Distance Measurements in Biological Systems by EPR PDF
Preview Distance Measurements in Biological Systems by EPR
Biological Magnetic Resonance Volume 19 Distance Measurements in Biological Systems by EPR A Continuation Order Plan is available for this series. A continuation orderwill bring delivery of each new volume immediately upon publication. Volumes are billed only upon actual shipment. For further information please contact the publisher. Biological Magnetic Resonance Volume 19 Distance Measurements in Biological Systems by EPR Edited by Lawrence J. Berliner OhioStateUniversity Columbus, Ohio Gareth R. Eaton and Sandra S. Eaton University of Denver Denver, Colorado KLUWER ACADEMIC PUBLISHERS NEW YORK, BOSTON, DORDRECHT, LONDON, MOSCOW eBookISBN: 0-306-47109-4 Print ISBN: 0-306-46533-7 ©2002 Kluwer Academic Publishers New York, Boston, Dordrecht, London, Moscow All rights reserved No part of this eBook may be reproduced or transmitted in any form or by any means, electronic, mechanical, recording, or otherwise, without written consent from the Publisher Created in the United States of America Visit Kluwer Online at: http://www.kluweronline.com and Kluwer's eBookstore at: http://www.ebooks.kluweronline.com To Pier Luigi Nordio CONTRIBUTORS Albert H. Beth • DepartmentofMolecularPhysiologyandBiophysics, VanderbiltUniversity, Nashville, Tennessee 37232 Petr P. Borbat • BakerLaboratory ofChemistry and ChemicalBiology, Cornell University, Ithaca, New York 14853 Gary W. Brudvig • DepartmentofChemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107 Sergei A.Dzuba • InstituteofChemical Kinetics andCombustion, Russian Academy of Sciences,Novosibirsk, Russia Gareth R. Eaton • Department ofChemistry and Biochemistry, University of Denver, Denver, Colorado 80208 Sandra S. Eaton • DepartmentofChemistry and Biochemistry, University of Denver, Denver, Colorado 80208 Jack H. Freed • BakerLaboratory ofChemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 Arnold J. Hoff• DepartmentofBiophysics, LeidenUniversity, Leiden, the Netherlands Eric J. Hustedt • Department ofMolecular PhysiologyandBiophysics, Vanderbilt University, Nashville, Tennessee 37232 GunnarJeschke• Max-Planck-Institute forPolymerResearch, Postfach 3148, D-55021 Mainz, Germany K. V. Lakshmi • Department ofChemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107 Gertz I. Likhtenshtein • DepartmentofChemistry, Ben-GurionUniversity of the Negev, P.O.B. 653, Beer-Sheva 84105, Israel vii viii Contributors Hassane S. Mchaourab • DepartmentofMolecularPhysiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232 Joseph C. McNulty • Departmentof Chemistry and Biochemistry, University of California, Santa Cruz, California 95064 Glenn L. Millhauser • DepartmentofChemistry and Biochemistry, University of California, Santa Cruz, California 95064 EduardoPerozo • DepartmentofMolecularPhysiologyandBiological Physics, University of Virginia Health Science Center, Charlottesville, VA 22906 MartinPannier • Max-Planck-Institute forPolymerResearch, Postfach 3148, D-55021 Mainz, Germany Arnold Raitsimring • DepartmentofChemistry, UniversityofArizona, Tucson, Arizona 85721 Yeon-Kyun Shin • DepartmentofBiochemistry and Biophysics, Iowa State University, Ames, Iowa 50011 Hans W. Spiess• Max-Planck-Institute forPolymerResearch,Postfach 3148, D-55021 Mainz, Germany Wenzhong Xiao • Department ofChemistry, University ofCalifornia, Berkeley, California 94270 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 withexamples 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 Batons, 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 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 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-inducedradical 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, Huttermann, Möbius, 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 Contents Section I. Introduction Chapter 1 Distance Measurements by CW and Pulsed EPR Sandra S. Eaton and Gareth R. Eaton 1. Structural StudiesofBiomolecules............................................................. 2 1.1. Structure andDynamics....................................................................... 3 1.2. Rationale forDistance Measurements byEPR.................................... 4 2. DipolarInteractions................................................................................... 6 3. ExchangeInteraction.................................................................................. 9 4. Determination of Electron-Electron Distances from Dipolar Interaction Measured by EPR ...................................................................................... 10 4.1. Pairwise Interaction Between Two Slowly-Relaxing Spins in an Immobilized Sample .......................................................................... 12 4.2. Pairwise Interaction Between Two Slowly-Relaxing Spins in a Slowly- Tumbling Macromolecule in Fluid Solution...................................... 17 4.3. Pairwise Interaction Between a Slowly-Relaxing Spin and a More Rapidly-Relaxing Spin in an Immobilized Sample........................... 18 4.4. Out-of-Phase Echo for Spin-Polarized Radical Pairs......................... 20 4.5. Collisions Between Slowly-Relaxing Label and More Rapidly- Relaxing Spin in Fluid Solution......................................................... 20 5. Distributions of Distances........................................................................... 21 6. Accuracy and Precision of Distances Measured......................................... 21 References................................................................................................... 21 Chapter 2 Relaxation Times of Organic Radicals and Transition Metal Ions Sandra S. Eaton and Gareth R. Eaton 1. Introduction................................................................................................ 29 1.1. Scope of this Chapter.......................................................................... 29 1.2. Why You Should Care about Relaxation Times................................. 31 2. Terminology............................................................................................... 32 3. Experimental Measurements of Relaxation Times .................................... 36 xi
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