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Bowen AM, Johnson EOD, Mercuri F, Hoskins NJ, Qiao R, McCullagh JSO, Lovett JE, Bell SG, Zhou W, Timmel CR, Wong LL, Harmer JR. A Structural Model of a P450-Ferredoxin Complex from Orientation-Selective Double Electron-Electron Resonance Spectroscopy. J Am Chem Soc 2018; 140:2514-2527. [PMID: 29266939 DOI: 10.1021/jacs.7b11056] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cytochrome P450 (CYP) monooxygenases catalyze the oxidation of chemically inert carbon-hydrogen bonds in diverse endogenous and exogenous organic compounds by atmospheric oxygen. This C-H bond oxy-functionalization activity has huge potential in biotechnological applications. Class I CYPs receive the two electrons required for oxygen activation from NAD(P)H via a ferredoxin reductase and ferredoxin. The interaction of Class I CYPs with their cognate ferredoxin is specific. In order to reconstitute the activity of diverse CYPs, structural characterization of CYP-ferredoxin complexes is necessary, but little structural information is available. Here we report a structural model of such a complex (CYP199A2-HaPux) in frozen solution derived from distance and orientation restraints gathered by the EPR technique of orientation-selective double electron-electron resonance (os-DEER). The long-lived oscillations in the os-DEER spectra were well modeled by a single orientation of the CYP199A2-HaPux complex. The structure is different from the two known Class I CYP-Fdx structures: CYP11A1-Adx and CYP101A1-Pdx. At the protein interface, HaPux residues in the [Fe2S2] cluster-binding loop and the α3 helix and the C-terminus residue interact with CYP199A2 residues in the proximal loop and the C helix. These residue contacts are consistent with biochemical data on CYP199A2-ferredoxin binding and electron transfer. Electron-tunneling calculations indicate an efficient electron-transfer pathway from the [Fe2S2] cluster to the heme. This new structural model of a CYP-Fdx complex provides the basis for tailoring CYP enzymes for which the cognate ferredoxin is not known, to accept electrons from HaPux and display monooxygenase activity.
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Affiliation(s)
- Alice M Bowen
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Eachan O D Johnson
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Francesco Mercuri
- Consiglio Nazionale delle Ricerche (CNR), Istituto per lo Studio dei Materiali Nanostrutturati (ISMN) Via P. Gobetti 101, 40129 Bologna, Italy
| | - Nicola J Hoskins
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Ruihong Qiao
- College of Life Sciences, Nankai University , Tianjin 300071, China
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Janet E Lovett
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Stephen G Bell
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Weihong Zhou
- College of Life Sciences, Nankai University , Tianjin 300071, China
| | - Christiane R Timmel
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Luet Lok Wong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Jeffrey R Harmer
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
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Endeward B, Marko A, Denysenkov VP, Sigurdsson ST, Prisner TF. Advanced EPR Methods for Studying Conformational Dynamics of Nucleic Acids. Methods Enzymol 2015; 564:403-25. [PMID: 26477259 DOI: 10.1016/bs.mie.2015.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Pulsed electron paramagnetic resonance (EPR) spectroscopy has become an important tool for structural characterization of biomolecules allowing measurement of the distances between two paramagnetic spin labels attached to a biomolecule in the 2-8 nm range. In this chapter, we will focus on applications of this approach to investigate tertiary structure elements as well as conformational dynamics of nucleic acid molecules. Both aspects take advantage of using specific spin labels that are rigidly attached to the nucleobases, as they allow obtaining not only the distance but also the relative orientation between both nitroxide moieties with high accuracy. Thus, not only the distance but additionally the three Euler angles between both the nitroxide axis systems and the two polar angles of the interconnecting vector with respect to the nitroxide axis systems can be extracted from a single pair of spin labels. To extract all these parameters independently and unambiguously, a set of multifrequency/multifield pulsed EPR experiments have to be performed. We will describe the experimental procedure as well as newly developed spin labels, which are helpful to disentangle all these parameters, and tools which we have developed to analyze such data sets. The procedures and analyses will be illustrated by examples from our laboratory.
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Affiliation(s)
- B Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - A Marko
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - V P Denysenkov
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - S Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Reykjavık, Iceland
| | - T F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.
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Livada J, Martinie RJ, Dassama LMK, Krebs C, Bollinger JM, Silakov A. Direct Measurement of the Radical Translocation Distance in the Class I Ribonucleotide Reductase from Chlamydia trachomatis. J Phys Chem B 2015; 119:13777-84. [PMID: 26087051 DOI: 10.1021/acs.jpcb.5b04067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze conversion of ribonucleotides to deoxyribonucleotides in all organisms via a free-radical mechanism that is essentially conserved. In class I RNRs, the reaction is initiated and terminated by radical translocation (RT) between the α and β subunits. In the class Ic RNR from Chlamydia trachomatis (Ct RNR), the initiating event converts the active S = 1 Mn(IV)/Fe(III) cofactor to the S = 1/2 Mn(III)/Fe(III) "RT-product" form in the β subunit and generates a cysteinyl radical in the α active site. The radical can be trapped via the well-described decomposition reaction of the mechanism-based inactivator, 2'-azido-2'-deoxyuridine-5'-diphosphate, resulting in the generation of a long-lived, nitrogen-centered radical (N(•)) in α. In this work, we have determined the distance between the Mn(III)/Fe(III) cofactor in β and N(•) in α to be 43 ± 1 Å by using double electron-electron resonance experiments. This study provides the first structural data on the Ct RNR holoenzyme complex and the first direct experimental measurement of the inter-subunit RT distance in any class I RNR.
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Affiliation(s)
- Jovan Livada
- Departments of †Chemistry and ‡Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Ryan J Martinie
- Departments of †Chemistry and ‡Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Laura M K Dassama
- Departments of †Chemistry and ‡Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Departments of †Chemistry and ‡Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Departments of †Chemistry and ‡Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- Departments of †Chemistry and ‡Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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Ji M, Ruthstein S, Saxena S. Paramagnetic metal ions in pulsed ESR distance distribution measurements. Acc Chem Res 2014; 47:688-95. [PMID: 24289139 DOI: 10.1021/ar400245z] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The use of pulsed electron spin resonance (ESR) to measure interspin distance distributions has advanced biophysical research. The three major techniques that use pulsed ESR are relaxation rate based distance measurements, double quantum coherence (DQC), and double electron electron resonance (DEER). Among these methods, the DEER technique has become particularly popular largely because it is easy to implement on commercial instruments and because programs are available to analyze experimental data. Researchers have widely used DEER to measure the structure and conformational dynamics of molecules labeled with the methanethiosulfonate spin label (MTSSL). Recently, researchers have exploited endogenously bound paramagnetic metal ions as spin probes as a way to determine structural constraints in metalloproteins. In this context Cu(2+) has served as a useful paramagnetic metal probe at X-band for DEER based distance measurements. Sample preparation is simple, and a coordinated-Cu(2+) ion offers limited spatial flexibility, making it an attractive probe for DEER experiments. On the other hand, Cu(2+) has a broad absorption ESR spectrum at low temperature, which leads to two potential complications. First, the Cu(2+)-based DEER time domain data has lower signal to noise ratio compared with MTSSL. Second, accurate distance distribution analysis often requires high-quality experimental data at different external magnetic fields or with different frequency offsets. In this Account, we summarize characteristics of Cu(2+)-based DEER distance distribution measurements and data analysis methods. We highlight a novel application of such measurements in a protein-DNA complex to identify the metal ion binding site and to elucidate its chemical mechanism of function. We also survey the progress of research on other metal ions in high frequency DEER experiments.
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Affiliation(s)
- Ming Ji
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sharon Ruthstein
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Chemistry, Faculty of Exact Science, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Roy A, Sarrou I, Vaughn MD, Astashkin AV, Ghirlanda G. De Novo Design of an Artificial Bis[4Fe-4S] Binding Protein. Biochemistry 2013; 52:7586-94. [DOI: 10.1021/bi401199s] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anindya Roy
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Iosifina Sarrou
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Michael D. Vaughn
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Andrei V. Astashkin
- Department
of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Giovanna Ghirlanda
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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8
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Orientation-Selective DEER Using Rigid Spin Labels, Cofactors, Metals, and Clusters. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2013. [DOI: 10.1007/430_2013_115] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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9
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Abstract
Distance distributions between paramagnetic centers in the range of 1.8 to 6 nm in membrane proteins and up to 10 nm in deuterated soluble proteins can be measured by the DEER technique. The number of paramagnetic centers and their relative orientation can be characterized. DEER does not require crystallization and is not limited with respect to the size of the protein or protein complex. Diamagnetic proteins are accessible by site-directed spin labeling. To characterize structure or structural changes, experimental protocols were optimized and techniques for artifact suppression were introduced. Data analysis programs were developed, and it was realized that interpretation of the distance distributions must take into account the conformational distribution of spin labels. First methods have appeared for deriving structural models from a small number of distance constraints. The present scope and limitations of the technique are illustrated.
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Affiliation(s)
- Gunnar Jeschke
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, Switzerland.
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Metal-Based Spin Labeling for Distance Determination. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2012. [DOI: 10.1007/430_2011_63] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Yulikov M, Lueders P, Farooq Warsi M, Chechik V, Jeschke G. Distance measurements in Au nanoparticles functionalized with nitroxide radicals and Gd3+–DTPA chelate complexes. Phys Chem Chem Phys 2012; 14:10732-46. [DOI: 10.1039/c2cp40282c] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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12
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Pandelia ME, Ogata H, Lubitz W. Intermediates in the catalytic cycle of [NiFe] hydrogenase: functional spectroscopy of the active site. Chemphyschem 2010; 11:1127-40. [PMID: 20301175 DOI: 10.1002/cphc.200900950] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The [NiFe] hydrogenase from the anaerobic sulphate reducing bacterium Desulfovibrio vulgaris Miyazaki F is an excellent model for constructing a mechanism for the function of the so-called 'oxygen-sensitive' hydrogenases. The present review focuses on spectroscopic investigations of the active site intermediates playing a role in the activation/deactivation and catalytic cycle of this enzyme as well as in the inhibition by carbon monoxide or molecular oxygen and the light-sensitivity of the hydrogenase. The methods employed include magnetic resonance and vibrational (FTIR) techniques combined with electrochemistry that deliver information about details of the geometrical and electronic structure of the intermediates and their redox behaviour. Based on these data a mechanistic scheme is developed.
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Affiliation(s)
- Maria-Eirini Pandelia
- Max-Planck Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
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Roessler MM, King MS, Robinson AJ, Armstrong FA, Harmer J, Hirst J. Direct assignment of EPR spectra to structurally defined iron-sulfur clusters in complex I by double electron-electron resonance. Proc Natl Acad Sci U S A 2010; 107:1930-5. [PMID: 20133838 PMCID: PMC2808219 DOI: 10.1073/pnas.0908050107] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In oxidative phosphorylation, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. Complex I contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters, in several subunits, to transfer the electrons to quinone. Understanding coupled electron transfer in complex I requires a detailed knowledge of the properties of individual clusters and of the cluster ensemble, and so it requires the correlation of spectroscopic and structural data: This has proved a challenging task. EPR studies on complex I from Bos taurus have established that EPR signals N1b, N2 and N3 arise, respectively, from the 2Fe cluster in the 75 kDa subunit, and from 4Fe clusters in the PSST and 51 kDa subunits (positions 2, 7, and 1 along the seven-cluster chain extending from the flavin). The other clusters have either evaded detection or definitive signal assignments have not been established. Here, we combine double electron-electron resonance (DEER) spectroscopy on B. taurus complex I with the structure of the hydrophilic domain of Thermus thermophilus complex I. By considering the magnetic moments of the clusters and the orientation selectivity of the DEER experiment explicitly, signal N4 is assigned to the first 4Fe cluster in the TYKY subunit (position 5), and N5 to the all-cysteine ligated 4Fe cluster in the 75 kDa subunit (position 3). The implications of our assignment for the mechanisms of electron transfer and energy transduction by complex I are discussed.
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Affiliation(s)
- Maxie M. Roessler
- Center for Advanced Electron Spin Resonance, and
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, United Kingdom; and
| | - Martin S. King
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Alan J. Robinson
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Fraser A. Armstrong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, United Kingdom; and
| | | | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge, CB2 0XY, United Kingdom
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Lovett JE, Bowen AM, Timmel CR, Jones MW, Dilworth JR, Caprotti D, Bell SG, Wong LL, Harmer J. Structural information from orientationally selective DEER spectroscopy. Phys Chem Chem Phys 2009; 11:6840-8. [DOI: 10.1039/b907010a] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Astashkin AV, Kawamori A. Distance Measurements in Photosynthetic Reaction Centers by Pulsed EPR. BIOPHYSICAL TECHNIQUES IN PHOTOSYNTHESIS 2008. [DOI: 10.1007/978-1-4020-8250-4_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Lubitz W, Reijerse E, van Gastel M. [NiFe] and [FeFe] Hydrogenases Studied by Advanced Magnetic Resonance Techniques. Chem Rev 2007; 107:4331-65. [PMID: 17845059 DOI: 10.1021/cr050186q] [Citation(s) in RCA: 376] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wolfgang Lubitz
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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Schiemann O, Prisner TF. Long-range distance determinations in biomacromolecules by EPR spectroscopy. Q Rev Biophys 2007; 40:1-53. [PMID: 17565764 DOI: 10.1017/s003358350700460x] [Citation(s) in RCA: 428] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy provides a variety of tools to study structures and structural changes of large biomolecules or complexes thereof. In order to unravel secondary structure elements, domain arrangements or complex formation, continuous wave and pulsed EPR methods capable of measuring the magnetic dipole coupling between two unpaired electrons can be used to obtain long-range distance constraints on the nanometer scale. Such methods yield reliably and precisely distances of up to 80 A, can be applied to biomolecules in aqueous buffer solutions or membranes, and are not size limited. They can be applied either at cryogenic or physiological temperatures and down to amounts of a few nanomoles. Spin centers may be metal ions, metal clusters, cofactor radicals, amino acid radicals, or spin labels. In this review, we discuss the advantages and limitations of the different EPR spectroscopic methods, briefly describe their theoretical background, and summarize important biological applications. The main focus of this article will be on pulsed EPR methods like pulsed electron-electron double resonance (PELDOR) and their applications to spin-labeled biosystems.
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Affiliation(s)
- Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, J. W. Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany.
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