypeptides Evaluating the Structure of Short Helical Peptides Structure of the a-helix The Trichogin GA IV Peptide: Resolving Multiple Conformations Summary and Outlook References

14 Contents xv Chapter 7 Depth of Immersion of Paramagnetic Centers in Biological Systems Gertz I. Likhtenshtein 1. Introduction Spin-Spin Metal-Radical Interaction Distances Between Isolated Pairs Distance of Closest Approach Investigation of Electrostatic Effects in Molecules in Solutions Effect of Charge on Dipolar Interactions Between Protons and a Paramagnetic Species Impact of Charge on Spin Exchange Interactions between Radicals and Paramagnetic Complexes Experimental Data on Biological Systems Photosynthetic Reaction Centers Cytochrome P Flavin-Dependent Alcohol Oxidase Determination of Electrostatic Potential Around Molecules of Biological Importance Conclusions References Section III. Pulsed EPR Measurements of Electron-Electron Interactions Chapter 8 Determination of Distances Based on T 1 and T m Effects Sandra S. Eaton and Gareth R. Eaton 1. Effect of Rapidly-Relaxing Metal on TI for Slowly-Relaxing Spin Application of Bloembergen Equation Based on an Average Value of Tis"""""""""""""""""""""""'" Application of Bloembergen Equation Based on Analysis of Saturation Recovery Curves without Knowledge of T If and T 2f Application of Bloembergen Equation Based on Analysis of the Saturation Recovery Curve with Knowledge of T If and T 2f Application to Slowly-Tumbling Macromolecules in Fluid Solution Modification to Explicitly Treat S=5/ Predicted Frequency Dependence Distance Determination Based on T I Effects - Experimental Data High-spin Fe(II) Low-spin Heme Fe(III)

15 xvi Contents 2.3. High-spin Heme Fe(III) with Zero-Field Splitting Greater than the X-band EPR Quantum Effect of Rapidly-Relaxing Metal on Spin Echo Dephasing, T m' for Slowly-Relaxing Spin Distance Determination Based on T m Effects - Experimental Data Effect of Low-Spin Fe(III) Effect of High-spin Fe(III) on Echo Dephasing Summary and Guide to Application of These Techniques References Chapter 9 Double-Quantum ESR and Distance Measurements Petr P. Barbat and Jack H. Freed 1. Introduction Theory of Double Quantum Coherence Multiple Quantum Coherences in ESR Product Operator Analysis for Arbitrary Pulses Approach for General Analysis Relation to Other ESR Techniques Instrumentation D-FT Pulse ESR Spectrometer Examples Random Radicals (E' Centers in Fused Silica) Bilabeled Organic Molecules Bilabeled Peptides "Forbidden" Coherences Discussion Comparison with Other Pulsed ESR Techniques Improvements in the Future Appendices A. Effects of the Pseudo-Secular Terms B. Sensitivity and the Upper Range of Measurable Distances C. 5-Pulse SQ Sequence D. Phase Cycles References

16 Contents xvii Chapter 10 "2+1" Pulse Sequence as Applied for Distance and Spatial Distribution Measurements of Paramagnetic Centers A. Raitsimring 1. Introduction Theory Experiment Conclusion References Chapter 11 Double Electron-Electron Resonance Gunnar Jeschke, Martin Pannier, and Hans W. Spiess 1. Introduction Three-Pulse DEER Four-Pulse DEER Technical Requirements Limitations and Comparisons with Other Methods DEER on Nitroxides Cluster Size and Intercluster Distances in Ionomers Conclusions References Section IV. Applications to Photosynthesis Chapter 12 Electron Paramagnetic Resonance Distance Measurements in Photosynthetic Reaction Centers K. V. Lakshmi and Gary W. Brudvig 1. Introduction Photosynthetic Reaction Centers EPR Distance Measurements Theory Distance Measurements in Photosynthetic Reaction Centers Lineshape Analysis in the Static Limit Spin-Lattice Relaxation Enhancement Measurements

17 xviii Contents 3.3. Pulsed Electron-Electron Double-Resonance Distance Measurements Summary References Chapter 13 Photo-Induced Radical Pairs Investigated using Out-of-Phase Electron Spin Echo Sergei A. Dzuba and Arnold J. Hoff 1. Introduction Electron Spin Echo Envelope Modulation of a Photoinduced Radical Pair Energy Levels of the Interacting Radical Pair Electron Spin Echo Formation Echo Amplitudes and Pulse Angle Dependence Zero-Quantum and Double Quantum Coherences Fourier Transformation and Distance Determination Sequential Electron Transfer Contributions to Nuclear ESEEM Structural Investigations in Photosynthetic Reaction Centers Bacterial Reaction Centers Photosystem I Reaction Centers Photosystem II Reaction Centers The Energy Landscape of a Reaction Center Protein Kleinfeld Effect Conclusion References Contents of Prior Related Volumes Index