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Eills J, Budker D, Cavagnero S, Chekmenev EY, Elliott SJ, Jannin S, Lesage A, Matysik J, Meersmann T, Prisner T, Reimer JA, Yang H, Koptyug IV. Spin Hyperpolarization in Modern Magnetic Resonance. Chem Rev 2023; 123:1417-1551. [PMID: 36701528 PMCID: PMC9951229 DOI: 10.1021/acs.chemrev.2c00534] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Magnetic resonance techniques are successfully utilized in a broad range of scientific disciplines and in various practical applications, with medical magnetic resonance imaging being the most widely known example. Currently, both fundamental and applied magnetic resonance are enjoying a major boost owing to the rapidly developing field of spin hyperpolarization. Hyperpolarization techniques are able to enhance signal intensities in magnetic resonance by several orders of magnitude, and thus to largely overcome its major disadvantage of relatively low sensitivity. This provides new impetus for existing applications of magnetic resonance and opens the gates to exciting new possibilities. In this review, we provide a unified picture of the many methods and techniques that fall under the umbrella term "hyperpolarization" but are currently seldom perceived as integral parts of the same field. Specifically, before delving into the individual techniques, we provide a detailed analysis of the underlying principles of spin hyperpolarization. We attempt to uncover and classify the origins of hyperpolarization, to establish its sources and the specific mechanisms that enable the flow of polarization from a source to the target spins. We then give a more detailed analysis of individual hyperpolarization techniques: the mechanisms by which they work, fundamental and technical requirements, characteristic applications, unresolved issues, and possible future directions. We are seeing a continuous growth of activity in the field of spin hyperpolarization, and we expect the field to flourish as new and improved hyperpolarization techniques are implemented. Some key areas for development are in prolonging polarization lifetimes, making hyperpolarization techniques more generally applicable to chemical/biological systems, reducing the technical and equipment requirements, and creating more efficient excitation and detection schemes. We hope this review will facilitate the sharing of knowledge between subfields within the broad topic of hyperpolarization, to help overcome existing challenges in magnetic resonance and enable novel applications.
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Affiliation(s)
- James Eills
- Institute
for Bioengineering of Catalonia, Barcelona
Institute of Science and Technology, 08028Barcelona, Spain,
| | - Dmitry Budker
- Johannes
Gutenberg-Universität Mainz, 55128Mainz, Germany,Helmholtz-Institut,
GSI Helmholtzzentrum für Schwerionenforschung, 55128Mainz, Germany,Department
of Physics, UC Berkeley, Berkeley, California94720, United States
| | - Silvia Cavagnero
- Department
of Chemistry, University of Wisconsin, Madison, Madison, Wisconsin53706, United States
| | - Eduard Y. Chekmenev
- Department
of Chemistry, Integrative Biosciences (IBio), Karmanos Cancer Institute
(KCI), Wayne State University, Detroit, Michigan48202, United States,Russian
Academy of Sciences, Moscow119991, Russia
| | - Stuart J. Elliott
- Molecular
Sciences Research Hub, Imperial College
London, LondonW12 0BZ, United Kingdom
| | - Sami Jannin
- Centre
de RMN à Hauts Champs de Lyon, Université
de Lyon, CNRS, ENS Lyon, Université Lyon 1, 69100Villeurbanne, France
| | - Anne Lesage
- Centre
de RMN à Hauts Champs de Lyon, Université
de Lyon, CNRS, ENS Lyon, Université Lyon 1, 69100Villeurbanne, France
| | - Jörg Matysik
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstr. 3, 04103Leipzig, Germany
| | - Thomas Meersmann
- Sir
Peter Mansfield Imaging Centre, University Park, School of Medicine, University of Nottingham, NottinghamNG7 2RD, United Kingdom
| | - Thomas Prisner
- Institute
of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic
Resonance, Goethe University Frankfurt, , 60438Frankfurt
am Main, Germany
| | - Jeffrey A. Reimer
- Department
of Chemical and Biomolecular Engineering, UC Berkeley, and Materials Science Division, Lawrence Berkeley National
Laboratory, Berkeley, California94720, United States
| | - Hanming Yang
- Department
of Chemistry, University of Wisconsin, Madison, Madison, Wisconsin53706, United States
| | - Igor V. Koptyug
- International Tomography Center, Siberian
Branch of the Russian Academy
of Sciences, 630090Novosibirsk, Russia,
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2
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Dai D, Wang X, Liu Y, Yang XL, Glaubitz C, Denysenkov V, He X, Prisner T, Mao J. Room-temperature dynamic nuclear polarization enhanced NMR spectroscopy of small biological molecules in water. Nat Commun 2021; 12:6880. [PMID: 34824218 PMCID: PMC8616939 DOI: 10.1038/s41467-021-27067-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 11/01/2021] [Indexed: 11/15/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful and popular technique for probing the molecular structures, dynamics and chemical properties. However the conventional NMR spectroscopy is bottlenecked by its low sensitivity. Dynamic nuclear polarization (DNP) boosts NMR sensitivity by orders of magnitude and resolves this limitation. In liquid-state this revolutionizing technique has been restricted to a few specific non-biological model molecules in organic solvents. Here we show that the carbon polarization in small biological molecules, including carbohydrates and amino acids, can be enhanced sizably by in situ Overhauser DNP (ODNP) in water at room temperature and at high magnetic field. An observed connection between ODNP 13C enhancement factor and paramagnetic 13C NMR shift has led to the exploration of biologically relevant heterocyclic compound indole. The QM/MM MD simulation underscores the dynamics of intermolecular hydrogen bonds as the driving force for the scalar ODNP in a long-living radical-substrate complex. Our work reconciles results obtained by DNP spectroscopy, paramagnetic NMR and computational chemistry and provides new mechanistic insights into the high-field scalar ODNP.
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Affiliation(s)
- Danhua Dai
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Xianwei Wang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang, 310023, China
| | - Yiwei Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Xiao-Liang Yang
- Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Clemens Glaubitz
- Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Vasyl Denysenkov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China.
| | - Thomas Prisner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jiafei Mao
- Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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3
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Gurinov A, Sieland B, Kuzhelev A, Elgabarty H, Kühne TD, Prisner T, Paradies J, Baldus M, Ivanov KL, Pylaeva S. Gemischtvalente Verbindungen als polarisierende Mittel für die dynamische Kern‐Overhauser‐Polarisation in Festkörpern**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Andrei Gurinov
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584CH Utrecht Niederlande
| | - Benedikt Sieland
- Department of Chemistry Paderborn University Warburger Straße 100 Paderborn 33098 Deutschland
| | - Andrey Kuzhelev
- Goethe University Frankfurt am Main Institute of Physical and Theoretical Chemistry Center for Biomolecular Magnetic Resonance Max von Laue Straße 7 60438 Frankfurt am Main Deutschland
| | - Hossam Elgabarty
- Dynamics of Condensed Matter and Center for Sustainable Systems Design Chair of Theoretical Chemistry University of Paderborn Warburger Straße 100 33098 Paderborn Deutschland
| | - Thomas D. Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design Chair of Theoretical Chemistry University of Paderborn Warburger Straße 100 33098 Paderborn Deutschland
| | - Thomas Prisner
- Goethe University Frankfurt am Main Institute of Physical and Theoretical Chemistry Center for Biomolecular Magnetic Resonance Max von Laue Straße 7 60438 Frankfurt am Main Deutschland
| | - Jan Paradies
- Department of Chemistry Paderborn University Warburger Straße 100 Paderborn 33098 Deutschland
| | - Marc Baldus
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584CH Utrecht Niederlande
| | - Konstantin L. Ivanov
- International Tomography Center Siberian Branch of the Russian Academy of Sciences Novosibirsk 630090 Russland
- Novosibirsk State University Novosibirsk 630090 Russland
| | - Svetlana Pylaeva
- Dynamics of Condensed Matter and Center for Sustainable Systems Design Chair of Theoretical Chemistry University of Paderborn Warburger Straße 100 33098 Paderborn Deutschland
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4
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Gurinov A, Sieland B, Kuzhelev A, Elgabarty H, Kühne TD, Prisner T, Paradies J, Baldus M, Ivanov KL, Pylaeva S. Mixed-Valence Compounds as Polarizing Agents for Overhauser Dynamic Nuclear Polarization in Solids*. Angew Chem Int Ed Engl 2021; 60:15371-15375. [PMID: 33908694 PMCID: PMC8361920 DOI: 10.1002/anie.202103215] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Indexed: 11/25/2022]
Abstract
Herein, we investigate a novel set of polarizing agents—mixed‐valence compounds—by theoretical and experimental methods and demonstrate their performance in high‐field dynamic nuclear polarization (DNP) NMR experiments in the solid state. Mixed‐valence compounds constitute a group of molecules in which molecular mobility persists even in solids. Consequently, such polarizing agents can be used to perform Overhauser‐DNP experiments in the solid state, with favorable conditions for dynamic nuclear polarization formation at ultra‐high magnetic fields.
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Affiliation(s)
- Andrei Gurinov
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Benedikt Sieland
- Department of Chemistry, Paderborn University, Warburger Strasse 100, Paderborn, 33098, Germany
| | - Andrey Kuzhelev
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, Max von Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Hossam Elgabarty
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Strasse 100, 33098, Paderborn, Germany
| | - Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Strasse 100, 33098, Paderborn, Germany
| | - Thomas Prisner
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, Max von Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Jan Paradies
- Department of Chemistry, Paderborn University, Warburger Strasse 100, Paderborn, 33098, Germany
| | - Marc Baldus
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Konstantin L Ivanov
- International Tomography Center, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Svetlana Pylaeva
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Strasse 100, 33098, Paderborn, Germany
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5
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Zapp C, Obarska-Kosinska A, Rennekamp B, Kurth M, Hudson DM, Mercadante D, Barayeu U, Dick TP, Denysenkov V, Prisner T, Bennati M, Daday C, Kappl R, Gräter F. Mechanoradicals in tensed tendon collagen as a source of oxidative stress. Nat Commun 2020; 11:2315. [PMID: 32385229 PMCID: PMC7210969 DOI: 10.1038/s41467-020-15567-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 03/10/2020] [Indexed: 12/31/2022] Open
Abstract
As established nearly a century ago, mechanoradicals originate from homolytic bond scission in polymers. The existence, nature and biological relevance of mechanoradicals in proteins, instead, are unknown. We here show that mechanical stress on collagen produces radicals and subsequently reactive oxygen species, essential biological signaling molecules. Electron-paramagnetic resonance (EPR) spectroscopy of stretched rat tail tendon, atomistic molecular dynamics simulations and quantum-chemical calculations show that the radicals form by bond scission in the direct vicinity of crosslinks in collagen. Radicals migrate to adjacent clusters of aromatic residues and stabilize on oxidized tyrosyl radicals, giving rise to a distinct EPR spectrum consistent with a stable dihydroxyphenylalanine (DOPA) radical. The protein mechanoradicals, as a yet undiscovered source of oxidative stress, finally convert into hydrogen peroxide. Our study suggests collagen I to have evolved as a radical sponge against mechano-oxidative damage and proposes a mechanism for exercise-induced oxidative stress and redox-mediated pathophysiological processes. The existence, nature and biological relevance of mechanoradicals in proteins are unknown. Here authors show that mechanical stress on collagen produces radicals and subsequently reactive oxygen species and suggest that collagen I evolved as a radical sponge against mechano-oxidative damage.
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Affiliation(s)
- Christopher Zapp
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.,Institute for Theoretical Physics, Heidelberg University, Philosophenweg 16, 69120, Heidelberg, Germany
| | - Agnieszka Obarska-Kosinska
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.,Hamburg Unit c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22607, Hamburg, Germany
| | - Benedikt Rennekamp
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.,Institute for Theoretical Physics, Heidelberg University, Philosophenweg 16, 69120, Heidelberg, Germany
| | - Markus Kurth
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - David M Hudson
- Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Davide Mercadante
- Biochemical Institute, University of Zuerich, Winterthurerstr. 190, 8057, Zuerich, Switzerland
| | - Uladzimir Barayeu
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany.,Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Tobias P Dick
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Vasyl Denysenkov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Thomas Prisner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Csaba Daday
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120, Heidelberg, Germany
| | - Reinhard Kappl
- Institute for Biophysics, Saarland University Medical Center, CIPMM Geb. 48, 66421, Homburg/Saar, Germany
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany. .,Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120, Heidelberg, Germany.
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6
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Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure 2019; 27:1745-1759. [PMID: 31780431 DOI: 10.1016/j.str.2019.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/31/2019] [Accepted: 11/06/2019] [Indexed: 12/23/2022]
Abstract
Structures of biomolecular systems are increasingly computed by integrative modeling. In this approach, a structural model is constructed by combining information from multiple sources, including varied experimental methods and prior models. In 2019, a Workshop was held as a Biophysical Society Satellite Meeting to assess progress and discuss further requirements for archiving integrative structures. The primary goal of the Workshop was to build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validating integrative structures. The summary of the Workshop and the recommendations that emerged are presented here.
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Affiliation(s)
- Helen M Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Bridge Institute, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA.
| | - Paul D Adams
- Physical Biosciences Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Alexandre A Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Wah Chiu
- Department of Bioengineering, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305-5447, USA; SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Thomas E Ferrin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Margaret J Gabanyi
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Thomas D Goddard
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | | | - Juergen Haas
- Swiss Institute of Bioinformatics and Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Christian A Hanke
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Jeffrey C Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Genji Kurisu
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Catherine L Lawson
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - John L Markley
- BioMagResBank (BMRB), Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37221, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytech Institute, Troy, NY 12180, USA
| | - George N Phillips
- BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX 77251, USA
| | - Thomas Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3JR, Scotland
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Torsten Schwede
- Swiss Institute of Bioinformatics and Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Claus A M Seidel
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | | | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Brinda Vallat
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK
| | - Geerten W Vuister
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Benjamin Webb
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kate L White
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Bridge Institute, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrej Sali
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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7
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Kaur H, Abreu B, Akhmetzyanov D, Lakatos-Karoly A, Soares CM, Prisner T, Glaubitz C. Unexplored Nucleotide Binding Modes for the ABC Exporter MsbA. J Am Chem Soc 2018; 140:14112-14125. [PMID: 30289253 DOI: 10.1021/jacs.8b06739] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The ATP-binding cassette (ABC) transporter MsbA is an ATP-driven lipid-A flippase. It belongs to the ABC protein superfamily whose members are characterized by conserved motifs in their nucleotide binding domains (NBDs), which are responsible for ATP hydrolysis. Recently, it was found that MsbA could catalyze a reverse adenylate kinase (rAK)-like reaction in addition to ATP hydrolysis. Both reactions are connected and mediated by the same conserved NBD domains. Here, the structural foundations underlying the nucleotide binding to MsbA were therefore explored using a concerted approach based on conventional- and DNP-enhanced solid-state NMR, pulsed-EPR, and MD simulations. MsbA reconstituted into lipid bilayers was trapped in various catalytic states corresponding to intermediates of the coupled ATPase-rAK mechanism. The analysis of nucleotide-binding dependent chemical shift changes, and the detection of through-space contacts between bound nucleotides and MsbA within these states provides evidence for an additional nucleotide-binding site in close proximity to the Q-loop and the His-Switch. By replacing Mg2+ with Mn2+ and employing pulsed EPR spectroscopy, evidence is provided that this newly found nucleotide binding site does not interfere with the coordination of the required metal ion. Molecular dynamic (MD) simulations of nucleotide and metal binding required for the coupled ATPase-rAK mechanism have been used to corroborate these experimental findings and provide additional insight into nucleotide location, orientation, and possible binding modes.
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Affiliation(s)
- Hundeep Kaur
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
| | - Bárbara Abreu
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , 2780-157 Oeiras , Portugal
| | - Dmitry Akhmetzyanov
- Institute for Physical and Theoretical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
| | - Andrea Lakatos-Karoly
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
| | - Cláudio M Soares
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , 2780-157 Oeiras , Portugal
| | - Thomas Prisner
- Institute for Physical and Theoretical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
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8
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Leone V, Waclawska I, Endeward B, Prisner T, Ziegler C, Forrest LR. Coupling Spectroscopic Data for a Secondary Transporter with Simulations to Assess the Role of a Key Acidic Residue. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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9
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Kuzhelev A, Akhmetzyanov D, Denysenkov V, Shevelev G, Krumkacheva O, Bagryanskaya E, Prisner T. High-frequency pulsed electron–electron double resonance spectroscopy on DNA duplexes using trityl tags and shaped microwave pulses. Phys Chem Chem Phys 2018; 20:26140-26144. [DOI: 10.1039/c8cp03951h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Distances between trityl spin labels attached to DNA duplexes were determined by 180 GHz and 260 GHz PELDOR spectroscopy applying broadband pump pulse at higher frequency.
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Affiliation(s)
- A. Kuzhelev
- Novosibirsk State University
- 630090 Novosibirsk
- Russia
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- 630090 Novosibirsk
| | - D. Akhmetzyanov
- Goethe University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry
- Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
| | - V. Denysenkov
- Goethe University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry
- Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
| | - G. Shevelev
- Novosibirsk State University
- 630090 Novosibirsk
- Russia
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- 630090 Novosibirsk
| | - O. Krumkacheva
- Novosibirsk State University
- 630090 Novosibirsk
- Russia
- International Tomography Center SB RAS
- Novosibirsk
| | - E. Bagryanskaya
- Novosibirsk State University
- 630090 Novosibirsk
- Russia
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- 630090 Novosibirsk
| | - T. Prisner
- Goethe University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry
- Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
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10
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Leone V, Waclawska I, Endeward B, Prisner T, Ziegler C, Forrest LR. Describing the Thermodynamics of the Secondary Transporter BetP by Coupling Spectroscopic Measurements to Molecular Dynamics Simulations. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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11
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Haeri HH, Spindler P, Plackmeyer J, Prisner T. Double quantum coherence ESR spectroscopy and quantum chemical calculations on a BDPA biradical. Phys Chem Chem Phys 2016; 18:29164-29169. [PMID: 27730235 DOI: 10.1039/c6cp05847g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Carbon-centered radicals are interesting alternatives to otherwise commonly used nitroxide spin labels for dipolar spectroscopy techniques because of their narrow ESR linewidth. Herein, we present a novel BDPA biradical, where two BDPA (α,α,γ,γ-bisdiphenylene-β-phenylallyl) radicals are covalently tethered by a saturated biphenyl acetylene linker. The inter-spin distance between the two spin carrier fragments was measured using double quantum coherence (DQC) ESR methodology. The DQC experiment revealed a mean distance of only 1.8 nm between the two unpaired electron spins. This distance is shorter than the predictions based on a simple modelling of the biradical geometry with the electron spins located at the central carbon atoms. Therefore, DFT (density functional theory) calculations were performed to obtain a picture of the spin delocalization, which may give rise to a modified dipolar interaction tensor, and to find those conformations that correspond best to the experimentally observed inter-spin distance. Quantum chemical calculations showed that the attachment of the biphenyl acetylene linker at the second position of the fluorenyl ring of BDPA did not affect the spin population or geometry of the BDPA radical. Therefore, spin delocalization and geometry optimization of each BDPA moiety could be performed on the monomeric unit alone. The allylic dihedral angle θ1 between the fluorenyl rings in the monomer subunit was determined to be 30° or 150° using quantum chemical calculations. The proton hyperfine coupling constant calculated from both energy minima was in very good agreement with literature values. Based on the optimal monomer geometries and spin density distributions, the dipolar coupling interaction between both BDPA units could be calculated for several dimer geometries. It was shown that the rotation of the BDPA units around the linker axis (θ2) does not significantly influence the dipolar coupling strength when compared to the allylic dihedral angle θ1. A good agreement between the experimental and calculated dipolar coupling was found for θ1 = 30°.
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Affiliation(s)
- Haleh Hashemi Haeri
- Institute of Physical und Theoretical Chemistry, Goethe University Frankfurt, Max von Laue Straße 7, 60438 Frankfurt am Main, Germany.
| | - Philipp Spindler
- Institute of Physical und Theoretical Chemistry, Goethe University Frankfurt, Max von Laue Straße 7, 60438 Frankfurt am Main, Germany.
| | - Jörn Plackmeyer
- Institute of Physical und Theoretical Chemistry, Goethe University Frankfurt, Max von Laue Straße 7, 60438 Frankfurt am Main, Germany.
| | - Thomas Prisner
- Institute of Physical und Theoretical Chemistry, Goethe University Frankfurt, Max von Laue Straße 7, 60438 Frankfurt am Main, Germany.
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12
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Sauvée C, Casano G, Abel S, Rockenbauer A, Akhmetzyanov D, Karoui H, Siri D, Aussenac F, Maas W, Weber RT, Prisner T, Rosay M, Tordo P, Ouari O. Tailoring of Polarizing Agents in the bTurea Series for Cross-Effect Dynamic Nuclear Polarization in Aqueous Media. Chemistry 2016; 22:5598-606. [PMID: 26992052 DOI: 10.1002/chem.201504693] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Indexed: 11/10/2022]
Abstract
A series of 18 nitroxide biradicals derived from bTurea has been prepared, and their enhancement factors ɛ ((1)H) in cross-effect dynamic nuclear polarization (CE DNP) NMR experiments at 9.4 and 14.1 T and 100 K in a DNP-optimized glycerol/water matrix ("DNP juice") have been studied. We observe that ɛ ((1)H) is strongly correlated with the substituents on the polarizing agents, and its trend is discussed in terms of different molecular parameters: solubility, average e-e distance, relative orientation of the nitroxide moieties, and electron spin relaxation times. We show that too short an e-e distance or too long a T1e can dramatically limit ɛ ((1)H). Our study also shows that the molecular structure of AMUPol is not optimal and its ɛ ((1)H) could be further improved through stronger interaction with the glassy matrix and a better orientation of the TEMPO moieties. A new AMUPol derivative introduced here provides a better ɛ ((1)H) than AMUPol itself (by a factor of ca. 1.2).
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Affiliation(s)
- Claire Sauvée
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France
| | - Gilles Casano
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France
| | - Sébastien Abel
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry, Hungarian Academy of Sciences, Department of Physics, Budapest University of Technology and Economics and MTA-BME Condensed Matter Research Group, Budafoki ut 8, 1111, Budapest, Hungary
| | - Dimitry Akhmetzyanov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438, Frankfurt-am-Main, Germany
| | - Hakim Karoui
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France
| | - Didier Siri
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France
| | - Fabien Aussenac
- Bruker BioSpin S.A.S., 34 rue de l'industrie, 67166, Wissembourg, France
| | - Werner Maas
- Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, Massachusetts, 01821, USA
| | - Ralph T Weber
- Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, Massachusetts, 01821, USA
| | - Thomas Prisner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438, Frankfurt-am-Main, Germany
| | - Mélanie Rosay
- Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, Massachusetts, 01821, USA
| | - Paul Tordo
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France.
| | - Olivier Ouari
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France.
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13
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Prisner T, Denysenkov V, Sezer D. Liquid state DNP at high magnetic fields: Instrumentation, experimental results and atomistic modelling by molecular dynamics simulations. J Magn Reson 2016; 264:68-77. [PMID: 26920832 DOI: 10.1016/j.jmr.2015.11.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/11/2015] [Accepted: 11/12/2015] [Indexed: 05/14/2023]
Abstract
Dynamic nuclear polarization (DNP) at high magnetic fields has recently become one of the major research areas in magnetic resonance spectroscopy and imaging. Whereas much work has been devoted to experiments where the polarization transfer from the electron spin to the nuclear spin is performed in the solid state, only a few examples exist of experiments where the polarization transfer is performed in the liquid state. Here we describe such experiments at a magnetic field of 9.2 T, corresponding to a nuclear Larmor frequency of 400 MHz for proton spins and an excitation frequency of 263 GHz for the electron spins. The technical requirements to perform such experiments are discussed in the context of the double resonance structures that we have implemented. The experimental steps that allowed access to the enhancement factors for proton spins of several organic solvents with nitroxide radicals as polarizing agents are described. A computational scheme for calculating the coupling factors from molecular dynamics (MD) simulations is outlined and used to highlight the limitations of the classical models based on translational and rotational motion that are typically employed to quantify the observed coupling factors. The ability of MD simulations to predict enhancements for a variety of radicals and solvent molecules at any magnetic field strength should prove useful in optimizing experimental conditions for DNP in the liquid state.
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Affiliation(s)
- Thomas Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany.
| | - Vasyl Denysenkov
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany
| | - Deniz Sezer
- Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı-Tuzla, 34956 Istanbul, Turkey.
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14
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Geiger MA, Orwick-Rydmark M, Märker K, Franks WT, Akhmetzyanov D, Stöppler D, Zinke M, Specker E, Nazaré M, Diehl A, van Rossum BJ, Aussenac F, Prisner T, Akbey Ü, Oschkinat H. Temperature dependence of cross-effect dynamic nuclear polarization in rotating solids: advantages of elevated temperatures. Phys Chem Chem Phys 2016; 18:30696-30704. [DOI: 10.1039/c6cp06154k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNP on proteins at 200 K.
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15
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Barthelmes D, Gränz M, Barthelmes K, Allen KN, Imperiali B, Prisner T, Schwalbe H. Encoded loop-lanthanide-binding tags for long-range distance measurements in proteins by NMR and EPR spectroscopy. J Biomol NMR 2015; 63:275-282. [PMID: 26341230 DOI: 10.1007/s10858-015-9984-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 09/01/2015] [Indexed: 06/05/2023]
Abstract
We recently engineered encodable lanthanide binding tags (LBTs) into proteins and demonstrated their applicability in Nuclear Magnetic Resonance (NMR) spectroscopy, X-ray crystallography and luminescence studies. Here, we engineered two-loop-LBTs into the model protein interleukin-1β (IL1β) and measured (1)H, (15)N-pseudocontact shifts (PCSs) by NMR spectroscopy. We determined the Δχ-tensors associated with each Tm(3+)-loaded loop-LBT and show that the experimental PCSs yield structural information at the interface between the two metal ion centers at atomic resolution. Such information is very valuable for the determination of the sites of interfaces in protein-protein-complexes. Combining the experimental PCSs of the two-loop-LBT construct IL1β-S2R2 and the respective single-loop-LBT constructs IL1β-S2, IL1β-R2 we additionally determined the distance between the metal ion centers. Further, we explore the use of two-loop LBTs loaded with Gd(3+) as a novel tool for distance determination by Electron Paramagnetic Resonance spectroscopy and show the NMR-derived distances to be remarkably consistent with distances derived from Pulsed Electron-Electron Dipolar Resonance.
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Affiliation(s)
- Dominic Barthelmes
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt Am Main, Germany
| | - Markus Gränz
- Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt Am Main, Germany
| | - Katja Barthelmes
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt Am Main, Germany
- Department of Chemistry, Munich Center for Integrated Protein Science and Chair Biomolecular NMR, Technical University Munich, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Karen N Allen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Barbara Imperiali
- Departments of Chemistry and Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Thomas Prisner
- Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt Am Main, Germany.
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt Am Main, Germany.
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16
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Ardenkjaer-Larsen JH, Boebinger GS, Comment A, Duckett S, Edison AS, Engelke F, Griesinger C, Griffin RG, Hilty C, Maeda H, Parigi G, Prisner T, Ravera E, van Bentum J, Vega S, Webb A, Luchinat C, Schwalbe H, Frydman L. Facing and Overcoming Sensitivity Challenges in Biomolecular NMR Spectroscopy. Angew Chem Int Ed Engl 2015; 54:9162-85. [PMID: 26136394 PMCID: PMC4943876 DOI: 10.1002/anie.201410653] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 01/26/2015] [Indexed: 11/07/2022]
Abstract
In the Spring of 2013, NMR spectroscopists convened at the Weizmann Institute in Israel to brainstorm on approaches to improve the sensitivity of NMR experiments, particularly when applied in biomolecular settings. This multi-author interdisciplinary Review presents a state-of-the-art description of the primary approaches that were considered. Topics discussed included the future of ultrahigh-field NMR systems, emerging NMR detection technologies, new approaches to nuclear hyperpolarization, and progress in sample preparation. All of these are orthogonal efforts, whose gains could multiply and thereby enhance the sensitivity of solid- and liquid-state experiments. While substantial advances have been made in all these areas, numerous challenges remain in the quest of endowing NMR spectroscopy with the sensitivity that has characterized forms of spectroscopies based on electrical or optical measurements. These challenges, and the ways by which scientists and engineers are striving to solve them, are also addressed.
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Affiliation(s)
- Jan-Henrik Ardenkjaer-Larsen
- GE Healthcare, Broendby, Denmark; Department of Electrical Engineering, Technical University of Denmark, Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital Hvidovre (Denmark)
| | - Gregory S Boebinger
- U.S. National High Magnetic Field Lab, Florida State University, Tallahassee, FL 32310 (USA)
| | - Arnaud Comment
- Institute of Physics of Biological Systems, Ecole Polytechnique Fédérale de Lausanne, Lausanne (Switzerland)
| | - Simon Duckett
- Department of Chemistry, University of York, Heslington, York, YO10 5DD (UK)
| | - Arthur S Edison
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32610 (USA)
| | | | | | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Lab, MIT, Cambridge, MA 02139-4703 (USA)
| | - Christian Hilty
- Department of Chemistry, Texas A&M University, College Station (USA)
| | - Hidaeki Maeda
- Riken Center for Life Science Technologies, Yokohama, Kanagawa (Japan)
| | - Giacomo Parigi
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy)
| | - Thomas Prisner
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Enrico Ravera
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy)
| | | | - Shimon Vega
- Chemical Physics Department, Weizmann Institute of Science, Rehovot (Israel)
| | - Andrew Webb
- Department of Radiology, C. J. Gorter Center for High Field MRI, Leiden University Medical Center (The Netherlands)
| | - Claudio Luchinat
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy).
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany).
| | - Lucio Frydman
- Chemical Physics Department, Weizmann Institute of Science, Rehovot (Israel).
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17
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Ardenkjaer-Larsen JH, Boebinger GS, Comment A, Duckett S, Edison AS, Engelke F, Griesinger C, Griffin RG, Hilty C, Maeda H, Parigi G, Prisner T, Ravera E, van Bentum J, Vega S, Webb A, Luchinat C, Schwalbe H, Frydman L. Neue Ansätze zur Empfindlichkeitssteigerung in der biomolekularen NMR-Spektroskopie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410653] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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Terekhov M, Krummenacker J, Denysenkov V, Gerz K, Prisner T, Schreiber LM. Characterization and optimization of the visualization performance of continuous flow overhauser DNP hyperpolarized water MRI: Inversion recovery approach. Magn Reson Med 2015; 75:985-96. [PMID: 25884985 DOI: 10.1002/mrm.25574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 11/11/2014] [Accepted: 11/15/2014] [Indexed: 01/08/2023]
Abstract
PURPOSE Overhauser dynamic nuclear polarization (DNP) allows the production of liquid hyperpolarized substrate inside the MRI magnet bore as well as its administration in continuous flow mode to acquire MR images with enhanced signal-to-noise ratio. We implemented inversion recovery preparation in order to improve contrast-to-noise ratio and to quantify the overall imaging performance of Overhauser DNP-enhanced MRI. METHOD The negative enhancement created by DNP in combination with inversion recovery (IR) preparation allows canceling selectively the signal originated from Boltzmann magnetization and visualizing only hyperpolarized fluid. The theoretical model describing gain of MR image intensity produced by steady-state continuous flow DNP hyperpolarized magnetization was established and proved experimentally. RESULTS A precise quantification of signal originated purely from DNP hyperpolarization was achieved. A temperature effect on longitudinal relaxation had to be taken into account to fit experimental results with numerical prediction. CONCLUSION Using properly adjusted IR preparation, the complete zeroing of thermal background magnetization was achieved, providing an essential increase of contrast-to-noise ratio of DNP-hyperpolarized water images. To quantify and optimize the steady-state conditions for MRI with continuous flow DNP, an approach similar to that incorporating transient-state thermal magnetization equilibrium in spoiled fast field echo imaging sequences can be used.
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Affiliation(s)
- Maxim Terekhov
- Section of Medical Physics, Department of Radiology, University Medical Center Mainz, Mainz, Germany
| | - Jan Krummenacker
- Section of Medical Physics, Department of Radiology, University Medical Center Mainz, Mainz, Germany.,Institute of Physical and Theoretical Chemistry, Center for Bimolecular Magnetic Resonance Goethe-University, Frankfurt am Main, Germany
| | - Vasyl Denysenkov
- Institute of Physical and Theoretical Chemistry, Center for Bimolecular Magnetic Resonance Goethe-University, Frankfurt am Main, Germany
| | - Kathrin Gerz
- Section of Medical Physics, Department of Radiology, University Medical Center Mainz, Mainz, Germany
| | - Thomas Prisner
- Institute of Physical and Theoretical Chemistry, Center for Bimolecular Magnetic Resonance Goethe-University, Frankfurt am Main, Germany
| | - Laura Maria Schreiber
- Section of Medical Physics, Department of Radiology, University Medical Center Mainz, Mainz, Germany
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19
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Budanow A, Haeri HH, Sänger I, Schödel F, Bolte M, Prisner T, Wagner M, Lerner HW. Disupersilylperoxo radical anion [tBu3 SiOOSitBu3 ](⋅-) : an intermediate of supersilanide oxidation. Chemistry 2014; 20:10236-9. [PMID: 25042609 DOI: 10.1002/chem.201403854] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Indexed: 11/07/2022]
Abstract
In the oxidative process of the supersilanide anion [SitBu3 ](-) , radical species are generated. The continuous wave (cw)-EPR spectrum of the reaction solution of Na[SitBu3 ] with O2 revealed a signal, which could be characterized as disupersilylperoxo radical anion [tBu3 SiOOSitBu3 ](⋅-) affected by sodium ions though ion-pair formation. A mechanism is suggested for the oxidative process of supersilanide, which in a further step can be helpful in a better understanding of the oxidation process of isoelectronic phosphanes.
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Affiliation(s)
- Alexandra Budanow
- Institut für Anorganische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany), Fax: (+49) 69-798-29252
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20
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Denysenkov V, Prisner T. Liquid state Dynamic Nuclear Polarization probe with Fabry-Perot resonator at 9.2 T. J Magn Reson 2012; 217:1-5. [PMID: 22386647 DOI: 10.1016/j.jmr.2012.01.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 01/23/2012] [Accepted: 01/25/2012] [Indexed: 05/31/2023]
Abstract
Recent achievements in liquid state DNP at high magnetic fields showing significant enhancements on aqueous solutions have initiated strong interest in possible applications of this method to biomolecular research. However, in situ DNP of biomolecules at ambient temperatures is a challenging task due to high microwave losses leading to excessive sample heating. To avoid such heating the sample volume has to be reduced strongly to keep it away from the electric component of the microwave field. A helical double resonance structure, used for the first demonstrations of the applicability of Overhauser DNP to aqueous solutions at high magnetic fields (9.2 T), restricted the sample size to a very small volume of 2 nl. Together with a poor spectral resolution this resulted in small overall signal amplitude, hampering observations of biomolecules. Here we present a new type of the double resonance structure for liquid-state DNP which consists of a Fabry-Perot resonator for the microwave excitation and a stripline resonator for the NMR detection. This new double resonance structure (260 GHz/400 MHz) offers a 30-fold increase in aqueous sample volume (80 nl) with respect to the helical probe and exhibits improved NMR sensitivity and linewidth.
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Affiliation(s)
- Vasyl Denysenkov
- Institute for Physical Chemistry, Goethe University Frankfurt, Max von Laue Str. 7, 60438 Frankfurt am Main, Germany
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21
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van de Linde S, Krstić I, Prisner T, Doose S, Heilemann M, Sauer M. Photoinduced formation of reversible dye radicals and their impact on super-resolution imaging. Photochem Photobiol Sci 2011; 10:499-506. [DOI: 10.1039/c0pp00317d] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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22
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Arias-Cartin R, Lyubenova S, Ceccaldi P, Prisner T, Magalon A, Guigliarelli B, Grimaldi S. HYSCORE Evidence That Endogenous Mena- and Ubisemiquinone Bind at the Same Q Site (QD) of Escherichia coli Nitrate Reductase A. J Am Chem Soc 2010; 132:5942-3. [DOI: 10.1021/ja1009234] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rodrigo Arias-Cartin
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Sevdalina Lyubenova
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Pierre Ceccaldi
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Thomas Prisner
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Axel Magalon
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Bruno Guigliarelli
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Stéphane Grimaldi
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
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Lyubenova S, Maly T, Zwicker K, Brandt U, Ludwig B, Prisner T. Multifrequency pulsed electron paramagnetic resonance on metalloproteins. Acc Chem Res 2010; 43:181-9. [PMID: 19842617 DOI: 10.1021/ar900050d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metalloproteins often contain metal centers that are paramagnetic in some functional state of the protein; hence electron paramagnetic resonance (EPR) spectroscopy can be a powerful tool for studying protein structure and function. Dipolar spectroscopy allows the determination of the dipole-dipole interactions between metal centers in protein complexes, revealing the structural arrangement of different paramagnetic centers at distances of up to 8 nm. Hyperfine spectroscopy can be used to measure the interaction between an unpaired electron spin and nuclear spins within a distance of 0.8 nm; it therefore permits the characterization of the local structure of the paramagnetic center's ligand sphere with very high precision. In this Account, we review our laboratory's recent applications of both dipolar and hyperfine pulsed EPR methods to metalloproteins. We used pulsed dipolar relaxation methods to investigate the complex of cytochrome c and cytochrome c oxidase, a noncovalent protein-protein complex involved in mitochondrial electron-transfer reactions. Hyperfine sublevel correlation spectroscopy (HYSCORE) was used to study the ligand sphere of iron-sulfur clusters in complex I of the mitochondrial respiratory chain and substrate binding to the molybdenum enzyme polysulfide reductase. These examples demonstrate the potential of the two techniques; however, they also highlight the difficulties of data interpretation when several paramagnetic species with overlapping spectra are present in the protein. In such cases, further approaches and data are very useful to enhance the information content. Relaxation filtered hyperfine spectroscopy (REFINE) can be used to separate the individual components of overlapping paramagnetic species on the basis of differences in their longitudinal relaxation rates; it is applicable to any kind of pulsed hyperfine or dipolar spectroscopy. Here, we show that the spectra of the iron-sulfur clusters in complex I can be separated by this method, allowing us to obtain hyperfine (and dipolar) information from the individual species. Furthermore, performing pulsed EPR experiments at different magnetic fields is another important tool to disentangle the spectral components in such complex systems. Despite the fact that high magnetic fields do not usually lead to better spectral separation for metal centers, they provide additional information about the relative orientation of different paramagnetic centers. Our high-field EPR studies on cytochrome c oxidase reveal essential information regarding the structural arrangement of the binuclear Cu(A) center with respect to both the manganese ion within the enzyme and the cytochrome in the protein-protein complex with cytochrome c.
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Affiliation(s)
- Sevdalina Lyubenova
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Thorsten Maly
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Klaus Zwicker
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Ulrich Brandt
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Bernd Ludwig
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Thomas Prisner
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
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Matsuki Y, Maly T, Ouari O, Karoui H, Le Moigne F, Rizzato E, Lyubenova S, Herzfeld J, Prisner T, Tordo P, Griffin RG. Dynamic nuclear polarization with a rigid biradical. Angew Chem Int Ed Engl 2009; 48:4996-5000. [PMID: 19492374 DOI: 10.1002/anie.200805940] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A new polarizing agent with superior performance in dynamic nuclear polarization experiments is introduced, and utilizes two TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl) moieties connected through a rigid spiro tether (see structure). The observed NMR signal intensities were enhanced by a factor of 1.4 compared to those of TOTAPOL, a previously described TEMPO-based biradical with a flexible tether.
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Affiliation(s)
- Yoh Matsuki
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Matsuki Y, Maly T, Ouari O, Karoui H, Le Moigne F, Rizzato E, Lyubenova S, Herzfeld J, Prisner T, Tordo P, Griffin R. Dynamic Nuclear Polarization with a Rigid Biradical. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805940] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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Marko A, Margraf D, Yu H, Mu Y, Stock G, Prisner T. Molecular orientation studies by pulsed electron-electron double resonance experiments. J Chem Phys 2009; 130:064102. [DOI: 10.1063/1.3073040] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Maly T, Grgic L, Zwicker K, Zickermann V, Brandt U, Prisner T. Cluster N1 of complex I from Yarrowia lipolytica studied by pulsed EPR spectroscopy. J Biol Inorg Chem 2006; 11:343-50. [PMID: 16502321 DOI: 10.1007/s00775-006-0081-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Accepted: 01/16/2006] [Indexed: 11/27/2022]
Abstract
After reduction with nicotinamide adenine dinucleotide (NADH), NADH:ubiquinone oxidoreductase (complex I) of the strictly aerobic yeast Yarrowia lipolytica shows clear signals from five different paramagnetic iron-sulfur (FeS) clusters (N1-N5) which can be detected using electron paramagnetic resonance (EPR) spectroscopy. The ligand environment and the assignment of several FeS clusters to specific binding motifs found in several subunits of the complex are still under debate. In order to characterize the hyperfine interaction of the surrounding nuclei with FeS cluster N1, one- and two-dimensional electron spin echo envelope modulation experiments were performed at a temperature of 30 K. At this temperature only cluster N1 contributes to the overall signal in a pulsed EPR experiment. The hyperfine and quadrupole tensors of a nitrogen nucleus and the isotropic and dipolar hyperfine couplings of two sets of protons could be determined by numerical simulation of the one- and two-dimensional spectra. The values obtained are in perfect agreement with a ferredoxin-like binding structure by four cysteine amino acid residues and allow the assignment of the nitrogen couplings to a backbone nitrogen nucleus and the proton couplings to the beta-protons of the bound cysteine residues.
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Affiliation(s)
- T Maly
- Institut für Physikalische und Theoretische Chemie and Center for Biological Magnetic Resonance, Johann-Wolfgang-Goethe-Universität Frankfurt, 60439, Frankfurt am Main, Germany
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Piton N, Schiemann O, Mu Y, Stock G, Prisner T, Engels JW. Synthesis of spin-labeled RNAs for long range distance measurements by peldor. Nucleosides Nucleotides Nucleic Acids 2005; 24:771-5. [PMID: 16248034 DOI: 10.1081/ncn-200060139] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Site directed spin labeled RNA duplexes with different interspin distances were synthesized. The radical 2,2,5,5-tetramethyl-pyrrolin- 1-yloxyl-3-acetylene (TPA) was introduced during the solid-phase synthesis through a Sonogashira cross-coupling with 5-iodo-uridine. Tm and CD studies showed that the spin label does not to disturb significantly the A-form of these duplexes. 4-Pulse Electron Double Resonance (PELDOR) was then used to measure intramolecular spin-spin distances of 19.3, 33.0 and 40.9 A, which are in very good agreement with the calculated values of 17.6, 32.1 and 39.1 A, obtained from Molecular Dynamics (MD) simulations.
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Affiliation(s)
- Nelly Piton
- Institut für Organische Chemie und Chemische Biologie (OCCB), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
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29
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Prisner T, Lyubenova S, Atabay Y, MacMillan F, Kröger A, Klimmek O. Multifrequency cw-EPR investigation of the catalytic molybdenum cofactor of polysulfide reductase from Wolinella succinogenes. J Biol Inorg Chem 2003; 8:419-26. [PMID: 12761663 DOI: 10.1007/s00775-002-0432-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2002] [Accepted: 11/11/2002] [Indexed: 11/30/2022]
Abstract
Electron paramagnetic resonance (EPR) spectra of the molybdenum centre in polysulfide reductase (Psr) from Wolinella succinogenes with unusually high G-tensor values have been observed for the first time. Three different Mo(V) states have been generated (by the addition of the substrate polysulfide and different redox agents) and analysed by their G- and hyperfine tensors using multifrequency (S-, X- and Q-band) cw-EPR spectroscopy. The unusually high G-tensor values are attributed to a large number of sulfur ligands. Four sulfur ligands are assumed to arise from two pterin cofactors; one additional sulfur ligand was identified from mutagenesis studies to be a cysteine residue of the protein backbone. One further sulfur ligand is proposed for two of the Mo(V) states, based on the experimentally observed shift of the g(av) value. This sixth sulfur ligand is postulated to belong to the polysulfide substrate consumed within the catalytic reaction cycle of the enzyme. The influence of the co-protein sulfur transferase on the Mo(V) G-tensor supports this assignment.
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Affiliation(s)
- Thomas Prisner
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University Frankfurt, Marie-Curie-Strasse 11, 60439, Frankfurt am Main, Germany.
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Fuhs M, Schnegg A, Prisner T, Köhne I, Hanley J, Rutherford A, Möbius K. Orientation selection in photosynthetic PS I multilayers: structural investigation of the charge separated state P(700)(+z.rad;)A(1)(-z.rad;) by high-field/high-frequency time-resolved EPR at 3.4 T/95 GHz. Biochim Biophys Acta 2002; 1556:81-8. [PMID: 12351221 DOI: 10.1016/s0005-2728(02)00338-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The radical-pair state of the primary electron donor and the secondary electron acceptor (P(700)(+z.rad;)A(1)(-z.rad;)) of the photosynthetic reaction center (RC) photosystem I (PS I) of Synechocystis PCC 6803 was studied by time-resolved electron paramagnetic resonance (TREPR) at high field/high frequency (3.4 T/95 GHz) using orientation selection in multilayers. The goal of the present article is to work out the basis for future studies, in which the improved resolution of such multilayers may be used to detect mutation-induced structural changes of PS I in membrane preparations. This approach is particularly interesting for systems that cannot be prepared as single crystals. However, in order to use such multilayers for structural investigations of protein complexes, it is necessary to know their orientation distribution. PS I was chosen as a test example because the wild type was recently crystallized and its X-ray structure determined to 2.5 A resolution [Nature 411 (2001) 909]. On the basis of our experimental results we determined the orientation distribution. Furthermore, a simulation model for the general case in which the orientation distribution is not axially symmetric about the C(2) symmetry axis of the RC is developed and discussed. Spectra simulations show that changes in the TREPR spectra of PS I are much more significant for these oriented multilayers than for disordered samples. In this way the use of oriented multilayers, in conjunction with multifrequency TREPR measurements on oriented as well as on disordered samples, is a promising approach for studies of structural changes of PS I systems that are induced by point mutations.
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Affiliation(s)
- M Fuhs
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, D-14195, Berlin, Germany.
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31
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Abstract
Pulsed electron paramagnetic resonance (EPR) methods such as ESEEM, PELDOR, relaxation time measurements, transient EPR, high-field/high-frequency EPR, and pulsed ENDOR, have been used successfully to investigate the local structure and dynamics of paramagnetic centers in biological samples. These methods allow different contributions to the EPR spectra to be distinguished and can help unravel complicated EPR spectra consisting of overlapping resonance lines, as are often found in disordered protein samples. The basic principles, specific potentials, technical requirements, and limitations of these advanced EPR techniques will be reviewed together with recent applications to metal centers, organic radicals, and spin labels in proteins.
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Affiliation(s)
- T Prisner
- Institute for Physical and Theoretical Chemistry, J. W. Goethe-University Frankfurt, Marie-Curie-Strasse 11, Frankfurt am Main, D-60439 Germany.
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Strube T, Schiemann O, MacMillan F, Prisner T, Engels JW. A new facile method for spin-labeling of oligonucleotides. Nucleosides Nucleotides Nucleic Acids 2001; 20:1271-4. [PMID: 11563001 DOI: 10.1081/ncn-100002534] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A new facile method for spin-labeling suitable for DNA and RNA oligonucleotides is presented. The nitroxide 3-ethenyl-2,2,5,5-tetramethyl-pyrrolin-1-yloxy was directly introduced during automated solid-phase synthesis by a Pd(0) cross coupling reaction. The main advantages of this procedure are the small amount of spin-label needed for the derivatisation of the oligonucleotide and the high coupling efficiency on the solid phase.
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Affiliation(s)
- T Strube
- Institut für Organische Chemie, Johann Wolfgang Goethe-Universität, Marie Curie Strasse 11, D-60439 Frankfurt am Main, Germany
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Fuhs M, Prisner T, Möbius K. Fourier-transform EPR at high-field/high-frequency (3.4 T/95 GHz) using broadband stochastic microwave excitation. J Magn Reson 2001; 149:67-73. [PMID: 11273753 DOI: 10.1006/jmre.2000.2272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Stochastic excitation with a full-width-half-maximum bandwidth of 250 MHz was used to perform Fourier-transform (FT) high-field/high-frequency electron paramagnetic resonance (EPR) at 3.4T/95 GHz (W-band). Thereby, the required microwave peak power is reduced by a factor of tau(p)/T1 as compared to equivalent pulsed FT EPR in which the spin system with spin-lattice relaxation time T1 is excited by a single microwave pulse of length tau(p). Stochastic EPR is particularly interesting under high-field/high-frequency conditions, because the limited output power of mm microwave sources, amplifiers, and mixers makes pulse FT EPR in that frequency domain impossible, at least for the near future. On the other hand, FT spectroscopy offers several advantages compared to field-swept magnetic resonance methods, as is demonstrated by its success in NMR and X-band EPR. In this paper we describe a novel stochastic W-band microwave bridge including a bimodal induction mode transmission resonator that serves for decoupling the microwave excitation and signal detection. We report first EPR measurements and discuss experimental difficulties as well as achieved sensitivity. Moreover, we discuss future improvements and the possibility for an application of stochastic W-band FT EPR to transient signals such as those of photoexcited radical pairs in photosynthetic reaction centers.
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Affiliation(s)
- M Fuhs
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, Berlin, D-14195, Germany
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Grimaldi S, MacMillan F, Ostermann T, Ludwig B, Michel H, Prisner T. QH*- ubisemiquinone radical in the bo3-type ubiquinol oxidase studied by pulsed electron paramagnetic resonance and hyperfine sublevel correlation spectroscopy. Biochemistry 2001; 40:1037-43. [PMID: 11170426 DOI: 10.1021/bi001641+] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The high-affinity QH ubiquinone-binding site in the bo(3) ubiquinol oxidase from Escherichia coli has been characterized by an investigation of the native ubiquinone radical anion QH(*-) by pulsed electron paramagnetic resonance (EPR) spectroscopy. One- and two-dimensional electron spin-echo envelope modulation (ESEEM) spectra reveal strong interactions of the unpaired electron of QH(*-) with a nitrogen nucleus from the surrounding protein matrix. From analysis of the experimental data, the (14)N nuclear quadrupolar parameters have been determined: kappa = e(2)qQ/4h = 0.93 MHz and eta = 0.50. This assignment is confirmed by hyperfine sublevel correlation (HYSCORE) spectroscopy. On the basis of a comparison of these data with those obtained previously for other membrane-protein bound semiquinone radicals and model systems, this nucleus is assigned to a protein backbone nitrogen. This result is discussed with regard to the location and potential function of QH in the enzyme.
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Affiliation(s)
- S Grimaldi
- Institut für Physikalische und Theoretische Chemie and Institut für Biochemie, J. W. Goethe Universität Frankfurt, D-60439 Frankfurt am Main, Germany
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MacMillan F, Kannt A, Behr J, Prisner T, Michel H. Direct evidence for a tyrosine radical in the reaction of cytochrome c oxidase with hydrogen peroxide. Biochemistry 1999; 38:9179-84. [PMID: 10413492 DOI: 10.1021/bi9911987] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome c oxidase (COX) catalyzes the reduction of oxygen to water, a process which is accompanied by the pumping of four protons across the membrane. Elucidation of the structures of intermediates in these processes is crucial for understanding the mechanism of oxygen reduction. In the work presented here, the reaction of H(2)O(2) with the fully oxidized protein at pH 6.0 has been investigated with electron paramagnetic resonance (EPR) spectroscopy. The results reveal an EPR signal with partially resolved hyperfine structure typical of an organic radical. The yield of this radical based on comparison with other paramagnetic centers in COX was approximately 20%. Recent crystallographic data have shown that one of the Cu(B) ligands, His 276 (in the bacterial case), is cross-linked to Tyr 280 and that this cross-linked tyrosine is ideally positioned to participate in dioxygen activation. Here selectively deuterated tyrosine has been incorporated into the protein, and a drastic change in the line shape of the EPR signal observed above has been detected. This would suggest that the observed EPR signal does indeed arise from a tyrosine radical species. It would seem also quite possible that this radical is an intermediate in the mechanism of oxygen reduction.
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Affiliation(s)
- F MacMillan
- Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität Frankfurt, Germany.
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Weis V, Mobius K, Prisner T. Optically detected electron spin echo envelope modulation on a photoexcited triplet state in zero magnetic field-A comparison between the zero-field and high-field limits. J Magn Reson 1998; 131:17-24. [PMID: 9533901 DOI: 10.1006/jmre.1997.1340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Electron spin echo envelope modulation (ESEEM) has been studied at zero and low magnetic fields (B </= 100 G) by means of optically detected magnetic resonance. Qualitative differences of the ESEEM effect for an electronic triplet state (S = 1) under low-field and high-field conditions are observed and discussed. They are related to the different properties of the total spin angular momentum operator S and the hyperfine interaction at zero and high magnetic field. The novel method was applied to the photoexcited triplet state of acridine-d9 in a fluorene-h10 matrix. An analysis of the observed nitrogen quadrupole splitting is done by a quantitative description of the ESEEM effect in zero field. Copyright 1998 Academic Press.
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Affiliation(s)
- V Weis
- Institut fur Experimentalphysik, Freie Universitat Berlin, Arnimallee 14, Berlin, 14 195, Germany
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38
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van der Est A, Prisner T, Bittl R, Fromme P, Lubitz W, Möbius K, Stehlik D. Time-Resolved X-, K-, and W-Band EPR of the Radical Pair State of Photosystem I in Comparison with in Bacterial Reaction Centers. J Phys Chem B 1997. [DOI: 10.1021/jp9622086] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. van der Est
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max Volmer Institut, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - T. Prisner
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max Volmer Institut, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - R. Bittl
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max Volmer Institut, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - P. Fromme
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max Volmer Institut, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - W. Lubitz
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max Volmer Institut, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - K. Möbius
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max Volmer Institut, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - D. Stehlik
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max Volmer Institut, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
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Weiland B, Hüttermann J, van Tol J, Johnen E, Fuhs M, Prisner T, Vrieze J, Roos BO, Vallance C, Wood BR. Primary Free Radical Formation in Randomly Oriented DNA: EPR Spectroscopy at 245 GHz. ACTA ACUST UNITED AC 1997. [DOI: 10.3891/acta.chem.scand.51-0585] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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40
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Elger G, Kurreck H, Wiehe A, Johnen E, Fuhs M, Prisner T, Vrieze J, Roos BO, Vallance C, Wood BR. Models for Photosynthesis: EPR Studies of Cyclohexylene-Linked Porphyrin Quinones. ACTA ACUST UNITED AC 1997. [DOI: 10.3891/acta.chem.scand.51-0593] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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41
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Geyer M, Schweins T, Herrmann C, Prisner T, Wittinghofer A, Kalbitzer HR. Conformational transitions in p21ras and in its complexes with the effector protein Raf-RBD and the GTPase activating protein GAP. Biochemistry 1996; 35:10308-20. [PMID: 8756686 DOI: 10.1021/bi952858k] [Citation(s) in RCA: 190] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
31P NMR revealed that the complex of p21ras with the GTP analog GppNHp.Mg2+ exists in two conformational states, states 1 and 2. In wild-type p21ras the equilibrium constant K1(12) between the two states is 1.09. The population of these states is different for various mutants but independent of temperature. The activation enthalpy delta H ++ and activation entropy delta S ++ for the conformational transitions were determined by full-exchange matrix analysis for wild-type p21ras and p21ras(S65P). For the wild-type protein one obtains delta H ++ = 89 +/- 2 kJ mol-1 and delta S ++ = 102 +/- 20 J mol-1 K-1 and for the mutant protein delta H ++ = 93 +/- 7 kJ mol-1 and delta S ++ = 138 +/- 30 J mol-1 K-1. The study of various p21ras mutants suggests that the two states correspond to different conformations of loop L2, with Tyr-32 in two different positions relative to the bound nucleotide. High-field EPR at 95 GHz suggest that the observed conformational transition does not directly influence the coordination sphere of the protein-bound metal ion. The influence of this transition on loop L4 was studied by 1H NMR with mutants E62H and E63H. There was no indication that L4 takes part in the transition described in L2, although a reversible conformational change could be induced by decreasing the pH value. The exchange between the two states is slow on the NMR time scale (< 10 s-1): at approximately pH 5 the population of the two states is equal. The interaction of p21ras-triphosphate complexes with the Ras-binding domain (RBD) of the effector protein c-Raf-1, Raf-RBD, and with the GTPase activating protein GAP was studied by 31P NMR spectroscopy. In complex with Raf-RBD the second conformation of p21ras (state 2) is stabilized. In this conformation Tyr-32 is located in close proximity to the phosphate groups of the nucleotide, and the beta-phosphate resonance is shifted upfield by 0.7 ppm. Spectra obtained in the presence of GAP suggest that in the ground state GAP does not interact directly with the nucleotide bound to p21ras and does not induce larger conformational changes in the neighborhood of the nucleotide. The experimental data are consistent with a picture where GAP accelerates the exchange process between the two states and simultaneously increases the population of state 1 at higher temperature.
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Affiliation(s)
- M Geyer
- Max-Planck-Institut für medizinische Forschung, Berlin, Germany
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Fuchs M, von Gersdorff J, Dieks H, Kurreck H, Möbius K, Prisner T. Transient optical absorption and time-resolved resonance Raman experiments on covalently linked porphyrin–quinone systems. ACTA ACUST UNITED AC 1996. [DOI: 10.1039/ft9969200949] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Prisner T, Dinse K. Determination of the deuteron quadrupole coupling tensor in the photo-excited triplet state of dibromobenzophenone by electron spin echo envelope modulation. Chem Phys 1990. [DOI: 10.1016/0301-0104(90)80036-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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