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Goldfarb D. Exploring protein conformations in vitro and in cell with EPR distance measurements. Curr Opin Struct Biol 2022; 75:102398. [PMID: 35667279 DOI: 10.1016/j.sbi.2022.102398] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/20/2022] [Accepted: 04/30/2022] [Indexed: 11/18/2022]
Abstract
The electron-electron double resonance (DEER) method, which provides distance distributions between two spin labels, attached site specifically to biomolecules (proteins and nucleic acids), is currently a well-recognized biophysical tool in structural biology. The most commonly used spin labels are based on nitroxide stable radicals, conjugated to the proteins primarily via native or engineered cysteine residues. However, in recent years, new spin labels, along with different labeling chemistries, have been introduced, driven in part by the desire to study structural and dynamical properties of biomolecules in their native environment, the cell. This mini-review focuses on these new spin labels, which allow for DEER on orthogonal spin labels, and on the state of the art methods for in-cell DEER distance measurements.
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Affiliation(s)
- Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 761001, Israel
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2
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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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3
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Bahrenberg T, Yardeni EH, Feintuch A, Bibi E, Goldfarb D. Substrate binding in the multidrug transporter MdfA in detergent solution and in lipid nanodiscs. Biophys J 2021; 120:1984-1993. [PMID: 33771471 PMCID: PMC8204392 DOI: 10.1016/j.bpj.2021.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 03/07/2021] [Accepted: 03/15/2021] [Indexed: 10/21/2022] Open
Abstract
MdfA from Escherichia coli is a prototypical secondary multi-drug (Mdr) transporter that exchanges drugs for protons. MdfA-mediated drug efflux is driven by the proton gradient and enabled by conformational changes that accompany the recruitment of drugs and their release. In this work, we applied distance measurements by W-band double electron-electron resonance (DEER) spectroscopy to explore the binding of mito-TEMPO, a nitroxide-labeled substrate analog, to Gd(III)-labeled MdfA. The choice of Gd(III)-nitroxide DEER enabled measurements in the presence of excess of mito-TEMPO, which has a relatively low affinity to MdfA. Distance measurements between mito-TEMPO and MdfA labeled at the periplasmic edges of either of three selected transmembrane helices (TM3101, TM5168, and TM9310) revealed rather similar distance distributions in detergent micelles (n-dodecyl-β-d-maltopyranoside, DDM)) and in lipid nanodiscs (ND). By grafting the predicted positions of the Gd(III) tag on the inward-facing (If) crystal structure, we looked for binding positions that reproduced the maxima of the distance distributions. The results show that the location of the mito-TEMPO nitroxide in DDM-solubilized or ND-reconstituted MdfA is similar (only 0.4 nm apart). In both cases, we located the nitroxide moiety near the ligand binding pocket in the If structure. However, according to the DEER-derived position, the substrate clashes with TM11, suggesting that for mito-TEMPO-bound MdfA, TM11 should move relative to the If structure. Additional DEER studies with MdfA labeled with Gd(III) at two sites revealed that TM9 also dislocates upon substrate binding. Together with our previous reports, this study demonstrates the utility of Gd(III)-Gd(III) and Gd(III)-nitroxide DEER measurements for studying the conformational behavior of transporters.
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Affiliation(s)
- Thorsten Bahrenberg
- Departments of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Eliane Hadas Yardeni
- Departments of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Akiva Feintuch
- Departments of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Eitan Bibi
- Departments of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - Daniella Goldfarb
- Departments of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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4
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Giannoulis A, Ben-Ishay Y, Goldfarb D. Characteristics of Gd(III) spin labels for the study of protein conformations. Methods Enzymol 2021; 651:235-290. [PMID: 33888206 DOI: 10.1016/bs.mie.2021.01.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gd(III) complexes are currently established as spin labels for structural studies of biomolecules using pulse dipolar electron paramagnetic resonance (PD-EPR) techniques. This has been achieved by the availability of medium- and high-field spectrometers, understanding the spin physics underlying the spectroscopic properties of high spin Gd(III) (S=7/2) pairs and their dipolar interaction, the design of well-defined model compounds and optimization of measurement techniques. In addition, a variety of Gd(III) chelates and labeling schemes have allowed a broad scope of applications. In this review, we provide a brief background of the spectroscopic properties of Gd(III) pertinent for effective PD-EPR measurements and focus on the various labels available to date. We report on their use in PD-EPR applications and highlight their pros and cons for particular applications. We also devote a section to recent in-cell structural studies of proteins using Gd(III), which is an exciting new direction for Gd(III) spin labeling.
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Affiliation(s)
- Angeliki Giannoulis
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Yasmin Ben-Ishay
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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Abstract
Many applications of lanthanides exploit their electron spin relaxation properties. Double electron-electron measurements of distances are possible because of the relatively long relaxation times of Gd3+. Relaxation enhancement measurements of distance are possible because of the much shorter relaxation times of other lanthanides. Magnetic resonance imaging contrast agents use the long relaxation time of the S-state Gd3+ ion, and NMR shift reagents use the fast relaxation of selected other lanthanides. Other than Gd3+ and the isoelectronic Eu2+ ion, spin relaxation of the lanthanides is so fast that their EPR spectra can be observed only in the liquid helium temperature range. In this chapter the EPR properties of each of the lanthanides is briefly summarized, with an emphasis on electron spin relaxation.
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Affiliation(s)
- Joseph E McPeak
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, United States
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, United States
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, United States.
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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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7
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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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8
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Bordignon E, Seeger MA, Galazzo L, Meier G. From in vitro towards in situ: structure-based investigation of ABC exporters by electron paramagnetic resonance spectroscopy. FEBS Lett 2020; 594:3839-3856. [PMID: 33219535 DOI: 10.1002/1873-3468.14004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/30/2020] [Accepted: 11/15/2020] [Indexed: 12/12/2022]
Abstract
ATP-binding cassette (ABC) exporters have been studied now for more than four decades, and recent structural investigation has produced a large number of protein database entries. Yet, important questions about how ABC exporters function at the molecular level remain debated, such as which are the molecular recognition hotspots and the allosteric couplings dynamically regulating the communication between the catalytic cycle and the export of substrates. This conundrum mainly arises from technical limitations confining all research to in vitro analysis of ABC transporters in detergent solutions or embedded in membrane-mimicking environments. Therefore, a largely unanswered question is how ABC exporters operate in situ, namely in the native membrane context of a metabolically active cell. This review focuses on novel mechanistic insights into type I ABC exporters gained through a unique combination of structure determination, biochemical characterization, generation of conformation-specific nanobodies/sybodies and double electron-electron resonance.
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Affiliation(s)
- Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Switzerland
| | - Laura Galazzo
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Gianmarco Meier
- Institute of Medical Microbiology, University of Zurich, Switzerland
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9
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Han CT, Song J, Chan T, Pruett C, Han S. Electrostatic Environment of Proteorhodopsin Affects the pKa of Its Buried Primary Proton Acceptor. Biophys J 2020; 118:1838-1849. [PMID: 32197061 DOI: 10.1016/j.bpj.2020.02.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/27/2020] [Accepted: 02/27/2020] [Indexed: 01/18/2023] Open
Abstract
The protonation state of embedded charged residues in transmembrane proteins (TMPs) can control the onset of protein function. It is understood that interactions between an embedded charged residue and other charged or polar residues in the moiety would influence its pKa, but how the surrounding environment in which the TMP resides affects the pKa of these residues is unclear. Proteorhodopsin (PR), a light-responsive proton pump from marine bacteria, was used as a model to examine externally accessible factors that tune the pKa of its embedded charged residue, specifically its primary proton acceptor D97. The pKa of D97 was compared between PR reconstituted in liposomes with different net headgroup charges and equilibrated in buffer with different ion concentrations. For PR reconstituted in net positively charged compared to net negatively charged liposomes in low-salt buffer solutions, a drop of the apparent pKa from 7.6 to 5.6 was observed, whereas intrinsic pKa modeled with surface pH calculated from Gouy-Chapman predictions found an opposite trend for the pKa change, suggesting that surface pH does not account for the main changes observed in the apparent pKa. This difference in the pKa of D97 observed from PR reconstituted in oppositely charged liposome environments disappeared when the NaCl concentration was increased to 150 mM. We suggest that protein-intrinsic structural properties must play a role in adjusting the local microenvironment around D97 to affect its pKa, as corroborated with observations of changes in protein side-chain and hydration dynamics around the E-F loop of PR. Understanding the effect of externally controllable factors in tuning the pKa of TMP-embedded charged residues is important for bioengineering and biomedical applications relying on TMP systems, in which the onset of functions can be controlled by the protonation state of embedded residues.
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Affiliation(s)
- Chung-Ta Han
- Department of Chemical Engineering, University of California, Santa Barbara, California
| | - Jichao Song
- Department of Chemical Engineering, University of California, Santa Barbara, California
| | - Tristan Chan
- Department of Chemistry, University of California, Santa Barbara, California
| | - Christine Pruett
- Department of Chemical Engineering, University of California, Santa Barbara, California
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California; Department of Chemistry, University of California, Santa Barbara, California.
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10
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Abdullin D, Schiemann O. Pulsed Dipolar EPR Spectroscopy and Metal Ions: Methodology and Biological Applications. Chempluschem 2020; 85:353-372. [DOI: 10.1002/cplu.201900705] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/16/2020] [Indexed: 01/18/2023]
Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
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11
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Shah A, Roux A, Starck M, Mosely JA, Stevens M, Norman DG, Hunter RI, El Mkami H, Smith GM, Parker D, Lovett JE. A Gadolinium Spin Label with Both a Narrow Central Transition and Short Tether for Use in Double Electron Electron Resonance Distance Measurements. Inorg Chem 2019; 58:3015-3025. [DOI: 10.1021/acs.inorgchem.8b02892] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Anokhi Shah
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
- BSRC, University of St Andrews, St Andrews KY16 9ST, U.K
| | - Amandine Roux
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Matthieu Starck
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Jackie A. Mosely
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Michael Stevens
- College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - David G. Norman
- College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Robert I. Hunter
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - Hassane El Mkami
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - Graham M. Smith
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - David Parker
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Janet E. Lovett
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
- BSRC, University of St Andrews, St Andrews KY16 9ST, U.K
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12
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Wegner J, Valora G, Halbmair K, Kehl A, Worbs B, Bennati M, Diederichsen U. Semi-Rigid Nitroxide Spin Label for Long-Range EPR Distance Measurements of Lipid Bilayer Embedded β-Peptides. Chemistry 2019; 25:2203-2207. [DOI: 10.1002/chem.201805880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Janine Wegner
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
| | - Gabriele Valora
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
- Dipartimento di Scienze Chimiche; University of Catania; Italy
| | - Karin Halbmair
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
| | - Annemarie Kehl
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
| | - Brigitte Worbs
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
| | - Marina Bennati
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
| | - Ulf Diederichsen
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
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13
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Clayton JA, Keller K, Qi M, Wegner J, Koch V, Hintz H, Godt A, Han S, Jeschke G, Sherwin MS, Yulikov M. Quantitative analysis of zero-field splitting parameter distributions in Gd(iii) complexes. Phys Chem Chem Phys 2018; 20:10470-10492. [PMID: 29617015 DOI: 10.1039/c7cp08507a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The magnetic properties of paramagnetic species with spin S > 1/2 are parameterized by the familiar g tensor as well as "zero-field splitting" (ZFS) terms that break the degeneracy between spin states even in the absence of a magnetic field. In this work, we determine the mean values and distributions of the ZFS parameters D and E for six Gd(iii) complexes (S = 7/2) and critically discuss the accuracy of such determination. EPR spectra of the Gd(iii) complexes were recorded in glassy frozen solutions at 10 K or below at Q-band (∼34 GHz), W-band (∼94 GHz) and G-band (240 GHz) frequencies, and simulated with two widely used models for the form of the distributions of the ZFS parameters D and E. We find that the form of the distribution of the ZFS parameter D is bimodal, consisting roughly of two Gaussians centered at D and -D with unequal amplitudes. The extracted values of D (σD) for the six complexes are, in MHz: Gd-NO3Pic, 485 ± 20 (155 ± 37); Gd-DOTA/Gd-maleimide-DOTA, -714 ± 43 (328 ± 99); iodo-(Gd-PyMTA)/MOMethynyl-(Gd-PyMTA), 1213 ± 60 (418 ± 141); Gd-TAHA, 1361 ± 69 (457 ± 178); iodo-Gd-PCTA-[12], 1861 ± 135 (467 ± 292); and Gd-PyDTTA, 1830 ± 105 (390 ± 242). The sign of D was adjusted based on the Gaussian component with larger amplitude. We relate the extracted P(D) distributions to the structure of the individual Gd(iii) complexes by fitting them to a model that superposes the contribution to the D tensor from each coordinating atom of the ligand. Using this model, we predict D, σD, and E values for several additional Gd(iii) complexes that were not measured in this work. The results of this paper may be useful as benchmarks for the verification of quantum chemical calculations of ZFS parameters, and point the way to designing Gd(iii) complexes for particular applications and estimating their magnetic properties a priori.
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Affiliation(s)
- Jessica A Clayton
- University of California, Santa Barbara, Department of Physics, Santa Barbara, CA, USA.
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14
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New limits of sensitivity of site-directed spin labeling electron paramagnetic resonance for membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:841-853. [DOI: 10.1016/j.bbamem.2017.12.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/27/2017] [Accepted: 12/09/2017] [Indexed: 01/27/2023]
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15
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Jassoy JJ, Meyer A, Spicher S, Wuebben C, Schiemann O. Synthesis of Nanometer Sized Bis- and Tris-trityl Model Compounds with Different Extent of Spin-Spin Coupling. Molecules 2018; 23:E682. [PMID: 29562622 PMCID: PMC6017437 DOI: 10.3390/molecules23030682] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 12/29/2022] Open
Abstract
Tris(2,3,5,6-tetrathiaaryl)methyl radicals, so-called trityl radicals, are emerging as spin labels for distance measurements in biological systems based on Electron Paramagnetic Resonance (EPR). Here, the synthesis and characterization of rigid model systems carrying either two or three trityl moieties is reported. The monofunctionalized trityl radicals are connected to the molecular bridging scaffold via an esterification reaction employing the Mukaiyama reagent 2-chloro-methylpyridinium iodide. The bis- and tris-trityl compounds exhibit different inter-spin distances, strength of electron-electron exchange and dipolar coupling and can give rise to multi-spin effects. They are to serve as benchmark systems in comparing EPR distance measurement methods.
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Affiliation(s)
- J Jacques Jassoy
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Andreas Meyer
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Sebastian Spicher
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Christine Wuebben
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
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Gmeiner C, Dorn G, Allain FHT, Jeschke G, Yulikov M. Spin labelling for integrative structure modelling: a case study of the polypyrimidine-tract binding protein 1 domains in complexes with short RNAs. Phys Chem Chem Phys 2018; 19:28360-28380. [PMID: 29034946 DOI: 10.1039/c7cp05822e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A combined method, employing NMR and EPR spectroscopies, has demonstrated its strength in solving structures of protein/RNA and other types of biomolecular complexes. This method works particularly well when the large biomolecular complex consists of a limited number of rigid building blocks, such as RNA-binding protein domains (RBDs). A variety of spin labels is available for such studies, allowing for conventional as well as spectroscopically orthogonal double electron-electron resonance (DEER) measurements in EPR. In this work, we compare different types of nitroxide-based and Gd(iii)-based spin labels attached to isolated RBDs of the polypyrimidine-tract binding protein 1 (PTBP1) and to short RNA fragments. In particular, we demonstrate experiments on spectroscopically orthogonal labelled RBD/RNA complexes. For all experiments we analyse spin labelling, DEER method performance, resulting distance distributions, and their consistency with the predictions from the spin label rotamers analysis. This work provides a set of intra-domain calibration DEER data, which can serve as a basis to start structure determination of the full length PTBP1 complex with an RNA derived from encephalomycarditis virus (EMCV) internal ribosomal entry site (IRES). For a series of tested labelling sites, we discuss their particular advantages and drawbacks in such a structure determination approach.
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Affiliation(s)
- Christoph Gmeiner
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland.
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17
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Meyer A, Jassoy JJ, Spicher S, Berndhäuser A, Schiemann O. Performance of PELDOR, RIDME, SIFTER, and DQC in measuring distances in trityl based bi- and triradicals: exchange coupling, pseudosecular coupling and multi-spin effects. Phys Chem Chem Phys 2018; 20:13858-13869. [DOI: 10.1039/c8cp01276h] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The performance of pulsed EPR methods for distance measurements is evaluated on three different trityl model systems.
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Affiliation(s)
- Andreas Meyer
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Jean Jacques Jassoy
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Sebastian Spicher
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Andreas Berndhäuser
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
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18
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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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19
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Gmeiner C, Klose D, Mileo E, Belle V, Marque SRA, Dorn G, Allain FHT, Guigliarelli B, Jeschke G, Yulikov M. Orthogonal Tyrosine and Cysteine Site-Directed Spin Labeling for Dipolar Pulse EPR Spectroscopy on Proteins. J Phys Chem Lett 2017; 8:4852-4857. [PMID: 28933855 DOI: 10.1021/acs.jpclett.7b02220] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Site-directed spin labeling of native tyrosine residues in isolated domains of the protein PTBP1, using a Mannich-type reaction, was combined with conventional spin labeling of cysteine residues. Double electron-electron resonance (DEER) EPR measurements were performed for both the nitroxide-nitroxide and Gd(III)-nitroxide label combinations within the same protein molecule. For the prediction of distance distributions from a structure model, rotamer libraries were generated for the two linker forms of the tyrosine-reactive isoindoline-based nitroxide radical Nox. Only moderate differences exist between the spatial spin distributions for the two linker forms of Nox. This strongly simplifies DEER data analysis, in particular, if only mean distances need to be predicted.
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Affiliation(s)
- Christoph Gmeiner
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
| | - Daniel Klose
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
| | - Elisabetta Mileo
- Aix Marseille Univ , CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Valérie Belle
- Aix Marseille Univ , CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Sylvain R A Marque
- Aix Marseille Univ , CNRS, ICR, Institut de Chimie Radicalaire, Marseille 13397, France
- N. N. Vorozhtsov Novosibirsk Insititute of Organic Chemistry , 630090 Novosibirsk, Russia
| | - Georg Dorn
- Institute of Molecular Biology and Biophysics, ETH Zurich , Zurich 8093, Switzerland
| | - Frédéric H T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich , Zurich 8093, Switzerland
| | - Bruno Guigliarelli
- Aix Marseille Univ , CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
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20
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Segawa TF, Doppelbauer M, Garbuio L, Doll A, Polyhach YO, Jeschke G. Water accessibility in a membrane-inserting peptide comparing Overhauser DNP and pulse EPR methods. J Chem Phys 2017; 144:194201. [PMID: 27208942 DOI: 10.1063/1.4948988] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Water accessibility is a key parameter for the understanding of the structure of biomolecules, especially membrane proteins. Several experimental techniques based on the combination of electron paramagnetic resonance (EPR) spectroscopy with site-directed spin labeling are currently available. Among those, we compare relaxation time measurements and electron spin echo envelope modulation (ESEEM) experiments using pulse EPR with Overhauser dynamic nuclear polarization (DNP) at X-band frequency and a magnetic field of 0.33 T. Overhauser DNP transfers the electron spin polarization to nuclear spins via cross-relaxation. The change in the intensity of the (1)H NMR spectrum of H2O at a Larmor frequency of 14 MHz under a continuous-wave microwave irradiation of the nitroxide spin label contains information on the water accessibility of the labeled site. As a model system for a membrane protein, we use the hydrophobic α-helical peptide WALP23 in unilamellar liposomes of DOPC. Water accessibility measurements with all techniques are conducted for eight peptides with different spin label positions and low radical concentrations (10-20 μM). Consistently in all experiments, the water accessibility appears to be very low, even for labels positioned near the end of the helix. The best profile is obtained by Overhauser DNP, which is the only technique that succeeds in discriminating neighboring positions in WALP23. Since the concentration of the spin-labeled peptides varied, we normalized the DNP parameter ϵ, being the relative change of the NMR intensity, by the electron spin concentration, which was determined from a continuous-wave EPR spectrum.
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Affiliation(s)
- Takuya F Segawa
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Maximilian Doppelbauer
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Luca Garbuio
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Andrin Doll
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Yevhen O Polyhach
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
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21
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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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22
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Di Valentin M, Albertini M, Dal Farra MG, Zurlo E, Orian L, Polimeno A, Gobbo M, Carbonera D. Light-Induced Porphyrin-Based Spectroscopic Ruler for Nanometer Distance Measurements. Chemistry 2016; 22:17204-17214. [DOI: 10.1002/chem.201603666] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Marilena Di Valentin
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Marco Albertini
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Maria Giulia Dal Farra
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Enrico Zurlo
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
- Leiden Institute of Physics; Leiden University; Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Laura Orian
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Antonino Polimeno
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Marina Gobbo
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Donatella Carbonera
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
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23
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Halbmair K, Wegner J, Diederichsen U, Bennati M. Pulse EPR Measurements of Intramolecular Distances in a TOPP-Labeled Transmembrane Peptide in Lipids. Biophys J 2016; 111:2345-2348. [PMID: 27836102 PMCID: PMC5153538 DOI: 10.1016/j.bpj.2016.10.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/12/2016] [Accepted: 10/19/2016] [Indexed: 11/15/2022] Open
Abstract
We present the performance of nanometer-range pulse electron paramagnetic resonance distance measurements (pulsed electron-electron double resonance/double electron-electron resonance, PELDOR/DEER) on a transmembrane WALP24 peptide labeled with the semirigid unnatural amino acid 4-(3,3,5,5-tetra-methyl-2,6-dioxo-4-oxylpiperazin-1-yl)-l-phenylglycine (TOPP). Distances reported by the TOPP label are compared to the ones reported by the more standard MTSSL spin label, commonly employed in protein studies. Using high-power pulse electron paramagnetic resonance spectroscopy at Q-band frequencies (34 GHz), we show that in contrast to MTSSL, our label reports one-peak, sharp (Δr ≤ 0.4 nm) intramolecular distances. Orientational selectivity is not observed. When spin-labeled WALP24 was inserted in two representative lipid bilayers with different bilayer thickness, i.e., DMPC and POPC, the intramolecular distance reported by TOPP did not change with the bilayer environment. In contrast, the distance measured with MTSSL was strongly affected by the hydrophobic thickness of the lipid. The results demonstrate that the TOPP label is well suited to study the intrinsic structure of peptides immersed in lipids.
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Affiliation(s)
- Karin Halbmair
- Electron Spin Resonance Spectroscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Janine Wegner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany
| | - Marina Bennati
- Electron Spin Resonance Spectroscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany.
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24
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Zhang S, Wang G, Lu Y, Zhu W, Peng C, Liu H. The Interactions between Imidazolium-Based Ionic Liquids and Stable Nitroxide Radical Species: A Theoretical Study. J Phys Chem A 2016; 120:6089-102. [DOI: 10.1021/acs.jpca.6b05770] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shaoze Zhang
- Key Laboratory for Advanced Materials and School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Guimin Wang
- Drug
Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Yunxiang Lu
- Key Laboratory for Advanced Materials and School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Weiliang Zhu
- Drug
Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Changjun Peng
- Key Laboratory for Advanced Materials and School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Honglai Liu
- Key Laboratory for Advanced Materials and School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
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25
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Collauto A, Feintuch A, Qi M, Godt A, Meade T, Goldfarb D. Gd(III) complexes as paramagnetic tags: Evaluation of the spin delocalization over the nuclei of the ligand. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 263:156-163. [PMID: 26802219 DOI: 10.1016/j.jmr.2015.12.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/28/2015] [Accepted: 12/30/2015] [Indexed: 05/15/2023]
Abstract
Complexes of the Gd(III) ion are currently being established as spin labels for distance determination in biomolecules by pulse dipolar spectroscopy. Because Gd(III) is an f ion, one expects electron spin density to be localized on the Gd(III) ion - an important feature for the mentioned application. Most of the complex ligands have nitrogens as Gd(III) coordinating atoms. Therefore, measurement of the (14)N hyperfine coupling gives access to information on the localization of the electron spin on the Gd(III) ion. We carried out W-band, 1D and 2D (14)N and (1)H ENDOR measurements on the Gd(III) complexes Gd-DOTA, Gd-538, Gd-595, and Gd-PyMTA that serve as spin labels for Gd-Gd distance measurements. The obtained (14)N spectra are particularly well resolved, revealing both the hyperfine and nuclear quadrupole splittings, which were assigned using 2D Mims ENDOR experiments. Additionally, the spectral contributions of the two different types of nitrogen atoms of Gd-PyMTA, the aliphatic N atom and the pyridine N atom, were distinguishable. The (14)N hyperfine interaction was found to have a very small isotropic hyperfine component of -0.25 to -0.37MHz. Furthermore, the anisotropic hyperfine interactions with the (14)N nuclei and with the non-exchangeable protons of the ligands are well described by the point-dipole approximation using distances derived from the crystal structures. We therefore conclude that the spin density is fully localized on the Gd(III) ion and that the spin density distribution over the nuclei of the ligands is rightfully ignored when analyzing distance measurements.
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Affiliation(s)
- A Collauto
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - A Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - M Qi
- University Bielefeld, Faculty of Chemistry and Center for Molecular Materials, D-33615 Bielefeld, Germany
| | - A Godt
- University Bielefeld, Faculty of Chemistry and Center for Molecular Materials, D-33615 Bielefeld, Germany
| | - T Meade
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - D Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel.
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26
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Collauto A, Frydman V, Lee MD, Abdelkader EH, Feintuch A, Swarbrick JD, Graham B, Otting G, Goldfarb D. RIDME distance measurements using Gd(iii) tags with a narrow central transition. Phys Chem Chem Phys 2016; 18:19037-49. [DOI: 10.1039/c6cp03299k] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Methods based on pulse electron paramagnetic resonance allow measurement of the electron–electron dipolar coupling between two high-spin labels.
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Affiliation(s)
- A. Collauto
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - V. Frydman
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - M. D. Lee
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - E. H. Abdelkader
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - A. Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - J. D. Swarbrick
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - B. Graham
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - G. Otting
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - D. Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
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27
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Abdelkader EH, Lee MD, Feintuch A, Cohen MR, Swarbrick JD, Otting G, Graham B, Goldfarb D. A New Gd(3+) Spin Label for Gd(3+)-Gd(3+) Distance Measurements in Proteins Produces Narrow Distance Distributions. J Phys Chem Lett 2015; 6:5016-5021. [PMID: 26623480 DOI: 10.1021/acs.jpclett.5b02451] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Gd(3+) tags have been shown to be useful for performing distance measurements in biomolecules via the double electron-electron resonance (DEER) technique at Q- and W-band frequencies. We introduce a new cyclen-based Gd(3+) tag that exhibits a relatively narrow electron paramagnetic resonance (EPR) spectrum, affording high sensitivity, and which yields exceptionally narrow Gd(3+)-Gd(3+) distance distributions in doubly tagged proteins owing to a very short tether. Both the maxima and widths of distance distributions measured for tagged mutants of the proteins ERp29 and T4 lysozyme, featuring Gd(3+)-Gd(3+) distances of ca. 6 and 4 nm, respectively, were well reproduced by simulated distance distributions based on available crystal structures and sterically allowed rotamers of the tag. The precision of the position of the Gd(3+) ion is comparable to that of the nitroxide radical in an MTSL-tagged protein and thus the new tag represents an attractive tool for performing accurate distance measurements and potentially probing protein conformational equilibria.
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Affiliation(s)
- Elwy H Abdelkader
- Research School of Chemistry, Australian National University , Canberra, ACT 2601, Australia
| | - Michael D Lee
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Marie Ramirez Cohen
- Department of Chemical Physics, Weizmann Institute of Science , Rehovot 76100, Israel
| | - James D Swarbrick
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University , Canberra, ACT 2601, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science , Rehovot 76100, Israel
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28
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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. JOURNAL OF BIOMOLECULAR 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] [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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29
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Doll A, Qi M, Wili N, Pribitzer S, Godt A, Jeschke G. Gd(III)-Gd(III) distance measurements with chirp pump pulses. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 259:153-62. [PMID: 26340436 DOI: 10.1016/j.jmr.2015.08.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/13/2015] [Accepted: 08/14/2015] [Indexed: 05/15/2023]
Abstract
The broad EPR spectrum of Gd(III) spin labels restricts the dipolar modulation depth in distance measurements between Gd(III) pairs to a few percent. To overcome this limitation, frequency-swept chirp pulses are utilized as pump pulses in the DEER experiment. Using a model system with 3.4 nm Gd-Gd distance, application of one single chirp pump pulse at Q-band frequencies leads to modulation depths beyond 10%. However, the larger modulation depth is counteracted by a reduction of the absolute echo intensity due to the pump pulse. As supported by spin dynamics simulations, this effect is primarily driven by signal loss to double-quantum coherence and specific to the Gd(III) high spin state of S=7/2. In order to balance modulation depth and echo intensity for optimum sensitivity, a simple experimental procedure is proposed. An additional improvement by 25% in DEER sensitivity is achieved with two consecutive chirp pump pulses. These pulses pump the Gd(III) spectrum symmetrically around the observation position, therefore mutually compensating for dynamical Bloch-Siegert phase shifts at the observer spins. The improved sensitivity of the DEER data with modulation depths on the order of 20% is due to mitigation of the echo reduction effects by the consecutive pump pulses. In particular, the second pump pulse does not lead to additional signal loss if perfect inversion is assumed. Moreover, the compensation of the dynamical Bloch-Siegert phase prevents signal loss due to spatial dependence of the dynamical phase, which is caused by inhomogeneities in the driving field. The new methodology is combined with pre-polarization techniques to measure long distances up to 8.6 nm, where signal intensity and modulation depth become attenuated by long dipolar evolution windows. In addition, the influence of the zero-field splitting parameters on the echo intensity is studied with simulations. Herein, larger sensitivity is anticipated for Gd(III) complexes with zero-field splitting that is smaller than for the employed Gd-PyMTA complex.
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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
| | - Nino Wili
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Stephan Pribitzer
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - 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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30
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Garbuio L, Zimmermann K, Häussinger D, Yulikov M. Gd(III) complexes for electron-electron dipolar spectroscopy: Effects of deuteration, pH and zero field splitting. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 259:163-73. [PMID: 26342680 DOI: 10.1016/j.jmr.2015.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/06/2015] [Accepted: 08/07/2015] [Indexed: 05/15/2023]
Abstract
Spectral parameters of Gd(III) complexes are intimately linked to the performance of the Gd(III)-nitroxide or Gd(III)-Gd(III) double electron-electron resonance (DEER or PELDOR) techniques, as well as to that of relaxation induced dipolar modulation enhancement (RIDME) spectroscopy with Gd(III) ions. These techniques are of interest for applications in structural biology, since they can selectively detect site-to-site distances in biomolecules or biomolecular complexes in the nanometer range. Here we report relaxation properties, echo detected EPR spectra, as well as the magnitude of the echo reduction effect in Gd(III)-nitroxide DEER for a series of Gadolinium(III) complexes with chelating agents derived from tetraazacyclododecane. We observed that solvent deuteration does not only lengthen the relaxation times of Gd(III) centers but also weakens the DEER echo reduction effect. Both of these phenomena lead to an improved signal-to-noise ratios or, alternatively, longer accessible distance range in pulse EPR measurements. The presented data enrich the knowledge on paramagnetic Gd(III) chelate complexes in frozen solutions, and can help optimize the experimental conditions for most types of the pulse measurements of the electron-electron dipolar interactions.
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Affiliation(s)
- Luca Garbuio
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | | | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland.
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31
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Wojciechowski F, Groß A, Holder IT, Knörr L, Drescher M, Hartig JS. Pulsed EPR spectroscopy distance measurements of DNA internally labelled with Gd(3+)-DOTA. Chem Commun (Camb) 2015; 51:13850-3. [PMID: 26236790 DOI: 10.1039/c5cc04234h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gd(3+) is increasingly used in EPR spectroscopy due to its increased intracellular stability and signal-to-noise ratios. Here we present the incorporation of Gd(3+)-DOTA into internal positions in DNA. Distance measurements via pulsed Electron Paramagnetic Resonance (EPR) spectroscopy in vitro and in cellula proved enhanced stability and efficiency compared to nitroxide labels.
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Affiliation(s)
- Filip Wojciechowski
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, Konstanz, Germany.
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32
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Manukovsky N, Frydman V, Goldfarb D. Gd3+ Spin Labels Report the Conformation and Solvent Accessibility of Solution and Vesicle-Bound Melittin. J Phys Chem B 2015; 119:13732-41. [DOI: 10.1021/acs.jpcb.5b03523] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Nurit Manukovsky
- Departments of †Chemical Physics and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Veronica Frydman
- Departments of †Chemical Physics and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Daniella Goldfarb
- Departments of †Chemical Physics and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
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33
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Kuzhelev AA, Trukhin DV, Krumkacheva OA, Strizhakov RK, Rogozhnikova OY, Troitskaya TI, Fedin MV, Tormyshev VM, Bagryanskaya EG. Room-Temperature Electron Spin Relaxation of Triarylmethyl Radicals at the X- and Q-Bands. J Phys Chem B 2015; 119:13630-13640. [PMID: 26001103 DOI: 10.1021/acs.jpcb.5b03027] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Triarylmethyl radicals (trityls, TAMs) represent a relatively new class of spin labels. The long relaxation of trityls at room temperature in liquid solutions makes them a promising alternative for traditional nitroxides. In this work we have synthesized a series of TAMs including perdeuterated Finland trityl (D36 form), mono-, di-, and triester derivatives of Finland-D36 trityl, the deuterated form of OX63, the dodeca-n-butyl homologue of Finland trityl, and triamide derivatives of Finland trityl with primary and secondary amines attached. We have studied room-temperature relaxation properties of these TAMs in liquids using pulsed electron paramagnetic resonance (EPR) at two microwave frequency bands. We have found the clear dependence of phase memory time (Tm ∼ T2) on the magnetic field: room-temperature Tm values are ∼1.5-2.5 times smaller at the Q-band (34 GHz, 1.2 T) than at the X-band (9 GHz, 0.3 T). This trend is ascribed to the contribution from g-anisotropy that is negligible at lower magnetic fields but comes into play at the Q-band. In agreement with this, the difference between T1 and Tm becomes more pronounced at the Q-band than at the X-band due to increased contributions from incomplete motional averaging of g-anisotropy. Linear dependence of (1/Tm - 1/T1) on viscosity implies that g-anisotropy is modulated by rotational motion of the trityl radical. On the basis of the analysis of previous data and results of the present work, we conclude that, in the general situation where the spin label is at least partly mobile, the X-band is most suitable for application of trityls for room-temperature pulsed EPR distance measurements.
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Affiliation(s)
- Andrey A Kuzhelev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry V Trukhin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Olesya A Krumkacheva
- International Tomography Center SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Rodion K Strizhakov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Olga Yu Rogozhnikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Tatiana I Troitskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Matvey V Fedin
- International Tomography Center SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Victor M Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
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34
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Shevelev GY, Krumkacheva OA, Lomzov AA, Kuzhelev AA, Trukhin DV, Rogozhnikova OY, Tormyshev VM, Pyshnyi DV, Fedin MV, Bagryanskaya EG. Triarylmethyl Labels: Toward Improving the Accuracy of EPR Nanoscale Distance Measurements in DNAs. J Phys Chem B 2015; 119:13641-8. [PMID: 26011022 DOI: 10.1021/acs.jpcb.5b03026] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Triarylmethyl (trityl, TAM) based spin labels represent a promising alternative to nitroxides for EPR distance measurements in biomolecules. Herewith, we report synthesis and comparative study of series of model DNA duplexes, 5'-spin-labeled with TAMs and nitroxides. We have found that the accuracy (width) of distance distributions obtained by double electron-electron resonance (DEER/PELDOR) strongly depends on the type of radical. Replacement of both nitroxides by TAMs in the same spin-labeled duplex allows narrowing of the distance distributions by a factor of 3. Replacement of one nitroxide by TAM (orthogonal labeling) leads to a less pronounced narrowing but at the same time gains sensitivity in DEER experiment due to efficient pumping on the narrow EPR line of TAM. Distance distributions in nitroxide/nitroxide pairs are influenced by the structure of the linker: the use of a short amine-based linker improves the accuracy by a factor of 2. At the same time, a negligible dependence on the linker length is found for the distribution width in TAM/TAM pairs. Molecular dynamics calculations indicate greater conformational disorder of nitroxide labels compared to TAM ones, thus rationalizing the experimentally observed trends. Thereby, we conclude that double spin-labeling using TAMs allows obtaining narrower spin-spin distance distributions and potentially more precise distances between labeling sites compared to traditional nitroxides.
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Affiliation(s)
- Georgiy Yu Shevelev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Olesya A Krumkacheva
- International Tomography Center, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Andrey A Kuzhelev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Dmitry V Trukhin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Olga Yu Rogozhnikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Victor M Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Matvey V Fedin
- International Tomography Center, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
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35
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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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36
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Bagryanskaya EG, Krumkacheva OA, Fedin MV, Marque SR. Development and Application of Spin Traps, Spin Probes, and Spin Labels. Methods Enzymol 2015; 563:365-96. [DOI: 10.1016/bs.mie.2015.06.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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37
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Feintuch A, Otting G, Goldfarb D. Gd3+ Spin Labeling for Measuring Distances in Biomacromolecules. Methods Enzymol 2015; 563:415-57. [DOI: 10.1016/bs.mie.2015.07.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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38
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Combining NMR and EPR to Determine Structures of Large RNAs and Protein–RNA Complexes in Solution. Methods Enzymol 2015; 558:279-331. [DOI: 10.1016/bs.mie.2015.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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39
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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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40
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Raitsimring A, Dalaloyan A, Collauto A, Feintuch A, Meade T, Goldfarb D. Zero field splitting fluctuations induced phase relaxation of Gd3+ in frozen solutions at cryogenic temperatures. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 248:71-80. [PMID: 25442776 PMCID: PMC4495766 DOI: 10.1016/j.jmr.2014.09.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 09/14/2014] [Accepted: 09/16/2014] [Indexed: 05/18/2023]
Abstract
Distance measurements using double electron-electron resonance (DEER) and Gd(3+) chelates for spin labels (GdSL) have been shown to be an attractive alternative to nitroxide spin labels at W-band (95GHz). The maximal distance that can be accessed by DEER measurements and the sensitivity of such measurements strongly depends on the phase relaxation of Gd(3+) chelates in frozen, glassy solutions. In this work, we explore the phase relaxation of Gd(3+)-DOTA as a representative of GdSL in temperature and concentration ranges typically used for W-band DEER measurements. We observed that in addition to the usual mechanisms of phase relaxation known for nitroxide based spin labels, GdSL are subjected to an additional phase relaxation mechanism that features an increase in the relaxation rate from the center to the periphery of the EPR spectrum. Since the EPR spectrum of GdSL is the sum of subspectra of the individual EPR transitions, we attribute this field dependence to transition dependent phase relaxation. Using simulations of the EPR spectra and its decomposition into the individual transition subspectra, we isolated the phase relaxation of each transition and found that its rate increases with |ms|. We suggest that this mechanism is due to transient zero field splitting (tZFS), where its magnitude and correlation time are scaled down and distributed as compared with similar situations in liquids. This tZFS induced phase relaxation mechanism becomes dominant (or at least significant) when all other well-known phase relaxation mechanisms, such as spectral diffusion caused by nuclear spin diffusion, instantaneous and electron spin spectral diffusion, are significantly suppressed by matrix deuteration and low concentration, and when the temperature is sufficiently low to disable spin lattice interaction as a source of phase relaxation.
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Affiliation(s)
| | - A Dalaloyan
- Weizmann Institute of Science, Rehovot, Israel
| | - A Collauto
- Weizmann Institute of Science, Rehovot, Israel
| | - A Feintuch
- Weizmann Institute of Science, Rehovot, Israel
| | - T Meade
- Northwestern University, Evanston, IL 60208, USA
| | - D Goldfarb
- Weizmann Institute of Science, Rehovot, Israel.
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41
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New developments in spin labels for pulsed dipolar EPR. Molecules 2014; 19:16998-7025. [PMID: 25342554 PMCID: PMC6271499 DOI: 10.3390/molecules191016998] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/07/2014] [Accepted: 10/13/2014] [Indexed: 11/17/2022] Open
Abstract
Spin labelling is a chemical technique that enables the integration of a molecule containing an unpaired electron into another framework for study. Given the need to understand the structure, dynamics, and conformational changes of biomacromolecules, spin labelling provides a relatively non-intrusive technique and has certain advantages over X-ray crystallography; which requires high quality crystals. The technique relies on the design of binding probes that target a functional group, for example, the thiol group of a cysteine residue within a protein. The unpaired electron is typically supplied through a nitroxide radical and sterically shielded to preserve stability. Pulsed electron paramagnetic resonance (EPR) techniques allow small magnetic couplings to be measured (e.g., <50 MHz) providing information on single label probes or the dipolar coupling between multiple labels. In particular, distances between spin labels pairs can be derived which has led to many protein/enzymes and nucleotides being studied. Here, we summarise recent examples of spin labels used for pulse EPR that serve to illustrate the contribution of chemistry to advancing discoveries in this field.
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42
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Upadhyay A, Das C, Shanmugam M, Langley SK, Murray KS, Shanmugam M. Electronic and Magnetic Properties of a Gadolinium(III) Schiff Base Complex. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402219] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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43
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Di Valentin M, Albertini M, Zurlo E, Gobbo M, Carbonera D. Porphyrin triplet state as a potential spin label for nanometer distance measurements by PELDOR spectroscopy. J Am Chem Soc 2014; 136:6582-5. [PMID: 24735449 DOI: 10.1021/ja502615n] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This work demonstrates, for the first time, the feasibility of applying pulsed electron-electron double resonance (PELDOR/DEER) to determine the interspin distance between a photoexcited porphyrin triplet state (S = 1) and a nitroxide spin label chemically incorporated into a small helical peptide. The PELDOR trace shows deep envelope modulation induced by electron-electron dipole interaction between the partners in the pair, providing an accurate distance measurement. This new labeling approach has a high potential for measuring nanometer distances in more complex biological systems due to the sensitivity acquired from the spin polarization of the photoexcited triplet state spectrum.
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Affiliation(s)
- Marilena Di Valentin
- Dipartimento di Scienze Chimiche, Università di Padova , via Marzolo 1, 35131 Padova, Italy
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44
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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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45
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Joseph B, Korkhov VM, Yulikov M, Jeschke G, Bordignon E. Conformational cycle of the vitamin B12 ABC importer in liposomes detected by double electron-electron resonance (DEER). J Biol Chem 2013; 289:3176-85. [PMID: 24362024 DOI: 10.1074/jbc.m113.512178] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Double electron-electron resonance is used here to investigate intermediates of the transport cycle of the Escherichia coli vitamin B12 ATP-binding cassette importer BtuCD-F. Previously, we showed the ATP-induced opening of the cytoplasmic gate I in TM5 helices, later confirmed by the AMP-PNP-bound BtuCD-F crystal structure. Here, other key residues are analyzed in TM10 helices (positions 307 and 322) and in the cytoplasmic gate II, i.e. the loop between TM2 and TM3 (positions 82 and 85). Without BtuF, binding of ATP induces detectable changes at positions 307 and 85 in BtuCD in liposomes. Together with BtuF, ATP triggers the closure of the cytoplasmic gate II in liposomes (reported by both positions 82 and 85). This forms a sealed cavity in the translocation channel in agreement with the AMP-PNP·BtuCD-F x-ray structure. When vitamin B12 and AMP-PNP are simultaneously present, the extent of complex formation is reduced, but the short 82-82 interspin distance detected indicates that the substrate does not affect the closed conformation of this gate. The existence of the BtuCD-F complex under these conditions is verified with spectroscopically orthogonal nitroxide and Gd(III)-based labels. The cytoplasmic gate II remains closed also in the vanadate-trapped state, but it reopens in the ADP-bound state of the complex. Therefore, we suggest that the substrate likely trapped in ATP·BtuCD-F can be released after ATP hydrolysis but before the occluded ADP-bound conformation is reached.
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Affiliation(s)
- Benesh Joseph
- From the Laboratory of Physical Chemistry, ETH Zurich, Wolfgang-Pauli-Strasse 10 and
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46
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Razzaghi S, Brooks EK, Bordignon E, Hubbell WL, Yulikov M, Jeschke G. EPR relaxation-enhancement-based distance measurements on orthogonally spin-labeled T4-lysozyme. Chembiochem 2013; 14:1883-90. [PMID: 23775845 PMCID: PMC3804414 DOI: 10.1002/cbic.201300165] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Indexed: 12/20/2022]
Abstract
Lanthanide-induced enhancement of the longitudinal relaxation of nitroxide radicals in combination with orthogonal site-directed spin labeling is presented as a systematic distance measurement method intended for studies of bio-macromolecules and bio-macromolecular complexes. The approach is tested on a water-soluble protein (T4-lysozyme) for two different commercially available lanthanide labels, and complemented by previously reported data on a membrane-inserted polypeptide. Single temperature measurements are shown to be sufficient for reliable distance determination, with an upper measurable distance limit of about 5-6 nm. The extracted averaged distances represent the closest approach in Ln(III) -nitroxide distance distributions. Studies of conformational changes and of bio-macromolecule association-dissociation are proposed as possible application area of the relaxation-enhancement-based distance measurements.
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Affiliation(s)
| | - Evan K. Brooks
- Jules Stein Eye Institute and the Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | | | - Wayne L. Hubbell
- Jules Stein Eye Institute and the Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
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47
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Matalon E, Huber T, Hagelueken G, Graham B, Frydman V, Feintuch A, Otting G, Goldfarb D. Gadolinium(III) Spin Labels for High-Sensitivity Distance Measurements in Transmembrane Helices. Angew Chem Int Ed Engl 2013; 52:11831-4. [DOI: 10.1002/anie.201305574] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/14/2013] [Indexed: 12/28/2022]
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48
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Matalon E, Huber T, Hagelueken G, Graham B, Frydman V, Feintuch A, Otting G, Goldfarb D. Gadolinium(III) Spin Labels for High-Sensitivity Distance Measurements in Transmembrane Helices. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305574] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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49
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Baldauf C, Schulze K, Lueders P, Bordignon E, Tampé R. In-situ spin labeling of his-tagged proteins: distance measurements under in-cell conditions. Chemistry 2013; 19:13714-9. [PMID: 24038571 DOI: 10.1002/chem.201301921] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Indexed: 12/29/2022]
Abstract
New spin labeling strategies have immense potential in studying protein structure and dynamics under physiological conditions with electron paramagnetic resonance (EPR) spectroscopy. Here, a new spin-labeled chemical recognition unit for switchable and concomitantly high affinity binding to His-tagged proteins was synthesized. In combination with an orthogonal site-directed spin label, this novel spin probe, Proxyl-trisNTA (P-trisNTA) allows the extraction of structural constraints within proteins and macromolecular complexes by EPR. By using the multisubunit maltose import system of E. coli: 1) the topology of the substrate-binding protein, 2) its substrate-dependent conformational change, and 3) the formation of the membrane multiprotein complex can be extracted. Notably, the same distance information was retrieved both in vitro and in situ allowing for site-specific spin labeling in cell lysates under in-cell conditions. This approach will open new avenues towards in-cell EPR.
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Affiliation(s)
- Christoph Baldauf
- Institute of Biochemistry, Biocenter, Cluster of Excellence-Macromolecular Complexes (CEF-MC), Goethe-University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt a.M. (Germany)
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50
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Ezhevskaya M, Bordignon E, Polyhach Y, Moens L, Dewilde S, Jeschke G, Van Doorslaer S. Distance determination between low-spin ferric haem and nitroxide spin label using DEER: the neuroglobin case. Mol Phys 2013. [DOI: 10.1080/00268976.2013.813592] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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