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Abstract
Different types of spin labels are currently available for structural studies of biomolecules both in vitro and in cells using Electron Paramagnetic Resonance (EPR) and pulse dipolar spectroscopy (PDS). Each type of label has its own advantages and disadvantages, that will be addressed in this chapter. The spectroscopically distinct properties of the labels have fostered new applications of PDS aimed to simultaneously extract multiple inter-label distances on the same sample. In fact, combining different labels and choosing the optimal strategy to address their inter-label distances can increase the information content per sample, and this is pivotal to better characterize complex multi-component biomolecular systems. In this review, we provide a brief background of the spectroscopic properties of the four most common orthogonal spin labels for PDS measurements and focus on the various methods at disposal to extract homo- and hetero-label distances in proteins. We also devote a section to possible artifacts arising from channel crosstalk and provide few examples of applications in structural biology.
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2
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Tkach I, Diederichsen U, Bennati M. Studies of transmembrane peptides by pulse dipolar spectroscopy with semi-rigid TOPP spin labels. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:143-157. [PMID: 33640998 PMCID: PMC8071797 DOI: 10.1007/s00249-021-01508-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 12/01/2022]
Abstract
Electron paramagnetic resonance (EPR)-based pulsed dipolar spectroscopy measures the dipolar interaction between paramagnetic centers that are separated by distances in the range of about 1.5-10 nm. Its application to transmembrane (TM) peptides in combination with modern spin labelling techniques provides a valuable tool to study peptide-to-lipid interactions at a molecular level, which permits access to key parameters characterizing the structural adaptation of model peptides incorporated in natural membranes. In this mini-review, we summarize our approach for distance and orientation measurements in lipid environment using novel semi-rigid TOPP [4-(3,3,5,5-tetramethyl-2,6-dioxo-4-oxylpiperazin-1-yl)-L-phenylglycine] labels specifically designed for incorporation in TM peptides. TOPP labels can report single peak distance distributions with sub-angstrom resolution, thus offering new capabilities for a variety of TM peptide investigations, such as monitoring of various helix conformations or measuring of tilt angles in membranes.
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Affiliation(s)
- Igor Tkach
- Max Planck Institute for Biophysical Chemistry, RG Electron-Spin Resonance Spectroscopy, 37077, Göttingen, Germany.
| | - Ulf Diederichsen
- Department of Organic and Biomolecular Chemistry, University of Göttingen, 37077, Göttingen, Germany
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, RG Electron-Spin Resonance Spectroscopy, 37077, Göttingen, Germany
- Department of Organic and Biomolecular Chemistry, University of Göttingen, 37077, Göttingen, Germany
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3
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Teucher M, Qi M, Cati N, Hintz H, Godt A, Bordignon E. Strategies to identify and suppress crosstalk signals in double electron-electron resonance (DEER) experiments with gadolinium III and nitroxide spin-labeled compounds. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:285-299. [PMID: 37904822 PMCID: PMC10500692 DOI: 10.5194/mr-1-285-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/31/2020] [Indexed: 11/01/2023]
Abstract
Double electron-electron resonance (DEER) spectroscopy applied to orthogonally spin-labeled biomolecular complexes simplifies the assignment of intra- and intermolecular distances, thereby increasing the information content per sample. In fact, various spin labels can be addressed independently in DEER experiments due to spectroscopically nonoverlapping central transitions, distinct relaxation times, and/or transition moments; hence, they are referred to as spectroscopically orthogonal. Molecular complexes which are, for example, orthogonally spin-labeled with nitroxide (NO) and gadolinium (Gd) labels give access to three distinct DEER channels that are optimized to selectively probe NO-NO, NO-Gd, and Gd-Gd distances. Nevertheless, it has been previously recognized that crosstalk signals between individual DEER channels can occur, for example, when a Gd-Gd distance appears in a DEER channel optimized to detect NO-Gd distances. This is caused by residual spectral overlap between NO and Gd spins which, therefore, cannot be considered as perfectly orthogonal. Here, we present a systematic study on how to identify and suppress crosstalk signals that can appear in DEER experiments using mixtures of NO-NO, NO-Gd, and Gd-Gd molecular rulers characterized by distinct, nonoverlapping distance distributions. This study will help to correctly assign the distance peaks in homo- and heterocomplexes of biomolecules carrying not perfectly orthogonal spin labels.
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Affiliation(s)
- Markus Teucher
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Ninive Cati
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Henrik Hintz
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
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4
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Wu Z, Feintuch A, Collauto A, Adams LA, Aurelio L, Graham B, Otting G, Goldfarb D. Selective Distance Measurements Using Triple Spin Labeling with Gd 3+, Mn 2+, and a Nitroxide. J Phys Chem Lett 2017; 8:5277-5282. [PMID: 28990781 DOI: 10.1021/acs.jpclett.7b01739] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Distance measurements by pulse electron paramagnetic resonance techniques, such as double electron-electron resonance (DEER, also called PELDOR), have become an established tool to explore structural properties of biomacromolecules and their assemblies. In such measurements a pair of spin labels provides a single distance constraint. Here we show that by employing three different types of spin labels that differ in their spectroscopic and spin dynamics properties it is possible to extract three independent distances from a single sample. We demonstrate this using the Antennapedia homeodomain orthogonally labeled with Gd3+ and Mn2+ tags in complex with its cognate DNA binding site labeled with a nitroxide.
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Affiliation(s)
- Zuyan Wu
- Research School of Chemistry, Australian National University , Canberra ACT 2601, Australia
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Alberto Collauto
- Department of Chemical Physics, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Luke A Adams
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
| | - Luigi Aurelio
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University , Canberra ACT 2601, Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science , Rehovot 76100, Israel
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5
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Tseytlin M. Concept of Phase Cycling in Pulsed Magnetic Resonance Using Sinusoidal Magnetic Field Modulation. ACTA ACUST UNITED AC 2017; 231:689-703. [PMID: 28751814 DOI: 10.1515/zpch-2016-0843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In conventional pulsed magnetic resonance suppression of unwanted signals is achieved by changing pulse phases with respect to the reference signal and spin magnetization phase. This method is called phase cycling. An alternative approach is suggested to separate the unwanted signals from the spin echo by using magnetic field modulation. Precession frequency of the spins, and therefore phases of free indication decays and echo signals, can be controlled by the selection of modulation parameters. This enables phase cycling. Since the signal is detected in the presence of the changing magnetic field, which drives spin precession, the echo signal is frequency-modulated. Numerical transformation into an accelerating reference frame associated with the Larmor frequency restores the signal to a form that would have been observed in the absence of modulation. The suggested phase cycling method is analyzed in detail for the two pulse spin echo case.
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Affiliation(s)
- Mark Tseytlin
- Department of Biochemistry, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Center for EPR Imaging In Vivo Physiology, Department of Radiation and Cellular Oncology, University of Chicago, IL, USA
- In vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, USA
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6
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Doll A, Qi M, Godt A, Jeschke G. CIDME: Short distances measured with long chirp pulses. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 273:73-82. [PMID: 27788378 DOI: 10.1016/j.jmr.2016.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/10/2016] [Accepted: 10/14/2016] [Indexed: 06/06/2023]
Abstract
Frequency-swept pulses have recently been introduced as pump pulses into double electron-electron resonance (DEER) experiments. A limitation of this approach is that the pump pulses need to be short in comparison to dipolar evolution periods. The "chirp-induced dipolar modulation enhancement" (CIDME) pulse sequence introduced in this work circumvents this limitation by means of longitudinal storage during the application of one single or two consecutive pump pulses. The resulting six-pulse sequence is closely related to the five-pulse "relaxation-induced dipolar modulation enhancement" (RIDME) pulse sequence: While dipolar modulation in RIDME is due to stochastic spin flips during longitudinal storage, modulation in CIDME is due to the pump pulse during longitudinal storage. Experimentally, CIDME is examined for Gd-Gd and nitroxide-nitroxide distance determination using a high-power Q-band spectrometer. Since longitudinal storage results in a 50% signal loss, comparisons between DEER using short chirp pump pulses of 64ns duration and CIDME using longer pump pulses are in favor of DEER. While the lower sensitivity restrains the applicability of CIDME for routine distance determination on high-power spectrometers, this result is not to be generalized to spectrometers having lower power and to specialized "non-routine" applications or different types of spin labels. In particular, the advantage of prolonged CIDME pump pulses is demonstrated for experiments at large frequency offset between the pumped and observed spins. At a frequency separation of 1GHz, where broadening due to dipolar pseudo-secular contributions becomes largely suppressed, a Gd-Gd modulation depth larger than 10% is achieved. Moreover, a CIDME experiment at deliberately reduced power underlines the potential of the new technique for spectrometers with lower power, as often encountered at higher microwave frequencies. With longitudinal storage times T below 10μs, however, CIDME appears rather susceptible to artifacts. For nitroxide-nitroxide experiments, these currently inhibit a faithful data analysis. To facilitate further developments, the artifacts are characterized experimentally. In addition, effects that are specific to the high spin of S=7/2 Gd-centers are examined. Herein, population transfer within the observer spin's multiplet due to the pump pulse as well as excitation of dipolar harmonics are discussed.
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Affiliation(s)
- Andrin Doll
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials, Bielefeld University, Unversitätsstraße 25, 33615 Bielefeld, Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials, Bielefeld University, Unversitätsstraße 25, 33615 Bielefeld, Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland.
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7
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Keller K, Zalibera M, Qi M, Koch V, Wegner J, Hintz H, Godt A, Jeschke G, Savitsky A, Yulikov M. EPR characterization of Mn(ii) complexes for distance determination with pulsed dipolar spectroscopy. Phys Chem Chem Phys 2016; 18:25120-25135. [DOI: 10.1039/c6cp04884f] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
EPR properties of four Mn(ii) complexes and Tikhonov regularization-based analysis of RIDME data containing dipolar overtones are presented.
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Affiliation(s)
- Katharina Keller
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Michal Zalibera
- Max Planck Institut for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
- Institute of Physical Chemistry and Chemical Physics
- Slovak University of Technology in Bratislava
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Vanessa Koch
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Julia Wegner
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Henrik Hintz
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Anton Savitsky
- Max Planck Institut for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Maxim Yulikov
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
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8
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Cohen MR, Frydman V, Milko P, Iron MA, Abdelkader EH, Lee MD, Swarbrick JD, Raitsimring A, Otting G, Graham B, Feintuch A, Goldfarb D. Overcoming artificial broadening in Gd3+–Gd3+ distance distributions arising from dipolar pseudo-secular terms in DEER experiments. Phys Chem Chem Phys 2016; 18:12847-59. [DOI: 10.1039/c6cp00829a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Double electron–electron resonance (DEER) is used to probe structure of Gd3+-tagged biomolecules by determining Gd3+–Gd3+ distances.
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Affiliation(s)
- Marie Ramirez Cohen
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Veronica Frydman
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Petr Milko
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Mark A. Iron
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Elwy H. Abdelkader
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | | | - Gottfried Otting
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Akiva Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
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9
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Endeward B, Marko A, Denysenkov VP, Sigurdsson ST, Prisner TF. Advanced EPR Methods for Studying Conformational Dynamics of Nucleic Acids. Methods Enzymol 2015; 564:403-25. [PMID: 26477259 DOI: 10.1016/bs.mie.2015.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Pulsed electron paramagnetic resonance (EPR) spectroscopy has become an important tool for structural characterization of biomolecules allowing measurement of the distances between two paramagnetic spin labels attached to a biomolecule in the 2-8 nm range. In this chapter, we will focus on applications of this approach to investigate tertiary structure elements as well as conformational dynamics of nucleic acid molecules. Both aspects take advantage of using specific spin labels that are rigidly attached to the nucleobases, as they allow obtaining not only the distance but also the relative orientation between both nitroxide moieties with high accuracy. Thus, not only the distance but additionally the three Euler angles between both the nitroxide axis systems and the two polar angles of the interconnecting vector with respect to the nitroxide axis systems can be extracted from a single pair of spin labels. To extract all these parameters independently and unambiguously, a set of multifrequency/multifield pulsed EPR experiments have to be performed. We will describe the experimental procedure as well as newly developed spin labels, which are helpful to disentangle all these parameters, and tools which we have developed to analyze such data sets. The procedures and analyses will be illustrated by examples from our laboratory.
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Affiliation(s)
- B Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - A Marko
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - V P Denysenkov
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - S Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Reykjavık, Iceland
| | - T F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.
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10
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Vincent Ching HY, Demay-Drouhard P, Bertrand HC, Policar C, Tabares LC, Un S. Nanometric distance measurements between Mn(ii)DOTA centers. Phys Chem Chem Phys 2015; 17:23368-77. [DOI: 10.1039/c5cp03487f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The distance between two Mn(ii)DOTA complexes attached to the ends of polyproline helices of varying lengths was measured by 94 GHz PELDOR spectroscopy with good accuracy demonstrating their effectiveness as spin-labels.
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Affiliation(s)
- H. Y. Vincent Ching
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
| | - Paul Demay-Drouhard
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Hélène C. Bertrand
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Clotilde Policar
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Leandro C. Tabares
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
| | - Sun Un
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
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11
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Dalaloyan A, Qi M, Ruthstein S, Vega S, Godt A, Feintuch A, Goldfarb D. Gd(iii)–Gd(iii) EPR distance measurements – the range of accessible distances and the impact of zero field splitting. Phys Chem Chem Phys 2015; 17:18464-76. [DOI: 10.1039/c5cp02602d] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gd rulers were designed in the 2–8 nm range for in-depth evaluation of Gd(iii) complexes as spin labels for EPR distance measurements.
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Affiliation(s)
- Arina Dalaloyan
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Mian Qi
- Bielefeld University
- Faculty of Chemistry and Center for Molecular Materials
- D-33615 Bielefeld
- Germany
| | - Sharon Ruthstein
- Department of Chemistry
- Faculty of Exact Sciences
- Bar-Ilan University
- Ramat Gan
- Israel
| | - Shimon Vega
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Adelheid Godt
- Bielefeld University
- Faculty of Chemistry and Center for Molecular Materials
- D-33615 Bielefeld
- Germany
| | - Akiva Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
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12
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Doll A, Qi M, Pribitzer S, Wili N, Yulikov M, Godt A, Jeschke G. Sensitivity enhancement by population transfer in Gd(iii) spin labels. Phys Chem Chem Phys 2015; 17:7334-44. [DOI: 10.1039/c4cp05893c] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Frequency-swept chirp pulses with bandwidths > 1 GHz rearrange electron spin populations in the S = 7/2 spin of Gd(iii) ions for better sensitivity, as demonstrated with distance measurements between Gd(iii) ions.
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Affiliation(s)
- Andrin Doll
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials
- Bielefeld University
- 33615 Bielefeld
- Germany
| | | | - Nino Wili
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
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13
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Goldfarb D. Gd3+ spin labeling for distance measurements by pulse EPR spectroscopy. Phys Chem Chem Phys 2014; 16:9685-99. [DOI: 10.1039/c3cp53822b] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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14
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Hubbell WL, López CJ, Altenbach C, Yang Z. Technological advances in site-directed spin labeling of proteins. Curr Opin Struct Biol 2013; 23:725-33. [PMID: 23850140 DOI: 10.1016/j.sbi.2013.06.008] [Citation(s) in RCA: 232] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/12/2013] [Indexed: 12/23/2022]
Abstract
Molecular flexibility over a wide time range is of central importance to the function of many proteins, both soluble and membrane. Revealing the modes of flexibility, their amplitudes, and time scales under physiological conditions is the challenge for spectroscopic methods, one of which is site-directed spin labeling EPR (SDSL-EPR). Here we provide an overview of some recent technological advances in SDSL-EPR related to investigation of structure, structural heterogeneity, and dynamics of proteins. These include new classes of spin labels, advances in measurement of long range distances and distance distributions, methods for identifying backbone and conformational fluctuations, and new strategies for determining the kinetics of protein motion.
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Affiliation(s)
- Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States.
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15
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Raitsimring A, Astashkin AV, Enemark J, Kaminker I, Goldfarb D, Walter ED, Song Y, Meade TJ. Optimization of pulsed DEER measurements for Gd-based labels: choice of operational frequencies, pulse durations and positions, and temperature. APPLIED MAGNETIC RESONANCE 2013; 44:649-670. [PMID: 23687407 PMCID: PMC3654798 DOI: 10.1007/s00723-012-0434-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In this work, the experimental conditions and parameters necessary to optimize the long-distance (≥ 60 Å) Double Electron-Electron Resonance (DEER) measurements of biomacromolecules labeled with Gd(III) tags are analyzed. The specific parameters discussed are the temperature, microwave band, the separation between the pumping and observation frequencies, pulse train repetition rate, pulse durations and pulse positioning in the electron paramagnetic resonance spectrum. It was found that: (i) in optimized DEER measurements, the observation pulses have to be applied at the maximum of the EPR spectrum; (ii) the optimal temperature range for Ka-band measurements is 14-17 K, while in W-band the optimal temperatures are between 6-9 K; (iii) W-band is preferable to Ka-band for DEER measurements. Recent achievements and the conditions necessary for short-distance measurements (<15 Å) are also briefly discussed.
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Affiliation(s)
- A. Raitsimring
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0041, USA
| | - A. V. Astashkin
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0041, USA
| | - J.H. Enemark
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0041, USA
| | - I. Kaminker
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - D. Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - E. D. Walter
- Pacific Northwest National Laboratory, EMSL, 3335 Q Ave, Richland, WA 99354, USA
| | - Y. Song
- Department of Chemistry; Department of Biochemistry, Cell Biology, and Molecular Biology; Neurobiology & Physiology; Department of Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - T. J. Meade
- Department of Chemistry; Department of Biochemistry, Cell Biology, and Molecular Biology; Neurobiology & Physiology; Department of Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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16
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Doll A, Pribitzer S, Tschaggelar R, Jeschke G. Adiabatic and fast passage ultra-wideband inversion in pulsed EPR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 230:27-39. [PMID: 23434533 DOI: 10.1016/j.jmr.2013.01.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 01/04/2013] [Accepted: 01/09/2013] [Indexed: 05/12/2023]
Abstract
We demonstrate that adiabatic and fast passage ultra-wideband (UWB) pulses can achieve inversion over several hundreds of MHz and thus enhance the measurement sensitivity, as shown by two selected experiments. Technically, frequency-swept pulses are generated by a 12 GS/s arbitrary waveform generator and upconverted to X-band frequencies. This pulsed UWB source is utilized as an incoherent channel in an ordinary pulsed EPR spectrometer. We discuss experimental methodologies and modeling techniques to account for the response of the resonator, which can strongly limit the excitation bandwidth of the entire non-linear excitation chain. Aided by these procedures, pulses compensated for bandwidth or variations in group delay reveal enhanced inversion efficiency. The degree of bandwidth compensation is shown to depend critically on the time available for excitation. As a result, we demonstrate optimized inversion recovery and double electron electron resonance (DEER) experiments. First, virtually complete inversion of the nitroxide spectrum with an adiabatic pulse of 128ns length is achieved. Consequently, spectral diffusion between inverted and non-inverted spins is largely suppressed and the observation bandwidth can be increased to increase measurement sensitivity. Second, DEER is performed on a terpyridine-based copper (II) complex with a nitroxide-copper distance of 2.5nm. As previously demonstrated on this complex, when pumping copper spins and observing nitroxide spins, the modulation depth is severely limited by the excitation bandwidth of the pump pulse. By using fast passage UWB pulses with a maximum length of 64ns, we achieve up to threefold enhancement of the modulation depth. Associated artifacts in distance distributions when increasing the bandwidth of the pump pulse are shown to be small.
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Affiliation(s)
- Andrin Doll
- ETH Zurich, Laboratory of Physical Chemistry, Wolfgang-Pauli-Str. 10, CH-8093 Zurich, Switzerland
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17
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Reichenwallner J, Hinderberger D. Using bound fatty acids to disclose the functional structure of serum albumin. Biochim Biophys Acta Gen Subj 2013; 1830:5382-93. [PMID: 23643928 DOI: 10.1016/j.bbagen.2013.04.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/23/2013] [Accepted: 04/24/2013] [Indexed: 11/16/2022]
Abstract
BACKGROUND Serum albumin is a major transport protein in mammals and is known to have at least seven binding sites for long-chain fatty acids (FAs). SCOPE OF REVIEW We have devised a new electron paramagnetic resonance (EPR) spectroscopic approach to gain information on the functional structure of serum albumin in solution in a "coarse-grained" manner from the ligands' point of view. Our approach is based on using spin labeled (paramagnetic) stearic acids self-assembled with albumin and subsequent nanoscale distance measurements between the FAs using double electron-electron resonance spectroscopy (DEER). Simple continuous wave (CW) EPR spectroscopy, which allows for quantification of bound ligands, complements our studies. MAJOR CONCLUSIONS Based on DEER nanoscale distance measurements, the functional solution structure of human serum albumin (HSA) has remarkably been found to have a much more symmetric distribution of entry points to the FA binding sites than expected from the crystal structure, indicating increased surface flexibility and plasticity for HSA in solution. In contrast, for bovine serum albumin (BSA), the entry point topology is in good agreement with that expected from the crystal structure of HSA. Changes in the solution structures between albumins can hence be revealed and extended to more albumins to detect functional differences at the nanoscale. Going beyond fundamental structural studies, our research platform is also excellently suited for general studies of protein-solvent interactions, temperature effects and ligand binding. GENERAL SIGNIFICANCE We discuss how our research platform helps illuminate protein dynamics and function and can be used to characterize albumin-based hybrid materials. This article is part of a Special Issue entitled Serum Albumin.
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Affiliation(s)
- Jörg Reichenwallner
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany; Institute for Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, Johann-Joachim-Becher-Weg 30, D-55128 Mainz, Germany
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18
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Synthesis of spin-labeled riboswitch RNAs using convertible nucleosides and DNA-catalyzed RNA ligation. Bioorg Med Chem 2013; 21:6171-80. [PMID: 23664496 DOI: 10.1016/j.bmc.2013.04.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/21/2013] [Accepted: 04/05/2013] [Indexed: 12/23/2022]
Abstract
Chemically stable nitroxide radicals that can be monitored by electron paramagnetic resonance (EPR) spectroscopy can provide information on structural and dynamic properties of functional RNA such as riboswitches. The convertible nucleoside approach is used to install 2,2,6,6-tetramethylpiperidin-1-oxyl (TEMPO) and 2,2,5,5-tetramethylpyrrolidin-1-oxyl (proxyl) labels at the exocyclic N(4)-amino group of cytidine and 2'-O-methylcytidine nucleotides in RNA. To obtain site-specifically labeled long riboswitch RNAs beyond the limit of solid-phase synthesis, we report the ligation of spin-labeled RNA using an in vitro selected deoxyribozyme as catalyst, and demonstrate the synthesis of TEMPO-labeled 53 nt SAM-III and 118 nt SAM-I riboswitch domains (SAM=S-adenosylmethionine).
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19
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Lueders P, Jäger H, Hemminga MA, Jeschke G, Yulikov M. Distance Measurements on Orthogonally Spin-Labeled Membrane Spanning WALP23 Polypeptides. J Phys Chem B 2013; 117:2061-8. [DOI: 10.1021/jp311287t] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Petra Lueders
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
| | - Heidrun Jäger
- Laboratory
of Biophysics, Wageningen University, Wageningen,
The Netherlands
| | - Marcus A. Hemminga
- Laboratory
of Biophysics, Wageningen University, Wageningen,
The Netherlands
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
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20
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Tkach I, Pornsuwan S, Höbartner C, Wachowius F, Sigurdsson ST, Baranova TY, Diederichsen U, Sicoli G, Bennati M. Orientation selection in distance measurements between nitroxide spin labels at 94 GHz EPR with variable dual frequency irradiation. Phys Chem Chem Phys 2013; 15:3433-7. [PMID: 23381580 DOI: 10.1039/c3cp44415e] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pulsed electron-electron double resonance (PELDOR, also known as DEER) has become a method of choice to measure distances in biomolecules. In this work we show how the performance of the method can be improved at high EPR frequencies (94 GHz) using variable dual frequency irradiation in a dual mode cavity in order to obtain enhanced resolution toward orientation selection. Dipolar evolution traces of a representative RNA duplex and an α-helical peptide were analysed in terms of possible bi-radical structures by considering the inherent ambiguity of symmetry-related solutions.
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Affiliation(s)
- Igor Tkach
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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21
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Kaminker I, Tkach I, Manukovsky N, Huber T, Yagi H, Otting G, Bennati M, Goldfarb D. W-band orientation selective DEER measurements on a Gd3+/nitroxide mixed-labeled protein dimer with a dual mode cavity. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 227:66-71. [PMID: 23314001 DOI: 10.1016/j.jmr.2012.11.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 11/29/2012] [Accepted: 11/29/2012] [Indexed: 06/01/2023]
Abstract
Double electron-electron resonance (DEER) at W-band (95 GHz) was applied to measure the distance between a pair of nitroxide and Gd(3+) chelate spin labels, about 6 nm apart, in a homodimer of the protein ERp29. While high-field DEER measurements on systems with such mixed labels can be highly attractive in terms of sensitivity and the potential to access long distances, a major difficulty arises from the large frequency spacing (about 700 MHz) between the narrow, intense signal of the Gd(3+) central transition and the nitroxide signal. This is particularly problematic when using standard single-mode cavities. Here we show that a novel dual-mode cavity that matches this large frequency separation dramatically increases the sensitivity of DEER measurements, allowing evolution times as long as 12 μs in a protein. This opens the possibility of accessing distances of 8 nm and longer. In addition, orientation selection can be resolved and analyzed, thus providing additional structural information. In the case of W-band DEER on a Gd(3+)-nitroxide pair, only two angles and their distributions have to be determined, which is a much simpler problem to solve than the five angles and their distributions associated with two nitroxide spin labels.
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Affiliation(s)
- Ilia Kaminker
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
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22
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Orientation-Selective DEER Using Rigid Spin Labels, Cofactors, Metals, and Clusters. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2013. [DOI: 10.1007/430_2013_115] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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23
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Borbat PP, Freed JH. Pulse Dipolar Electron Spin Resonance: Distance Measurements. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2013. [DOI: 10.1007/430_2012_82] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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Höbartner C, Sicoli G, Wachowius F, Gophane DB, Sigurdsson ST. Synthesis and Characterization of RNA Containing a Rigid and Nonperturbing Cytidine-Derived Spin Label. J Org Chem 2012; 77:7749-54. [DOI: 10.1021/jo301227w] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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Türke MT, Bennati M. Comparison of Overhauser DNP at 0.34 and 3.4 T with Frémy's Salt. APPLIED MAGNETIC RESONANCE 2012; 43:129-138. [PMID: 22815593 PMCID: PMC3396338 DOI: 10.1007/s00723-012-0362-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/11/2012] [Indexed: 05/05/2023]
Abstract
Dynamic nuclear polarization (DNP) is investigated in the liquid state using a model system of Frémy's salt dissolved in water. Nuclear magnetic resonance signal enhancements at 0.34 and 3.4 T of the bulk water protons are recorded as a function of the irradiation time and the polarizer concentration. The build-up rates are consistent with the T(1n) of the observed water protons at room temperature (for 9 GHz/0.34 T) and for about 50 ± 10 °C at 94 GHz/3.4 T. At 94 GHz/3.4 T, we observe in our setup a maximal enhancement of -50 at 25 mM polarizer concentration. The use of Frémy's salt allows the determination of the saturation factors at 94 GHz by pulsed ELDOR experiments. The results are well consistent with the Overhauser DNP mechanism and indicate that higher enhancements at this intermediate frequency require higher sample temperatures.
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Affiliation(s)
- M.-T. Türke
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - M. Bennati
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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26
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Raitsimring A, Astashkin A, Enemark JH, Blank A, Twig Y, Song Y, Meade TJ. Dielectric Resonator for Ka-Band Pulsed EPR Measurements at Cryogenic Temperatures: Probehead Construction and Applications. APPLIED MAGNETIC RESONANCE 2012; 42:441-452. [PMID: 23626406 PMCID: PMC3634706 DOI: 10.1007/s00723-012-0313-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The construction and performance of a Ka-band pulsed electron paramagnetic resonance (EPR) cryogenic probehead that incorporates dielectric resonator (DR) is presented. We demonstrate that the use of DR allows one to optimize pulsed double electron-electron resonance (DEER) measurements utilizing large resonator bandwidth and large amplitude of the microwave field B1 . In DEER measurements of Gd-based spin labels, use of this probe finally allows one to implement the potentials of Gd-based labels in distance measurements. Evidently, this DR is well suited to any applications requiring large B1-fields and resonator bandwidths, such as electron spin echo envelope modulation spectroscopy of nuclei having low magnetic moments and strong hyperfine interactions and double quantum coherence dipolar spectroscopy as was recently demonstrated in the application of a similar probe based on an loop-gap resonator and reported by Forrer et al. (J Magn Reson 190:280, 2008).
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Affiliation(s)
- A. Raitsimring
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd, Tucson, AZ 85721-0041, USA
| | - A. Astashkin
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd, Tucson, AZ 85721-0041, USA
| | - J. H. Enemark
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd, Tucson, AZ 85721-0041, USA
| | - A. Blank
- Schulich Faculty of Chemistry, Technion, Israel Institute of Technology, 32000 Haifa, Israel
| | - Y. Twig
- Schulich Faculty of Chemistry, Technion, Israel Institute of Technology, 32000 Haifa, Israel
| | - Y. Song
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. Department of Biochemistry, Cell Biology, and Molecular Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. Department of Neurobiology and Physiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. Department of Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - T. J. Meade
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. Department of Biochemistry, Cell Biology, and Molecular Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. Department of Neurobiology and Physiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. Department of Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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27
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Reginsson GW, Hunter RI, Cruickshank PAS, Bolton DR, Sigurdsson ST, Smith GM, Schiemann O. W-band PELDOR with 1 kW microwave power: molecular geometry, flexibility and exchange coupling. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 216:175-182. [PMID: 22386646 DOI: 10.1016/j.jmr.2012.01.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 01/09/2012] [Accepted: 01/29/2012] [Indexed: 05/31/2023]
Abstract
A technique that is increasingly being used to determine the structure and conformational flexibility of biomacromolecules is Pulsed Electron-Electron Double Resonance (PELDOR or DEER), an Electron Paramagnetic Resonance (EPR) based technique. At X-band frequencies (9.5 GHz), PELDOR is capable of precisely measuring distances in the range of 1.5-8 nm between paramagnetic centres but the orientation selectivity is weak. In contrast, working at higher frequencies increases the orientation selection but usually at the expense of decreased microwave power and PELDOR modulation depth. Here it is shown that a home-built high-power pulsed W-band EPR spectrometer (HiPER) with a large instantaneous bandwidth enables one to achieve PELDOR data with a high degree of orientation selectivity and large modulation depths. We demonstrate a measurement methodology that gives a set of PELDOR time traces that yield highly constrained data sets. Simulating the resulting time traces provides a deeper insight into the conformational flexibility and exchange coupling of three bisnitroxide model systems. These measurements provide strong evidence that W-band PELDOR may prove to be an accurate and quantitative tool in assessing the relative orientations of nitroxide spin labels and to correlate those orientations to the underlying biological structure and dynamics.
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Affiliation(s)
- Gunnar W Reginsson
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
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28
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Kaminker I, Yagi H, Huber T, Feintuch A, Otting G, Goldfarb D. Spectroscopic selection of distance measurements in a protein dimer with mixed nitroxide and Gd3+ spin labels. Phys Chem Chem Phys 2012; 14:4355-8. [DOI: 10.1039/c2cp40219j] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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