1
|
Bizet M, Byrne D, Biaso F, Gerbaud G, Etienne E, Briola G, Guigliarelli B, Urban P, Dorlet P, Kalai T, Truan G, Martinho M. Structural insights into the semiquinone form of human Cytochrome P450 reductase by DEER distance measurements between a native flavin and a spin labelled non-canonical amino acid. Chemistry 2024; 30:e202304307. [PMID: 38277424 DOI: 10.1002/chem.202304307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/28/2024]
Abstract
The flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a "locked/closed" to an "unlocked/open" state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site-Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non-canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH• and the nitroxide. The DEER data revealed a salt concentration-dependent distance distribution, evidence of an "open" CPR conformation at high salt concentrations exceeding previous reports. We also conducted molecular dynamics simulations which unveiled a diverse ensemble of conformations for the "open" semiquinone state of the CPR at high salt concentration. This study unravels the conformational landscape of the one electron reduced state of CPR, which had never been studied before.
Collapse
Affiliation(s)
- Maxime Bizet
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Deborah Byrne
- Protein Expression Facility, Aix Marseille Univ, CNRS, IMM, 13402, Marseille, France
| | - Frédéric Biaso
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Emilien Etienne
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Giuseppina Briola
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Philippe Urban
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Pierre Dorlet
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Tamas Kalai
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Pécs, PO Box 99 Szigeti st. 12, H-7602 7624, Pécs, Hungary
| | - Gilles Truan
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Marlène Martinho
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| |
Collapse
|
2
|
Nalepa A, Malferrari M, Lubitz W, Venturoli G, Möbius K, Savitsky A. Local water sensing: water exchange in bacterial photosynthetic reaction centers embedded in a trehalose glass studied using multiresonance EPR. Phys Chem Chem Phys 2017; 19:28388-28400. [DOI: 10.1039/c7cp03942e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Pulsed EPR spectroscopies and isotope labeled water are applied to detect and quantify the local water in a bacterial reaction center embedded into a trehalose glass.
Collapse
Affiliation(s)
- Anna Nalepa
- Max-Planck-Institut für Chemische Energiekonversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Marco Malferrari
- Laboratorio di Biochimica e Biofisica
- Dipartimento di Farmacia e Biotecnologie
- FaBiT
- Università di Bologna
- I-40126 Bologna
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Giovanni Venturoli
- Laboratorio di Biochimica e Biofisica
- Dipartimento di Farmacia e Biotecnologie
- FaBiT
- Università di Bologna
- I-40126 Bologna
| | - Klaus Möbius
- Max-Planck-Institut für Chemische Energiekonversion
- D-45470 Mülheim an der Ruhr
- Germany
- Department of Physics
- Free University Berlin
| | - Anton Savitsky
- Max-Planck-Institut für Chemische Energiekonversion
- D-45470 Mülheim an der Ruhr
- Germany
| |
Collapse
|
3
|
Modeling structural transitions from the periplasmic-open state of lactose permease and interpretations of spin label experiments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1541-52. [DOI: 10.1016/j.bbamem.2016.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/25/2016] [Accepted: 04/19/2016] [Indexed: 11/22/2022]
|
4
|
|
5
|
Ishara Silva K, Jagannathan B, Golbeck JH, Lakshmi KV. Elucidating the design principles of photosynthetic electron-transfer proteins by site-directed spin labeling EPR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:548-556. [PMID: 26334844 DOI: 10.1016/j.bbabio.2015.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 08/20/2015] [Indexed: 10/23/2022]
Abstract
Site-directed spin labeling electron paramagnetic resonance (SDSL EPR) spectroscopy is a powerful tool to determine solvent accessibility, side-chain dynamics, and inter-spin distances at specific sites in biological macromolecules. This information provides important insights into the structure and dynamics of both natural and designed proteins and protein complexes. Here, we discuss the application of SDSL EPR spectroscopy in probing the charge-transfer cofactors in photosynthetic reaction centers (RC) such as photosystem I (PSI) and the bacterial reaction center (bRC). Photosynthetic RCs are large multi-subunit proteins (molecular weight≥300 kDa) that perform light-driven charge transfer reactions in photosynthesis. These reactions are carried out by cofactors that are paramagnetic in one of their oxidation states. This renders the RCs unsuitable for conventional nuclear magnetic resonance spectroscopy investigations. However, the presence of native paramagnetic centers and the ability to covalently attach site-directed spin labels in RCs makes them ideally suited for the application of SDSL EPR spectroscopy. The paramagnetic centers serve as probes of conformational changes, dynamics of subunit assembly, and the relative motion of cofactors and peptide subunits. In this review, we describe novel applications of SDSL EPR spectroscopy for elucidating the effects of local structure and dynamics on the electron-transfer cofactors of photosynthetic RCs. Because SDSL EPR Spectroscopy is uniquely suited to provide dynamic information on protein motion, it is a particularly useful method in the engineering and analysis of designed electron transfer proteins and protein networks. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
Collapse
Affiliation(s)
- K Ishara Silva
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180; The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Bharat Jagannathan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802; Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802; Department of Chemistry, The Pennsylvania State University, University Park, PA 16802.
| | - K V Lakshmi
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180; The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180.
| |
Collapse
|
6
|
Malferrari M, Francia F, Venturoli G. Retardation of Protein Dynamics by Trehalose in Dehydrated Systems of Photosynthetic Reaction Centers. Insights from Electron Transfer and Thermal Denaturation Kinetics. J Phys Chem B 2015; 119:13600-18. [DOI: 10.1021/acs.jpcb.5b02986] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Malferrari
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di
Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Francesco Francia
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di
Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Giovanni Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di
Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
- Consorzio Nazionale
Interuniversitario per le Scienze Fisiche della Materia (CNISM), c/o
Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy
| |
Collapse
|
7
|
Möbius K, Lubitz W, Savitsky A. High-field EPR on membrane proteins - crossing the gap to NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 75:1-49. [PMID: 24160760 DOI: 10.1016/j.pnmrs.2013.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/15/2013] [Accepted: 07/15/2013] [Indexed: 06/02/2023]
Abstract
In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar quantities of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems - offering highly interesting applications for chemists, biochemists and molecular biologists. In three case studies, representative examples of advanced EPR spectroscopy are reviewed: (I) High-field PELDOR and ENDOR structure determination of cation-anion radical pairs in reaction centers from photosynthetic purple bacteria and cyanobacteria (Photosystem I); (II) High-field ENDOR and ELDOR-detected NMR spectroscopy on the oxygen-evolving complex of Photosystem II; and (III) High-field electron dipolar spectroscopy on nitroxide spin-labelled bacteriorhodopsin for structure-function studies. An extended conclusion with an outlook to further developments and applications is also presented.
Collapse
Affiliation(s)
- Klaus Möbius
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany; Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany.
| | | | | |
Collapse
|
8
|
Spindler PE, Glaser SJ, Skinner TE, Prisner TF. Broadband Inversion PELDOR Spectroscopy with Partially Adiabatic Shaped Pulses. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207777] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
9
|
Spindler PE, Glaser SJ, Skinner TE, Prisner TF. Broadband inversion PELDOR spectroscopy with partially adiabatic shaped pulses. Angew Chem Int Ed Engl 2013; 52:3425-9. [PMID: 23424088 DOI: 10.1002/anie.201207777] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Indexed: 12/14/2022]
Affiliation(s)
- Philipp E Spindler
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum, Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | | | | | | |
Collapse
|
10
|
Prasad Gajula MNV, Vogel KP, Rai A, Dietrich F, Steinhoff HJ. How far in-silico computing meets real experiments. A study on the structure and dynamics of spin labeled vinculin tail protein by molecular dynamics simulations and EPR spectroscopy. BMC Genomics 2013; 14 Suppl 2:S4. [PMID: 23445506 PMCID: PMC3582443 DOI: 10.1186/1471-2164-14-s2-s4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Investigation of conformational changes in a protein is a prerequisite to understand its biological function. To explore these conformational changes in proteins we developed a strategy with the combination of molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy. The major goal of this work is to investigate how far computer simulations can meet the experiments. Methods Vinculin tail protein is chosen as a model system as conformational changes within the vinculin protein are believed to be important for its biological function at the sites of cell adhesion. MD simulations were performed on vinculin tail protein both in water and in vacuo environments. EPR experimental data is compared with those of the simulated data for corresponding spin label positions. Results The calculated EPR spectra from MD simulations trajectories of selected spin labelled positions are comparable to experimental EPR spectra. The results show that the information contained in the spin label mobility provides a powerful means of mapping protein folds and their conformational changes. Conclusions The results suggest the localization of dynamic and flexible regions of the vinculin tail protein. This study shows MD simulations can be used as a complementary tool to interpret experimental EPR data.
Collapse
Affiliation(s)
- M N V Prasad Gajula
- CABin division, DST Ramanujan Fellow, Indian Agricultural Statistics Research Institute, PUSA campus, New Delhi-110012, India.
| | | | | | | | | |
Collapse
|
11
|
Sarver JL, Townsend JE, Rajapakse G, Jen-Jacobson L, Saxena S. Simulating the dynamics and orientations of spin-labeled side chains in a protein-DNA complex. J Phys Chem B 2012; 116:4024-33. [PMID: 22404310 PMCID: PMC3325110 DOI: 10.1021/jp211094n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-directed spin labeling, wherein a nitroxide side chain is introduced into a protein at a selected mutant site, is increasingly employed to investigate biological systems by electron spin resonance (ESR) spectroscopy. An understanding of the packing and dynamics of the spin label is needed to extract the biologically relevant information about the macromolecule from ESR measurements. In this work, molecular dynamics (MD) simulations were performed on the spin-labeled restriction endonuclease, EcoRI in complex with DNA. Mutants of this homodimeric enzyme were previously constructed, and distance measurements were performed using the double electron electron resonance experiment. These correlated distance constraints have been leveraged with MD simulations to learn about side chain packing and preferred conformers of the spin label on sites in an α-helix and a β-strand. We found three dihedral angles of the spin label side chain to be most sensitive to the secondary structure where the spin label was located. Conformers sampled by the spin label differed between secondary structures as well. C(α)-C(α) distance distributions were constructed and used to extract details about the protein backbone mobility at the two spin labeled sites. These simulation studies enhance our understanding of the behavior of spin labels in proteins and thus expand the ability of ESR spectroscopy to contribute to knowledge of protein structure and dynamics.
Collapse
Affiliation(s)
- Jessica L. Sarver
- Department of Chemistry, University of Pittsburgh 219 Parkman Ave., Pittsburgh, PA 15260
| | - Jacqueline E. Townsend
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA 15260
| | - Gayathri Rajapakse
- Department of Chemistry, University of Pittsburgh 219 Parkman Ave., Pittsburgh, PA 15260
| | - Linda Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh 219 Parkman Ave., Pittsburgh, PA 15260
| |
Collapse
|
12
|
McHaourab HS, Steed PR, Kazmier K. Toward the fourth dimension of membrane protein structure: insight into dynamics from spin-labeling EPR spectroscopy. Structure 2012; 19:1549-61. [PMID: 22078555 DOI: 10.1016/j.str.2011.10.009] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 10/19/2011] [Accepted: 10/21/2011] [Indexed: 12/26/2022]
Abstract
Trapping membrane proteins in the confines of a crystal lattice obscures dynamic modes essential for interconversion between multiple conformations in the functional cycle. Moreover, lattice forces could conspire with detergent solubilization to stabilize a minor conformer in an ensemble thus confounding mechanistic interpretation. Spin labeling in conjunction with electron paramagnetic resonance (EPR) spectroscopy offers an exquisite window into membrane protein dynamics in the native-like environment of a lipid bilayer. Systematic application of spin labeling and EPR identifies sequence-specific secondary structures, defines their topology and their packing in the tertiary fold. Long range distance measurements (60 Å-80 Å) between pairs of spin labels enable quantitative analysis of equilibrium dynamics and triggered conformational changes. This review highlights the contribution of spin labeling to bridging structure and mechanism. Efforts to develop methods for determining structures from EPR restraints and to increase sensitivity and throughput promise to expand spin labeling applications in membrane protein structural biology.
Collapse
Affiliation(s)
- Hassane S McHaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA.
| | | | | |
Collapse
|
13
|
Song Y, Meade TJ, Astashkin A, Klein E, Enemark J, Raitsimring A. Pulsed dipolar spectroscopy distance measurements in biomacromolecules labeled with Gd(III) markers. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 210:59-68. [PMID: 21388847 PMCID: PMC3081411 DOI: 10.1016/j.jmr.2011.02.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 02/03/2011] [Accepted: 02/08/2011] [Indexed: 05/11/2023]
Abstract
This work demonstrates the feasibility of using Gd(III) tags for long-range Double Electron Electron Resonance (DEER) distance measurements in biomacromolecules. Double-stranded 14- base pair Gd(III)-DNA conjugates were synthesized and investigated at K(a) band. For the longest Gd(III) tag the average distance and average deviation between Gd(III) ions determined from the DEER time domains was about 59±12Å. This result demonstrates that DEER measurements with Gd(III) tags can be routinely carried out for distances of at least 60Å, and analysis indicates that distance measurements up to 100Å are possible. Compared with commonly used nitroxide labels, Gd(III)-based labels will be most beneficial for the detection of distance variations in large biomacromolecules, with an emphasis on large scale changes in shape or distance. Tracking the folding/unfolding and domain interactions of proteins and the conformational changes in DNA are examples of such applications.
Collapse
Affiliation(s)
- Y. Song
- Departments of Chemistry; Molecular Biosciences; Neurobiology & Physiology; and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - T. J. Meade
- Departments of Chemistry; Molecular Biosciences; Neurobiology & Physiology; and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - A.V. Astashkin
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
| | - E.L. Klein
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
| | - J.H. Enemark
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
| | - A. Raitsimring
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
- Corresponding Author: Arnold Raitsimring, Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA.
| |
Collapse
|
14
|
Studying biomolecular complexes with pulsed electron–electron double resonance spectroscopy. Biochem Soc Trans 2011; 39:128-39. [DOI: 10.1042/bst0390128] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The function of biomolecules is intrinsically linked to their structure and the complexes they form during function. Techniques for the determination of structures and dynamics of these nanometre assemblies are therefore important for an understanding on the molecular level. PELDOR (pulsed electron–electron double resonance) is a pulsed EPR method that can be used to reliably and precisely measure distances in the range 1.5–8 nm, to unravel orientations and to determine the number of monomers in complexes. In conjunction with site-directed spin labelling, it can be applied to biomolecules of all sizes in aqueous solutions or membranes. PELDOR is therefore complementary to the methods of X-ray crystallography, NMR and FRET (fluorescence resonance energy transfer) and is becoming a powerful method for structural determination of biomolecules. In the present review, the methods of PELDOR are discussed and examples where PELDOR has been used to obtain structural information on biomolecules are summarized.
Collapse
|
15
|
Jeschke G. Interpretation of Dipolar EPR Data in Terms of Protein Structure. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2011. [DOI: 10.1007/430_2011_61] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
16
|
Kazmier K, Alexander NS, Meiler J, McHaourab HS. Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination. J Struct Biol 2010; 173:549-57. [PMID: 21074624 DOI: 10.1016/j.jsb.2010.11.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 10/25/2010] [Accepted: 11/04/2010] [Indexed: 11/29/2022]
Abstract
A hybrid protein structure determination approach combining sparse Electron Paramagnetic Resonance (EPR) distance restraints and Rosetta de novo protein folding has been previously demonstrated to yield high quality models (Alexander et al. (2008)). However, widespread application of this methodology to proteins of unknown structures is hindered by the lack of a general strategy to place spin label pairs in the primary sequence. In this work, we report the development of an algorithm that optimally selects spin labeling positions for the purpose of distance measurements by EPR. For the α-helical subdomain of T4 lysozyme (T4L), simulated restraints that maximize sequence separation between the two spin labels while simultaneously ensuring pairwise connectivity of secondary structure elements yielded vastly improved models by Rosetta folding. 54% of all these models have the correct fold compared to only 21% and 8% correctly folded models when randomly placed restraints or no restraints are used, respectively. Moreover, the improvements in model quality require a limited number of optimized restraints, which is determined by the pairwise connectivities of T4L α-helices. The predicted improvement in Rosetta model quality was verified by experimental determination of distances between spin labels pairs selected by the algorithm. Overall, our results reinforce the rationale for the combined use of sparse EPR distance restraints and de novo folding. By alleviating the experimental bottleneck associated with restraint selection, this algorithm sets the stage for extending computational structure determination to larger, traditionally elusive protein topologies of critical structural and biochemical importance.
Collapse
Affiliation(s)
- Kelli Kazmier
- Chemical and Physical Biology Program, 340 Light Hall, Vanderbilt University, Nashville, TN 37232, USA.
| | | | | | | |
Collapse
|
17
|
Savitsky A, Malferrari M, Francia F, Venturoli G, Möbius K. Bacterial Photosynthetic Reaction Centers in Trehalose Glasses: Coupling between Protein Conformational Dynamics and Electron-Transfer Kinetics as Studied by Laser-Flash and High-Field EPR Spectroscopies. J Phys Chem B 2010; 114:12729-43. [DOI: 10.1021/jp105801q] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anton Savitsky
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Marco Malferrari
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Francesco Francia
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Giovanni Venturoli
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Klaus Möbius
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| |
Collapse
|
18
|
Yang Z, Kise D, Saxena S. An Approach towards the Measurement of Nanometer Range Distances Based on Cu2+ Ions and ESR. J Phys Chem B 2010; 114:6165-74. [DOI: 10.1021/jp911637s] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhongyu Yang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Drew Kise
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| |
Collapse
|
19
|
Swanson MA, Kathirvelu V, Majtan T, Frerman FE, Eaton GR, Eaton SS. DEER distance measurement between a spin label and a native FAD semiquinone in electron transfer flavoprotein. J Am Chem Soc 2010; 131:15978-9. [PMID: 19886689 DOI: 10.1021/ja9059816] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human mitochondrial electron transfer flavoprotein (ETF) accepts electrons from at least 10 different flavoprotein dehydrogenases and transfers electrons to a single electron acceptor in the inner membrane. Paracoccus denitrificans ETF has the identical function, shares the same three-dimensional structure and functional domains, and exhibits the same conformational mobility. It has been proposed that the mobility of the alphaII domain permits the promiscuous behavior of ETF with respect to a variety of redox partners. Double electron-electron resonance (DEER) measurements between a spin label and an enzymatically reduced flavin adenine dinucleotide (FAD) cofactor in P. denitrificans ETF gave two distributions of distances: a major component centered at 4.2 +/- 0.1 nm and a minor component centered at 5.1 +/- 0.2 nm. Both components had widths of approximately 0.3 nm. A distance of 4.1 nm was calculated using the crystal structure of P. denitrificans ETF, which agrees with the major component obtained from the DEER measurement. The observation of a second distribution suggests that ETF, in the absence of substrate, adopts some conformations that are intermediate between the predominant free and substrate-bound states.
Collapse
Affiliation(s)
- Michael A Swanson
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, USA
| | | | | | | | | | | |
Collapse
|
20
|
Klare JP, Steinhoff HJ. Spin labeling EPR. PHOTOSYNTHESIS RESEARCH 2009; 102:377-390. [PMID: 19728138 DOI: 10.1007/s11120-009-9490-7] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2008] [Accepted: 08/14/2009] [Indexed: 05/28/2023]
Abstract
Site-directed spin labeling in combination with electron paramagnetic resonance spectroscopy has emerged as an efficient tool to elucidate the structure and conformational dynamics of biomolecules under native-like conditions. This article summarizes the basics as well as recent progress of site-directed spin labeling. Continuous wave EPR spectra analyses and pulse EPR techniques are reviewed with special emphasis on applications to the sensory rhodopsin-transducer complex mediating the photophobic response of the halophilic archaeum Natronomonas pharaonis and the photosynthetic reaction center from Rhodobacter sphaeroides R26.
Collapse
Affiliation(s)
- Johann P Klare
- Physics Department, University of Osnabrück, Barbarastr. 7, 49076, Osnabrück, Germany
| | | |
Collapse
|
21
|
van Gastel M. Pulsed EPR spectroscopy. PHOTOSYNTHESIS RESEARCH 2009; 102:367-373. [PMID: 19381861 DOI: 10.1007/s11120-009-9422-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Accepted: 04/06/2009] [Indexed: 05/27/2023]
Affiliation(s)
- Maurice van Gastel
- Insitut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Wegeler Strasse 12, 53115, Bonn, Germany.
| |
Collapse
|
22
|
Böhme S, Padmavathi PVL, Holterhues J, Ouchni F, Klare JP, Steinhoff HJ. Topology of the amphipathic helices of the colicin A pore-forming domain in E. coli lipid membranes studied by pulse EPR. Phys Chem Chem Phys 2009; 11:6770-7. [DOI: 10.1039/b907117m] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
23
|
Finiguerra MG, Prudêncio M, Ubbink M, Huber M. Accurate long-range distance measurements in a doubly spin-labeled protein by a four-pulse, double electron-electron resonance method. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:1096-1101. [PMID: 18932181 DOI: 10.1002/mrc.2290] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Distance determination in disordered systems by a four-pulse double electron-electron resonance method (DEER or PELDOR) is becoming increasingly popular because long distances (several nanometers) and their distributions can be measured. From the distance distributions eventual heterogeneities and dynamics can be deduced. To make full use of the method, typical distance distributions for structurally well-defined systems are needed. Here, the structurally well-characterized protein azurin is investigated by attaching two (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate spin labels (MTSL) by site-directed mutagenesis. Mutations at the surface sites of the protein Q12, K27, and N42 are combined in the double mutants Q12C/K27C and K27C/N42C. A distance of 4.3 nm is found for Q12C/K27C and 4.6 nm for K27C/N42C. For Q12C/K27C the width of the distribution (0.24 nm) is smaller than for the K27C/N42C mutant (0.36 nm). The shapes of the distributions are close to Gaussian. These distance distributions agree well with those derived from a model to determine the maximally accessible conformational space of the spin-label linker. Additionally, the expected distribution for the shorter distance variant Q12C/N42C was modeled. The width is larger than the calculated one for Q12C/K27C by 21%, revealing the effect of the different orientation and shorter distance. The widths and the shapes of the distributions are suited as a reference for two unperturbed MTSL labels at structurally well-defined sites.
Collapse
Affiliation(s)
- Michela G Finiguerra
- Department of Molecular Physics, Leiden University, 2300 RA Leiden, The Netherlands
| | | | | | | |
Collapse
|
24
|
DeSensi SC, Rangel DP, Beth AH, Lybrand TP, Hustedt EJ. Simulation of nitroxide electron paramagnetic resonance spectra from brownian trajectories and molecular dynamics simulations. Biophys J 2008; 94:3798-809. [PMID: 18234808 PMCID: PMC2367180 DOI: 10.1529/biophysj.107.125419] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 12/27/2007] [Indexed: 11/18/2022] Open
Abstract
A simulated continuous wave electron paramagnetic resonance spectrum of a nitroxide spin label can be obtained from the Fourier transform of a free induction decay. It has been previously shown that the free induction decay can be calculated by solving the time-dependent stochastic Liouville equation for a set of Brownian trajectories defining the rotational dynamics of the label. In this work, a quaternion-based Monte Carlo algorithm has been developed to generate Brownian trajectories describing the global rotational diffusion of a spin-labeled protein. Also, molecular dynamics simulations of two spin-labeled mutants of T4 lysozyme, T4L F153R1, and T4L K65R1 have been used to generate trajectories describing the internal dynamics of the protein and the local dynamics of the spin-label side chain. Trajectories from the molecular dynamics simulations combined with trajectories describing the global rotational diffusion of the protein are used to account for all of the dynamics of a spin-labeled protein. Spectra calculated from these combined trajectories correspond well to the experimental spectra for the buried site T4L F153R1 and the helix surface site T4L K65R1. This work provides a framework to further explore the modeling of the dynamics of the spin-label side chain in the wide variety of labeling environments encountered in site-directed spin labeling studies.
Collapse
Affiliation(s)
- Susan C DeSensi
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, USA
| | | | | | | | | |
Collapse
|
25
|
Hilger D, Polyhach Y, Padan E, Jung H, Jeschke G. High-resolution structure of a Na+/H+ antiporter dimer obtained by pulsed electron paramagnetic resonance distance measurements. Biophys J 2007; 93:3675-83. [PMID: 17704177 PMCID: PMC2072073 DOI: 10.1529/biophysj.107.109769] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transient or partial formation of complexes between biomacromolecules is a general mechanism used to control cellular functions. Several of these complexes escape structure determination by crystallographic means. We developed a new approach for determining the structure of protein dimers in the native environment (e.g., in the membrane) with high resolution in cases where the structure of the two monomers is known. The approach is based on measurements of distance distributions between spin labels in the range between 2 and 6 nanometers by a pulsed electron paramagnetic resonance technique and explicit modeling of spin label conformations. By applying this method to the membrane protein homodimer of the Na(+)/H(+) antiporter NhaA of Escherichia coli, the structure of the presumably physiological dimer was determined. It reveals two points of contact between the two monomers, with one of them confirming results of earlier cross-linking experiments.
Collapse
Affiliation(s)
- D Hilger
- Ludwig-Maximilians-Universität München, Department Biologie I, D-80638 Munich, Germany
| | | | | | | | | |
Collapse
|
26
|
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: 427] [Impact Index Per Article: 25.1] [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.
Collapse
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.
| | | |
Collapse
|
27
|
Savitsky A, Dubinskii AA, Flores M, Lubitz W, Möbius K. Orientation-Resolving Pulsed Electron Dipolar High-Field EPR Spectroscopy on Disordered Solids: I. Structure of Spin-Correlated Radical Pairs in Bacterial Photosynthetic Reaction Centers. J Phys Chem B 2007; 111:6245-62. [PMID: 17497913 DOI: 10.1021/jp070016c] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Distance and relative orientation of functional groups within protein domains and their changes during chemical reactions determine the efficiency of biological processes. In this work on disordered solid-state electron-transfer proteins, it is demonstrated that the combination of pulsed high-field EPR spectroscopy at the W band (95 GHz, 3.4 T) with its extensions to PELDOR (pulsed electron-electron double resonance) and RIDME (relaxation-induced dipolar modulation enhancement) offers a powerful tool for obtaining not only information on the electronic structure of the redox partners but also on the three-dimensional structure of radical-pair systems with large interspin distances (up to about 5 nm). Strategies are discussed both in terms of data collection and data analysis to extract unique solutions for the full radical-pair structure with only a minimum of additional independent structural information. By this novel approach, the three-dimensional structure of laser-flash-induced transient radical pairs P(865)(*+)Q(A)(*-) in frozen-solution reaction centers (RCs) from the photosynthetic bacterium Rhodobacter (Rb.) sphaeroides is solved. The measured positions and relative orientations of the weakly coupled ion radicals P(865)(*+) and Q(A)(*-) are compared with those of the precursor cofactors P865 and QA known from X-ray crystallography. A small but significant reorientation of the reduced ubiquinone QA is revealed and interpreted as being due to the photosynthetic electron transfer. In contrast to the large conformational change of Q(B)(*-) upon light illumination of the RCs, the small light-induced reorientation of Q(A)(*-) had escaped previous attempts to detect structural changes of photosynthetic cofactors upon charge separation. Although small, they still may be of functional importance for optimizing the electronic coupling of the redox partners in bacterial photosynthesis both for the charge-separation and charge-recombination processes.
Collapse
Affiliation(s)
- A Savitsky
- Department of Physics, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
| | | | | | | | | |
Collapse
|
28
|
Polyhach Y, Godt A, Bauer C, Jeschke G. Spin pair geometry revealed by high-field DEER in the presence of conformational distributions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 185:118-29. [PMID: 17188008 DOI: 10.1016/j.jmr.2006.11.012] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 11/29/2006] [Indexed: 05/13/2023]
Abstract
Orientation selection on two nitroxide-labelled shape-persistent molecules is demonstrated by high-field pulsed electron-electron double resonance experiments at a frequency of 95 GHz with a commercial spectrometer. The experiments are performed with fixed observer and pump frequencies by variation of the magnetic field, so that the variation of both the dipolar frequencies and the modulation depths can be analyzed. By applying the deadtime-free four-pulse double electron-electron resonance (DEER) sequence, the lineshapes of the dipolar spectra are obtained. In the investigated linear biradical and equilateral triradical the nitroxide labels undergo restricted dynamics, so that their relative orientations are not fixed, but are correlated to some extent. In this situation, the general dependence of the dipolar spectra on the observer field can be satisfyingly modelled by simple geometrical models that involve only one rotational degree of freedom for the biradical and two rotational degrees of freedom for the triradical. A somewhat better agreement of the dipolar lineshapes for the biradical is obtained by simulations based on a molecular dynamics trajectory. For the triradical, small but significant deviations of the lineshape are observed with both models, indicating that the technique can reveal deficiencies in modelling of the conformational ensemble of a macromolecule.
Collapse
Affiliation(s)
- Ye Polyhach
- Max Planck Institute for Polymer Research, Postfach 3148, 55021 Mainz, Germany
| | | | | | | |
Collapse
|
29
|
Jeschke G, Polyhach Y. Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance. Phys Chem Chem Phys 2007; 9:1895-910. [PMID: 17431518 DOI: 10.1039/b614920k] [Citation(s) in RCA: 460] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biological function of protein, DNA, and RNA molecules often depends on relative movements of domains with dimensions of a few nanometers. This length scale can be accessed by distance measurements between spin labels if pulsed electron paramagnetic resonance (EPR) techniques such as electron-electron double resonance (ELDOR) and double-quantum EPR are used. The approach does not require crystalline samples and is well suited to biomacromolecules with an intrinsic flexibility as distributions of distances can be measured. Furthermore, oligomerization or complexation of biomacromolecules can also be studied, even if it is incomplete. The sensitivity of the technique and the reliability of the measured distance distribution depend on careful optimization of the experimental conditions and procedures for data analysis. Interpretation of spin-to-spin distance distributions in terms of the structure of the biomacromolecules furthermore requires a model for the conformational distribution of the spin labels.
Collapse
Affiliation(s)
- Gunnar Jeschke
- University of Konstanz, Universitätsstrasse, 78457 Konstanz, Germany.
| | | |
Collapse
|
30
|
Borbat PP, Freed JH. Measuring distances by pulsed dipolar ESR spectroscopy: spin-labeled histidine kinases. Methods Enzymol 2007; 423:52-116. [PMID: 17609127 DOI: 10.1016/s0076-6879(07)23003-4] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Applications of dipolar ESR spectroscopy to structural biology are rapidly expanding, and it has become a useful method that is aimed at resolving protein structure and functional mechanisms. The method of pulsed dipolar ESR spectroscopy (PDS) is outlined in the first half of the chapter, and it illustrates the simplicity and potential of this developing technology with applications to various biological systems. A more detailed description is presented of the implementation of PDS to reconstruct the ternary structure of a large dimeric protein complex from Thermotoga maritima, formed by the histidine kinase CheA and the coupling protein CheW. This protein complex is a building block of an extensive array composed of coupled supramolecular structures assembled from CheA/CheW proteins and transmembrane signaling chemoreceptors, which make up a sensor that is key to controlling the motility in bacterial chemotaxis. The reconstruction of the CheA/CheW complex has employed several techniques, including X-ray crystallography and pulsed ESR. Emphasis is on the role of PDS, which is part of a larger effort to reconstruct the entire signaling complex, including chemoreceptor, by means of PDS structural mapping. In order to precisely establish the mode of coupling of CheW to CheA and to globally map the complex, approximately 70 distances have already been determined and processed into molecular coordinates by readily available methods of distance geometry constraints.
Collapse
Affiliation(s)
- Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | | |
Collapse
|