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Vitali V, Ackermann K, Hagelueken G, Bode BE. Spectroscopically Orthogonal Labelling to Disentangle Site-Specific Nitroxide Label Distributions. APPLIED MAGNETIC RESONANCE 2023; 55:187-205. [PMID: 38357007 PMCID: PMC10861635 DOI: 10.1007/s00723-023-01611-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 02/16/2024]
Abstract
Biomolecular applications of pulse dipolar electron paramagnetic resonance spectroscopy (PDS) are becoming increasingly valuable in structural biology. Site-directed spin labelling of proteins is routinely performed using nitroxides, with paramagnetic metal ions and other organic radicals gaining popularity as alternative spin centres. Spectroscopically orthogonal spin labelling using different types of labels potentially increases the information content available from a single sample. When analysing experimental distance distributions between two nitroxide spin labels, the site-specific rotamer information has been projected into the distance and is not readily available, and the contributions of individual labelling sites to the width of the distance distribution are not obvious from the PDS data. Here, we exploit the exquisite precision of labelling double-histidine (dHis) motifs with CuII chelate complexes. The contribution of this label to the distance distribution widths in model protein GB1 has been shown to be negligible. By combining a dHis CuII labelling site with cysteine-specific nitroxide labelling, we gather insights on the label rotamers at two distinct sites, comparing their contributions to distance distributions based on different in silico modelling approaches and structural models. From this study, it seems advisable to consider discrepancies between different in silico modelling approaches when selecting labelling sites for PDS studies. Supplementary Information The online version contains supplementary material available at 10.1007/s00723-023-01611-1.
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Affiliation(s)
- Valentina Vitali
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST Scotland
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST Scotland
| | - Gregor Hagelueken
- Institute of Structural Biology, Biomedical Center, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Bela E. Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST Scotland
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2
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Ossadnik D, Kuzin S, Qi M, Yulikov M, Godt A. A Gd III-Based Spin Label at the Limits for Linewidth Reduction through Zero-Field Splitting Optimization. Inorg Chem 2023; 62:408-432. [PMID: 36525400 DOI: 10.1021/acs.inorgchem.2c03531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The remarkably narrow central line in the electron paramagnetic resonance spectrum and the very weak zero-field splitting (ZFS) make [GdIII(NO3Pic)] ([GdIII(TPATCN)]) an attractive starting point for the development of spin labels. For retaining the narrow line of this parent complex when modifying it with a substituent enabling bioconjugation, alkyl with a somehow remote functional group as a substituent at the picolinate moiety was found to be highly suitable because ZFS stayed weak, even if the threefold axial symmetry was broken. The ZFS is so weak that hyperfine coupling and/or g-value variations noticeably determine the linewidth in Q band and higher fields when the biomolecule is protonated, which is the standard situation, and in W band and higher fields for the protonated complex in a fully deuterated surrounding. Clearly, [NDSE-{GdIII(NO3Pic)}], a spin label targeting the cysteines in a peptide, is at a limit of linewidth narrowing through ZFS minimization. The labeling reaction is highly chemoselective and, applied to a polyproline with two cysteine units, it took no more than a minute at 7 °C and pH 7.8. Subsequent disulfide scrambling is very slow and can therefore be prevented. Double electron-electron resonance and relaxation-induced dipolar modulation enhancement applied to the spin-labeled polyproline proved the spin label useful for distance determination in peptides.
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Affiliation(s)
- Daniel Ossadnik
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615Bielefeld, Germany
| | - Sergei Kuzin
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, 8093Zurich, Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615Bielefeld, Germany
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, 8093Zurich, Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615Bielefeld, Germany
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3
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Buch CD, Kundu K, Marbey JJ, van Tol J, Weihe H, Hill S, Piligkos S. Spin–Lattice Relaxation Decoherence Suppression in Vanishing Orbital Angular Momentum Qubits. J Am Chem Soc 2022; 144:17597-17603. [DOI: 10.1021/jacs.2c07057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christian D. Buch
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Krishnendu Kundu
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Jonathan J. Marbey
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Johan van Tol
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Høgni Weihe
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Stephen Hill
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Stergios Piligkos
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
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4
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Mekkattu Tharayil S, Mahawaththa MC, Feintuch A, Maleckis A, Ullrich S, Morewood R, Maxwell MJ, Huber T, Nitsche C, Goldfarb D, Otting G. Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2022; 3:169-182. [PMID: 37904871 PMCID: PMC10539774 DOI: 10.5194/mr-3-169-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/18/2022] [Indexed: 11/01/2023]
Abstract
The paramagnetism of a lanthanoid tag site-specifically installed on a protein provides a rich source of structural information accessible by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy. Here we report a lanthanoid tag for selective reaction with cysteine or selenocysteine with formation of a (seleno)thioether bond and a short tether between the lanthanoid ion and the protein backbone. The tag is assembled on the protein in three steps, comprising (i) reaction with 4-fluoro-2,6-dicyanopyridine (FDCP); (ii) reaction of the cyano groups with α -cysteine, penicillamine or β -cysteine to complete the lanthanoid chelating moiety; and (iii) titration with a lanthanoid ion. FDCP reacts much faster with selenocysteine than cysteine, opening a route for selective tagging in the presence of solvent-exposed cysteine residues. Loaded with Tb 3 + and Tm 3 + ions, pseudocontact shifts were observed in protein NMR spectra, confirming that the tag delivers good immobilisation of the lanthanoid ion relative to the protein, which was also manifested in residual dipolar couplings. Completion of the tag with different 1,2-aminothiol compounds resulted in different magnetic susceptibility tensors. In addition, the tag proved suitable for measuring distance distributions in double electron-electron resonance experiments after titration with Gd 3 + ions.
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Affiliation(s)
| | - Mithun C. Mahawaththa
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Richard Morewood
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Michael J. Maxwell
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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5
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Peter MF, Gebhardt C, Mächtel R, Muñoz GGM, Glaenzer J, Narducci A, Thomas GH, Cordes T, Hagelueken G. Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET. Nat Commun 2022; 13:4396. [PMID: 35906222 PMCID: PMC9338047 DOI: 10.1038/s41467-022-31945-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Pulsed electron-electron double resonance spectroscopy (PELDOR/DEER) and single-molecule Förster resonance energy transfer spectroscopy (smFRET) are frequently used to determine conformational changes, structural heterogeneity, and inter probe distances in biological macromolecules. They provide qualitative information that facilitates mechanistic understanding of biochemical processes and quantitative data for structural modelling. To provide a comprehensive comparison of the accuracy of PELDOR/DEER and smFRET, we use a library of double cysteine variants of four proteins that undergo large-scale conformational changes upon ligand binding. With either method, we use established standard experimental protocols and data analysis routines to determine inter-probe distances in the presence and absence of ligands. The results are compared to distance predictions from structural models. Despite an overall satisfying and similar distance accuracy, some inconsistencies are identified, which we attribute to the use of cryoprotectants for PELDOR/DEER and label-protein interactions for smFRET. This large-scale cross-validation of PELDOR/DEER and smFRET highlights the strengths, weaknesses, and synergies of these two important and complementary tools in integrative structural biology.
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Affiliation(s)
- Martin F Peter
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Rebecca Mächtel
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gabriel G Moya Muñoz
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Janin Glaenzer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York, UK
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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6
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Herath ID, Breen C, Hewitt SH, Berki TR, Kassir AF, Dodson C, Judd M, Jabar S, Cox N, Otting G, Butler SJ. A Chiral Lanthanide Tag for Stable and Rigid Attachment to Single Cysteine Residues in Proteins for NMR, EPR and Time-Resolved Luminescence Studies. Chemistry 2021; 27:13009-13023. [PMID: 34152643 PMCID: PMC8518945 DOI: 10.1002/chem.202101143] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Indexed: 12/12/2022]
Abstract
A lanthanide-binding tag site-specifically attached to a protein presents a tool to probe the protein by multiple spectroscopic techniques, including nuclear magnetic resonance, electron paramagnetic resonance and time-resolved luminescence spectroscopy. Here a new stable chiral LnIII tag, referred to as C12, is presented for spontaneous and quantitative reaction with a cysteine residue to generate a stable thioether bond. The synthetic protocol of the tag is relatively straightforward, and the tag is stable for storage and shipping. It displays greatly enhanced reactivity towards selenocysteine, opening a route towards selective tagging of selenocysteine in proteins containing cysteine residues. Loaded with TbIII or TmIII ions, the C12 tag readily generates pseudocontact shifts (PCS) in protein NMR spectra. It produces a relatively rigid tether between lanthanide and protein, which is beneficial for interpretation of the PCSs by single magnetic susceptibility anisotropy tensors, and it is suitable for measuring distance distributions in double electron-electron resonance experiments. Upon reaction with cysteine or other thiol compounds, the TbIII complex exhibits a 100-fold enhancement in luminescence quantum yield, affording a highly sensitive turn-on luminescence probe for time-resolved FRET assays and enzyme reaction monitoring.
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Affiliation(s)
- Iresha D. Herath
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Colum Breen
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Sarah H. Hewitt
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Thomas R. Berki
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Ahmad F. Kassir
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Charlotte Dodson
- Department of Pharmacy & PharmacologyUniversity of Bath Claverton DownBathBA2 7AYUK
| | - Martyna Judd
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Shereen Jabar
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Nicholas Cox
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Gottfried Otting
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Stephen J. Butler
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
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7
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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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8
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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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9
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Abdelkader EH, Qianzhu H, Tan YJ, Adams LA, Huber T, Otting G. Genetic Encoding of N6-(((Trimethylsilyl)methoxy)carbonyl)-l-lysine for NMR Studies of Protein–Protein and Protein–Ligand Interactions. J Am Chem Soc 2021; 143:1133-1143. [DOI: 10.1021/jacs.0c11971] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Elwy H. Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Yi Jiun Tan
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Luke A. Adams
- ARC Training Centre for Fragment Based Design and Monash Fragment Platform, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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10
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Miao Q, Zurlo E, de Bruin D, Wondergem JAJ, Timmer M, Blok A, Heinrich D, Overhand M, Huber M, Ubbink M. A Two-Armed Probe for In-Cell DEER Measurements on Proteins*. Chemistry 2020; 26:17128-17133. [PMID: 33200852 PMCID: PMC7839491 DOI: 10.1002/chem.202002743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/27/2020] [Indexed: 12/21/2022]
Abstract
The application of double electron‐electron resonance (DEER) with site‐directed spin labeling (SDSL) to measure distances in proteins and protein complexes in living cells puts rigorous restraints on the spin‐label. The linkage and paramagnetic centers need to resist the reducing conditions of the cell. Rigid attachment of the probe to the protein improves precision of the measured distances. Here, three two‐armed GdIII complexes, GdIII‐CLaNP13a/b/c were synthesized. Rather than the disulfide linkage of most other CLaNP molecules, a thioether linkage was used to avoid reductive dissociation of the linker. The doubly GdIII labeled N55C/V57C/K147C/T151C variants of T4Lysozyme were measured by 95 GHz DEER. The constructs were measured in vitro, in cell lysate and in Dictyostelium discoideum cells. Measured distances were 4.5 nm, consistent with results from paramagnetic NMR. A narrow distance distribution and typical modulation depth, also in cell, indicate complete and durable labeling and probe rigidity due to the dual attachment sites.
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Affiliation(s)
- Qing Miao
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Enrico Zurlo
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Donny de Bruin
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Joeri A J Wondergem
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Monika Timmer
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Anneloes Blok
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Doris Heinrich
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands.,Fraunhofer Institute for Silicate Research ISC, 97082, Würzburg, Germany
| | - Mark Overhand
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
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11
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EL Mkami H, Hunter R, Cruickshank P, Taylor M, Lovett J, Feintuch A, Qi M, Godt A, Smith G. High-sensitivity Gd 3+-Gd 3+ EPR distance measurements that eliminate artefacts seen at short distances. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:301-313. [PMID: 37904818 PMCID: PMC10500690 DOI: 10.5194/mr-1-301-2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/18/2020] [Indexed: 11/01/2023]
Abstract
Gadolinium complexes are attracting increasing attention as spin labels for EPR dipolar distance measurements in biomolecules and particularly for in-cell measurements. It has been shown that flip-flop transitions within the central transition of the high-spin Gd3 + ion can introduce artefacts in dipolar distance measurements, particularly when measuring distances less than 3 nm. Previous work has shown some reduction of these artefacts through increasing the frequency separation between the two frequencies required for the double electron-electron resonance (DEER) experiment. Here we use a high-power (1 kW), wideband, non-resonant system operating at 94 GHz to evaluate DEER measurement protocols using two stiff Gd(III) rulers, consisting of two b i s -Gd3 + -PyMTA complexes, with separations of 2.1 nm and 6.0 nm, respectively. We show that by avoiding the - 1 2 → 1 2 central transition completely, and placing both the pump and the observer pulses on either side of the central transition, we can now observe apparently artefact-free spectra and narrow distance distributions, even for a Gd-Gd distance of 2.1 nm. Importantly we still maintain excellent signal-to-noise ratio and relatively high modulation depths. These results have implications for in-cell EPR measurements at naturally occurring biomolecule concentrations.
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Affiliation(s)
- Hassane EL Mkami
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Robert I. Hunter
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Paul A. S. Cruickshank
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Michael J. Taylor
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Janet E. Lovett
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science,
Rehovot, Israel
| | - Mian Qi
- Faculty of Chemistry and Center of Molecular Materials (CM2),
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld,
Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center of Molecular Materials (CM2),
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld,
Germany
| | - Graham M. Smith
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
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12
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Di Mauro GM, Hardin NZ, Ramamoorthy A. Lipid-nanodiscs formed by paramagnetic metal chelated polymer for fast NMR data acquisition. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2020; 1862:183332. [PMID: 32360741 PMCID: PMC7340147 DOI: 10.1016/j.bbamem.2020.183332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/21/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
Lipid-nanodiscs have been shown to be an exciting innovation as a membrane-mimicking system for studies on membrane proteins by a variety of biophysical techniques, including NMR spectroscopy. Although NMR spectroscopy is unique in enabling the atomic-resolution investigation of dynamic structures of membrane-associated molecules, it, unfortunately, suffers from intrinsically low sensitivity. The long data acquisition often used to enhance the sensitivity is not desirable for sensitive membrane proteins. Instead, paramagnetic relaxation enhancement (PRE) has been used to reduce NMR data acquisition time or to reduce the amount of sample required to acquire an NMR spectra. However, the PRE approach involves the introduction of external paramagnetic probes in the system, which can induce undesired changes in the sample and on the observed NMR spectra. For example, the addition of paramagnetic ions, as frequently used, can denature the protein via direct interaction and also through sample heating. In this study, we show how the introduction of paramagnetic tags on the outer belt of polymer-nanodiscs can be used to speed-up data acquisition by significantly reducing the spin-lattice relaxation (T1) times with minimum-to-no alteration of the spectral quality. Our results also demonstrate the feasibility of using different types of paramagnetic ions (Eu3+, Gd3+, Dy3+, Er3+, Yb3+) for NMR studies on lipid-nanodiscs. Experimental results characterizing the formation of lipid-nanodiscs by the metal-chelated polymer, and their increased tolerance toward metal ions are also reported.
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Affiliation(s)
- Giacomo M Di Mauro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Nathaniel Z Hardin
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Biophysics and Chemistry Department, The University of Michigan, Ann Arbor, MI 48109-1055, USA; Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA; Biomedical Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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13
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Accelerating structural life science by paramagnetic lanthanide probe methods. Biochim Biophys Acta Gen Subj 2020; 1864:129332. [DOI: 10.1016/j.bbagen.2019.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 02/08/2023]
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14
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Spin-labeled nanobodies as protein conformational reporters for electron paramagnetic resonance in cellular membranes. Proc Natl Acad Sci U S A 2020; 117:2441-2448. [PMID: 31964841 DOI: 10.1073/pnas.1913737117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Nanobodies are emerging tools in a variety of fields such as structural biology, cell imaging, and drug discovery. Here we pioneer the use of their spin-labeled variants as reporters of conformational dynamics of membrane proteins using DEER spectroscopy. At the example of the bacterial ABC transporter TM287/288, we show that two gadolinium-labeled nanobodies allow us to quantify, via analysis of the modulation depth of DEER traces, the fraction of transporters adopting the outward-facing state under different experimental conditions. Additionally, we quantitatively follow the interconversion from the outward- to the inward-facing state in the conformational ensemble under ATP turnover conditions. We finally show that the specificity of the nanobodies for the target protein allows the direct attainment of structural information on the wild-type TM287/288 expressed in cellular membranes without the need to purify or label the investigated membrane protein.
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15
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Yardeni EH, Bahrenberg T, Stein RA, Mishra S, Zomot E, Graham B, Tuck KL, Huber T, Bibi E, Mchaourab HS, Goldfarb D. Probing the solution structure of the E. coli multidrug transporter MdfA using DEER distance measurements with nitroxide and Gd(III) spin labels. Sci Rep 2019; 9:12528. [PMID: 31467343 PMCID: PMC6715713 DOI: 10.1038/s41598-019-48694-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 08/08/2019] [Indexed: 11/09/2022] Open
Abstract
Methodological and technological advances in EPR spectroscopy have enabled novel insight into the structural and dynamic aspects of integral membrane proteins. In addition to an extensive toolkit of EPR methods, multiple spin labels have been developed and utilized, among them Gd(III)-chelates which offer high sensitivity at high magnetic fields. Here, we applied a dual labeling approach, employing nitroxide and Gd(III) spin labels, in conjunction with Q-band and W-band double electron-electron resonance (DEER) measurements to characterize the solution structure of the detergent-solubilized multidrug transporter MdfA from E. coli. Our results identify highly flexible regions of MdfA, which may play an important role in its functional dynamics. Comparison of distance distribution of spin label pairs on the periplasm with those calculated using inward- and outward-facing crystal structures of MdfA, show that in detergent micelles, the protein adopts a predominantly outward-facing conformation, although more closed than the crystal structure. The cytoplasmic pairs suggest a small preference to the outward-facing crystal structure, with a somewhat more open conformation than the crystal structure. Parallel DEER measurements with the two types of labels led to similar distance distributions, demonstrating the feasibility of using W-band spectroscopy with a Gd(III) label for investigation of the structural dynamics of membrane proteins.
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Affiliation(s)
- Eliane H Yardeni
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, 76100, Israel
| | - Thorsten Bahrenberg
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Smriti Mishra
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Elia Zomot
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, 76100, Israel
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Kellie L Tuck
- School of Chemistry, Monash University, Wellington Road, Clayton, Victoria, Australia
| | - Thomas Huber
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Eitan Bibi
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, 76100, Israel.
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel.
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16
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Abstract
The DEER (double electron-electron resonance, also called PELDOR) experiment, which probes the dipolar interaction between two spins and thus reveals distance information, is an important tool for structural studies. In recent years, shaped pump pulses have become a valuable addition to the DEER experiment. Shaped pulses offer an increased excitation bandwidth and the possibility to precisely adjust pulse parameters, which is beneficial especially for demanding biological samples. We have noticed that on our home built W-band spectrometer, the dead-time free 4-pulse DEER sequence with chirped pump pulses suffers from distortions at the end of the DEER trace. Although minor, these are crucial for Gd(III)-Gd(III) DEER where the modulation depth is on the order of a few percent. Here we present a modified DEER sequence—referred to as reversed DEER (rDEER)—that circumvents the coherence pathway which gives rise to the distortion. We compare the rDEER (with two chirped pump pulses) performance values to regular 4-pulse DEER with one monochromatic as well as two chirped pulses and investigate the source of the distortion. We demonstrate the applicability and effectivity of rDEER on three systems, ubiquitin labeled with Gd(III)-DOTA-maleimide (DOTA, 1,4,7,10-Tetraazacyclododecane-1,4,7,10-tetraacetic acid) or with Gd(III)-DO3A (DO3A, 1,4,7,10-Tetraazacyclododecane-1,4,7-triyl) triacetic acid) and the multidrug transporter MdfA, labeled with a Gd(III)-C2 tag, and report an increase in the signal-to-noise ratio in the range of 3 to 7 when comparing the rDEER with two chirped pump pulses to standard 4-pulse DEER.
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17
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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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18
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Yang Y, Yang F, Li XY, Su XC, Goldfarb D. In-Cell EPR Distance Measurements on Ubiquitin Labeled with a Rigid PyMTA-Gd(III) Tag. J Phys Chem B 2019; 123:1050-1059. [DOI: 10.1021/acs.jpcb.8b11442] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Yin Yang
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Xia-Yan Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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19
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Gigli L, Andrałojć W, Dalaloyan A, Parigi G, Ravera E, Goldfarb D, Luchinat C. Assessing protein conformational landscapes: integration of DEER data in Maximum Occurrence analysis. Phys Chem Chem Phys 2018; 20:27429-27438. [PMID: 30357188 DOI: 10.1039/c8cp06195e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The properties of the conformational landscape of a biomolecule are of capital importance to understand its function. It is widely accepted that a statistical ensemble is far more representative than a single structure, especially for proteins with disordered regions. While experimental data provide the most important handle on the conformational variability that the system is experiencing, they usually report on either time or ensemble averages. Since the available conformations largely outnumber the (independent) available experimental data, the latter can be equally well reproduced by a variety of ensembles. We have proposed the Maximum Occurrence (MaxOcc) approach to provide an upper bound of the statistical weight of each conformation. This method is expected to converge towards the true statistical weights by increasing the number of independent experimental datasets. In this paper we explore the ability of DEER (Double Electron Electron Resonance) data, which report on the distance distribution between two spin labels attached to a biomolecule, to restrain the MaxOcc values and its complementarity to previously introduced experimental techniques such as NMR and Small-Angle X-ray Scattering. We here present the case of Ca2+ bound calmodulin (CaM) as a test case and show that DEER data impose a sizeable reduction of the conformational space described by high MaxOcc conformations.
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Affiliation(s)
- Lucia Gigli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.
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20
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Yang Y, Yang F, Gong YJ, Bahrenberg T, Feintuch A, Su XC, Goldfarb D. High Sensitivity In-Cell EPR Distance Measurements on Proteins using an Optimized Gd(III) Spin Label. J Phys Chem Lett 2018; 9:6119-6123. [PMID: 30277780 DOI: 10.1021/acs.jpclett.8b02663] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Distance measurements by electron-electron double resonance (DEER) carried out on spin-labeled proteins delivered into cells provide new insights into the conformational states of proteins in their native environment. Such measurements depend on spin labels that exhibit high redox stability and high DEER sensitivity. Here we present a new Gd(III)-based spin label, BrPSPy-DO3A-Gd(III), which was derived from an earlier label, BrPSPy-DO3MA-Gd(III), by removing the methyl group from the methyl acetate pending arms. The small chemical modification led to a reduction in the zero-field splitting and to a significant increase in the phase memory time, which together culminated in a remarkable improvement of in-cell DEER sensitivity, while maintaining the high distance resolution. The excellent performance of BrPSPy-DO3A-Gd(III) in in-cell DEER measurements was demonstrated on doubly labeled ubiquitin and GB1 delivered into HeLa cells by electroporation.
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Affiliation(s)
- Yin Yang
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Nankai University , Tianjin 300071 , China
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Nankai University , Tianjin 300071 , China
| | - Thorsten Bahrenberg
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Akiva Feintuch
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Nankai University , Tianjin 300071 , China
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
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21
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Prokopiou G, Lee MD, Collauto A, Abdelkader EH, Bahrenberg T, Feintuch A, Ramirez-Cohen M, Clayton J, Swarbrick JD, Graham B, Otting G, Goldfarb D. Small Gd(III) Tags for Gd(III)–Gd(III) Distance Measurements in Proteins by EPR Spectroscopy. Inorg Chem 2018; 57:5048-5059. [DOI: 10.1021/acs.inorgchem.8b00133] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Georgia Prokopiou
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Alberto Collauto
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elwy H. Abdelkader
- Research School of Chemistry, Australian National University, Canberra, ACT 2601,Australia
| | - Thorsten Bahrenberg
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - 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
| | - Jessica Clayton
- Department of Physics, University of California, Santa Barbara, California 93106-9530, United States
| | - James D. Swarbrick
- 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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22
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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: 20] [Impact Index Per Article: 3.3] [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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23
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Matveeva AG, Nekrasov VM, Maryasov AG. Analytical solution of the PELDOR inverse problem using the integral Mellin transform. Phys Chem Chem Phys 2018; 19:32381-32388. [PMID: 29185558 DOI: 10.1039/c7cp04059h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We describe a new model-free approach to solve the inverse problem in pulsed double electron-electron resonance (PELDOR, also known as DEER) spectroscopy and obtain the distance distribution function between two radicals from time-domain PELDOR data. The approach is based on analytical solutions of the Fredholm integral equations of the first kind using integral Mellin transforms to provide the distance distribution function directly. The approach appears to confine the noise in the computed distance distribution to short distances and does not introduce systematic distortions. Thus, the proposed analysis method can be a useful supplement to current methods to determine complicated distance distributions.
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Affiliation(s)
- Anna G Matveeva
- Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia.
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24
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Mahawaththa MC, Lee MD, Giannoulis A, Adams LA, Feintuch A, Swarbrick JD, Graham B, Nitsche C, Goldfarb D, Otting G. Small neutral Gd(iii) tags for distance measurements in proteins by double electron–electron resonance experiments. Phys Chem Chem Phys 2018; 20:23535-23545. [DOI: 10.1039/c8cp03532f] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small Gd(iii) tags based on DO3A deliver narrow and readily predictable distances by double electron–electron resonance (DEER) measurements.
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Affiliation(s)
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Angeliki Giannoulis
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Luke A. Adams
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Akiva Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Christoph Nitsche
- Research School of Chemistry
- The Australian National University
- Canberra
- Australia
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Gottfried Otting
- Research School of Chemistry
- The Australian National University
- Canberra
- Australia
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25
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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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26
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Welegedara AP, Yang Y, Lee MD, Swarbrick JD, Huber T, Graham B, Goldfarb D, Otting G. Double‐Arm Lanthanide Tags Deliver Narrow Gd
3+
–Gd
3+
Distance Distributions in Double Electron–Electron Resonance (DEER) Measurements. Chemistry 2017; 23:11694-11702. [DOI: 10.1002/chem.201702521] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Adarshi P. Welegedara
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Yin Yang
- Department of Chemical Physics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - Thomas Huber
- 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 7610001 Israel
| | - Gottfried Otting
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
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27
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Manukovsky N, Feintuch A, Kuprov I, Goldfarb D. Time domain simulation of Gd3+–Gd3+ distance measurements by EPR. J Chem Phys 2017; 147:044201. [DOI: 10.1063/1.4994084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nurit Manukovsky
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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28
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Clayton JA, Qi M, Godt A, Goldfarb D, Han S, Sherwin MS. Gd 3+-Gd 3+ distances exceeding 3 nm determined by very high frequency continuous wave electron paramagnetic resonance. Phys Chem Chem Phys 2017; 19:5127-5136. [PMID: 28139788 PMCID: PMC5394103 DOI: 10.1039/c6cp07119h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron paramagnetic resonance spectroscopy in combination with site-directed spin labeling is a very powerful tool for elucidating the structure and organization of biomolecules. Gd3+ complexes have recently emerged as a new class of spin labels for distance determination by pulsed EPR spectroscopy at Q- and W-band. We present CW EPR measurements at 240 GHz (8.6 Tesla) on a series of Gd-rulers of the type Gd-PyMTA-spacer-Gd-PyMTA, with Gd-Gd distances ranging from 1.2 nm to 4.3 nm. CW EPR measurements of these Gd-rulers show that significant dipolar broadening of the central |-1/2〉 → |1/2〉 transition occurs at 30 K for Gd-Gd distances up to ∼3.4 nm with Gd-PyMTA as the spin label. This represents a significant extension for distances accessible by CW EPR, as nitroxide-based spin labels at X-band frequencies can typically only access distances up to ∼2 nm. We show that this broadening persists at biologically relevant temperatures above 200 K, and that this method is further extendable up to room temperature by immobilizing the sample in glassy trehalose. We show that the peak-to-peak broadening of the central transition follows the expected 1/r3 dependence for the electron-electron dipolar interaction, from cryogenic temperatures up to room temperature. A simple procedure for simulating the dependence of the lineshape on interspin distance is presented, in which the broadening of the central transition is modeled as an S = 1/2 spin whose CW EPR lineshape is broadened through electron-electron dipolar interactions with a neighboring S = 7/2 spin.
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Affiliation(s)
- Jessica A Clayton
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, USA. and Institute for Terahertz Science and Technology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Bielefeld, Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Bielefeld, Germany
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Songi Han
- Institute for Terahertz Science and Technology, University of California, Santa Barbara, Santa Barbara, CA, USA and Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, USA and Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Mark S Sherwin
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, USA. and Institute for Terahertz Science and Technology, University of California, Santa Barbara, Santa Barbara, CA, USA
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29
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Suturina EA, Häussinger D, Zimmermann K, Garbuio L, Yulikov M, Jeschke G, Kuprov I. Model-free extraction of spin label position distributions from pseudocontact shift data. Chem Sci 2017; 8:2751-2757. [PMID: 28553510 PMCID: PMC5426344 DOI: 10.1039/c6sc03736d] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022] Open
Abstract
Not a point, but a cloud: advanced PCS data analysis using 3D probability density reconstruction provides more information.
A significant problem with paramagnetic tags attached to proteins and nucleic acids is their conformational mobility. Each tag is statistically distributed within a volume between 5 and 10 Angstroms across; structural biology conclusions from NMR and EPR work are necessarily diluted by this uncertainty. The problem is solved in electron spin resonance, but remains open in the other major branch of paramagnetic resonance – pseudocontact shift (PCS) NMR spectroscopy, where structural biologists have so far been reluctantly using the point paramagnetic centre approximation. Here we describe a new method for extracting probability densities of lanthanide tags from PCS data. The method relies on Tikhonov-regularised 3D reconstruction and opens a new window into biomolecular structure and dynamics because it explores a very different range of conditions from those accessible to double electron resonance work on paramagnetic tags: a room-temperature solution rather than a glass at cryogenic temperatures. The method is illustrated using four different Tm3+ DOTA-M8 tagged mutants of human carbonic anhydrase II; the results are in good agreement with rotamer library and DEER data. The wealth of high-quality pseudocontact shift data accumulated by the biological magnetic resonance community over the last 30 years, and so far only processed using point models, could now become a major source of useful information on conformational distributions of paramagnetic tags in biomolecules.
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Affiliation(s)
- Elizaveta A Suturina
- School of Chemistry , University of Southampton , Highfield Campus , Southampton , SO17 1BJ , UK .
| | - Daniel Häussinger
- Department of Chemistry , University of Basel , St. Johanns Ring 19 , CH-4056 Basel , Switzerland
| | - Kaspar Zimmermann
- Department of Chemistry , University of Basel , St. Johanns Ring 19 , CH-4056 Basel , Switzerland
| | - Luca Garbuio
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology in Zurich , Vladimir Prelog Weg 1-5/10 , CH-8093 Zürich , Switzerland
| | - Maxim Yulikov
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology in Zurich , Vladimir Prelog Weg 1-5/10 , CH-8093 Zürich , Switzerland
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology in Zurich , Vladimir Prelog Weg 1-5/10 , CH-8093 Zürich , Switzerland
| | - Ilya Kuprov
- School of Chemistry , University of Southampton , Highfield Campus , Southampton , SO17 1BJ , UK .
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30
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Yang Y, Gong YJ, Litvinov A, Liu HK, Yang F, Su XC, Goldfarb D. Generic tags for Mn(ii) and Gd(iii) spin labels for distance measurements in proteins. Phys Chem Chem Phys 2017; 19:26944-26956. [DOI: 10.1039/c7cp04311b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The coordination mode of the metal ion in the spin label affects the distance distribution determined by DEER distance measurements.
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Affiliation(s)
- Yin Yang
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Aleksei Litvinov
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Hong-Kai Liu
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
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31
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Kaushik M, Bahrenberg T, Can TV, Caporini MA, Silvers R, Heiliger J, Smith AA, Schwalbe H, Griffin RG, Corzilius B. Gd(iii) and Mn(ii) complexes for dynamic nuclear polarization: small molecular chelate polarizing agents and applications with site-directed spin labeling of proteins. Phys Chem Chem Phys 2016; 18:27205-27218. [PMID: 27545112 PMCID: PMC5053914 DOI: 10.1039/c6cp04623a] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate complexes of two paramagnetic metal ions Gd3+ and Mn2+ to serve as polarizing agents for solid-state dynamic nuclear polarization (DNP) of 1H, 13C, and 15N at magnetic fields of 5, 9.4, and 14.1 T. Both ions are half-integer high-spin systems with a zero-field splitting and therefore exhibit a broadening of the mS = -1/2 ↔ +1/2 central transition which scales inversely with the external field strength. We investigate experimentally the influence of the chelator molecule, strong hyperfine coupling to the metal nucleus, and deuteration of the bulk matrix on DNP properties. At small Gd-DOTA concentrations the narrow central transition allows us to polarize nuclei with small gyromagnetic ratio such as 13C and even 15N via the solid effect. We demonstrate that enhancements observed are limited by the available microwave power and that large enhancement factors of >100 (for 1H) and on the order of 1000 (for 13C) can be achieved in the saturation limit even at 80 K. At larger Gd(iii) concentrations (≥10 mM) where dipolar couplings between two neighboring Gd3+ complexes become substantial a transition towards cross effect as dominating DNP mechanism is observed. Furthermore, the slow spin-diffusion between 13C and 15N, respectively, allows for temporally resolved observation of enhanced polarization spreading from nuclei close to the paramagnetic ion towards nuclei further removed. Subsequently, we present preliminary DNP experiments on ubiquitin by site-directed spin-labeling with Gd3+ chelator tags. The results hold promise towards applications of such paramagnetically labeled proteins for DNP applications in biophysical chemistry and/or structural biology.
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Affiliation(s)
- Monu Kaushik
- Institute of Physical and Theoretical Chemistry and Institute of Biophysical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt am Main, Germany.
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32
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Meyer A, Schiemann O. PELDOR and RIDME Measurements on a High-Spin Manganese(II) Bisnitroxide Model Complex. J Phys Chem A 2016; 120:3463-72. [DOI: 10.1021/acs.jpca.6b00716] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Andreas Meyer
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstr. 12, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstr. 12, Bonn, Germany
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33
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Demay-Drouhard P, Ching HYV, Akhmetzyanov D, Guillot R, Tabares LC, Bertrand HC, Policar C. A Bis-Manganese(II)-DOTA Complex for Pulsed Dipolar Spectroscopy. Chemphyschem 2016; 17:2066-78. [DOI: 10.1002/cphc.201600234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Paul Demay-Drouhard
- Ecole Normale Supérieure-PSL Research University; Département de Chimie, Sorbonne Universités-UPMC Univ Paris 06; CNRS UMR 7203 LBM; 24 rue Lhomond 75005 Paris France
| | - H. Y. Vincent Ching
- Institute for Integrative Biology of the Cell (I2BC); Department of Biochemistry, Biophysics and Structural Biology; Université Paris-Saclay, CEA, CNRS UMR 9198; Gif-sur-Yvette F-91198 France
| | - Dmitry Akhmetzyanov
- Goethe-University Frankfurt am Main; Institute of Physical and Theoretical Chemistry and; Center for Biomolecular Magnetic Resonance; Max von Laue Str. 7 60438 Frankfurt am Main Germany
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux O'Orsay; Université Paris-Sud, UMR CNRS 8182, Université Paris-Saclay; 91405 Orsay France
| | - Leandro C. Tabares
- Institute for Integrative Biology of the Cell (I2BC); Department of Biochemistry, Biophysics and Structural Biology; Université Paris-Saclay, CEA, CNRS UMR 9198; Gif-sur-Yvette F-91198 France
| | - Hélène C. Bertrand
- Ecole Normale Supérieure-PSL Research University; Département de Chimie, Sorbonne Universités-UPMC Univ Paris 06; CNRS UMR 7203 LBM; 24 rue Lhomond 75005 Paris France
| | - Clotilde Policar
- Ecole Normale Supérieure-PSL Research University; Département de Chimie, Sorbonne Universités-UPMC Univ Paris 06; CNRS UMR 7203 LBM; 24 rue Lhomond 75005 Paris France
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34
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Qi M, Hülsmann M, Godt A. Spacers for Geometrically Well-Defined Water-Soluble Molecular Rulers and Their Application. J Org Chem 2016; 81:2549-71. [DOI: 10.1021/acs.joc.6b00125] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mian Qi
- Faculty of Chemistry and
Center for Molecular Materials (MC2), Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
| | - Miriam Hülsmann
- Faculty of Chemistry and
Center for Molecular Materials (MC2), Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
| | - Adelheid Godt
- Faculty of Chemistry and
Center for Molecular Materials (MC2), Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
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35
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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: 10] [Impact Index Per Article: 1.3] [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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36
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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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37
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Roser P, Schmidt MJ, Drescher M, Summerer D. Site-directed spin labeling of proteins for distance measurements in vitro and in cells. Org Biomol Chem 2016; 14:5468-76. [DOI: 10.1039/c6ob00473c] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We here review strategies for site-directed spin labeling (SDSL) of proteins and discuss their potential for EPR distance measurements to study protein function in vitro and in cells.
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Affiliation(s)
- P. Roser
- Department of Chemistry
- Zukunftskolleg
- and Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
| | - M. J. Schmidt
- Department of Chemistry
- Zukunftskolleg
- and Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
| | - M. Drescher
- Department of Chemistry
- Zukunftskolleg
- and Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
| | - D. Summerer
- Department of Chemistry and Chemical Biology
- Technical University of Dortmund
- 44227 Dortmund
- Germany
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38
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Cohen MR, Frydman V, Milko P, Iron MA, Abdelkader EH, Lee MD, Swarbrick JD, Raitsimring A, Otting G, Graham B, Feintuch A, Goldfarb D. Overcoming artificial broadening in Gd3+–Gd3+ distance distributions arising from dipolar pseudo-secular terms in DEER experiments. Phys Chem Chem Phys 2016; 18:12847-59. [DOI: 10.1039/c6cp00829a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Double electron–electron resonance (DEER) is used to probe structure of Gd3+-tagged biomolecules by determining Gd3+–Gd3+ distances.
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Affiliation(s)
- Marie Ramirez Cohen
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Veronica Frydman
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Petr Milko
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Mark A. Iron
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Elwy H. Abdelkader
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | | | - Gottfried Otting
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Akiva Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
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39
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Abdelkader EH, Yao X, Feintuch A, Adams LA, Aurelio L, Graham B, Goldfarb D, Otting G. Pulse EPR-enabled interpretation of scarce pseudocontact shifts induced by lanthanide binding tags. JOURNAL OF BIOMOLECULAR NMR 2016; 64:39-51. [PMID: 26597990 DOI: 10.1007/s10858-015-0003-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
Pseudocontact shifts (PCS) induced by tags loaded with paramagnetic lanthanide ions provide powerful long-range structure information, provided the location of the metal ion relative to the target protein is known. Usually, the metal position is determined by fitting the magnetic susceptibility anisotropy (Δχ) tensor to the 3D structure of the protein in an 8-parameter fit, which requires a large set of PCSs to be reliable. In an alternative approach, we used multiple Gd(3+)-Gd(3+) distances measured by double electron-electron resonance (DEER) experiments to define the metal position, allowing Δχ-tensor determinations from more robust 5-parameter fits that can be performed with a relatively sparse set of PCSs. Using this approach with the 32 kDa E. coli aspartate/glutamate binding protein (DEBP), we demonstrate a structural transition between substrate-bound and substrate-free DEBP, supported by PCSs generated by C3-Tm(3+) and C3-Tb(3+) tags attached to a genetically encoded p-azidophenylalanine residue. The significance of small PCSs was magnified by considering the difference between the chemical shifts measured with Tb(3+) and Tm(3+) rather than involving a diamagnetic reference. The integrative sparse data approach developed in this work makes poorly soluble proteins of limited stability amenable to structural studies in solution, without having to rely on cysteine mutations for tag attachment.
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Affiliation(s)
- Elwy H Abdelkader
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Xuejun Yao
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, 76100, Rehovot, 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
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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40
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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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41
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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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42
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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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43
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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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44
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Copper-based pulsed dipolar ESR spectroscopy as a probe of protein conformation linked to disease states. Biophys J 2015; 107:1669-74. [PMID: 25296320 DOI: 10.1016/j.bpj.2014.07.068] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 07/18/2014] [Accepted: 07/30/2014] [Indexed: 11/21/2022] Open
Abstract
We demonstrate the ability of pulsed dipolar electron spin resonance (ESR) spectroscopy (PDS) to report on the conformation of Cu-Zn superoxide dismutase (SOD1) through the sensitive measurement of dipolar interactions between inherent Cu(2+) ions. Although the extent and the anisotropy of the Cu ESR spectrum provides challenges for PDS, Ku-band (17.3 GHz) double electron-electron resonance and double-quantum coherence variants of PDS coupled with distance reconstruction methods recover Cu-Cu distances in good agreement with crystal structures. Moreover, Cu-PDS measurements expose distinct differences between the conformational properties of wild-type SOD1 and a single-residue variant (I149T) that leads to the disease amyotrophic lateral sclerosis (ALS). The I149T protein displays a broader Cu-Cu distance distribution within the SOD1 dimer compared to wild-type. In a nitroxide (NO)-labeled sample, distance distributions obtained from Cu-Cu, Cu-NO, and NO-NO separations reveal increased structural heterogeneity within the protein and a tendency for mutant dimers to associate. In contrast, perturbations caused by the ALS mutation are completely masked in the crystal structure of I149T. Thus, PDS readily detects alterations in metalloenzyme solution properties not easily deciphered by other methods and in doing so supports the notion that increased range of motion and associations of SOD1 ALS variants contribute to disease progression.
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45
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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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46
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Lee MD, Loh CT, Shin J, Chhabra S, Dennis ML, Otting G, Swarbrick JD, Graham B. Compact, hydrophilic, lanthanide-binding tags for paramagnetic NMR spectroscopy. Chem Sci 2015; 6:2614-2624. [PMID: 29560247 PMCID: PMC5812434 DOI: 10.1039/c4sc03892d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/25/2015] [Indexed: 01/18/2023] Open
Abstract
The design, synthesis and evaluation of four novel lanthanide-binding tags for paramagnetic NMR spectroscopy are reported.
The design, synthesis and evaluation of four novel lanthanide-binding tags for paramagnetic NMR spectroscopy are reported. Each tag is based on the ((2S,2′S,2′′S,2′′′S)-1,1′,1′′,1′′′-(1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrayl)tetrakis(propan-2-ol)) scaffold, featuring small chiral alcohol coordinating pendants to minimise the size and hydrophobic character of each tag. The tags feature different linkers of variable length for conjugation to protein via a single cysteine residue. Each tag's ability to induce pseudocontact shifts (PCS) was assessed on a ubiquitin A28C mutant. Two enantiomeric tags of particular note, C7 and C8, produced significantly larger Δχ-tensors compared to a previously developed tag, C1, attributed to the extremely short linker utilised, limiting the mobility of the bound lanthanide ion. The C7 and C8 tags' capacity to induce PCSs was further demonstrated on GB1 Q32C and 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) S112C/C80A mutants. Whilst factors such as the choice of lanthanide ion, pH and site of conjugation influence the size of the PCSs obtained, the tags represent a significant advance in the field.
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Affiliation(s)
- M D Lee
- Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , VIC 3052 , Australia . ;
| | - C-T Loh
- Research School of Chemistry , Australian National University , Canberra , ACT 0200 , Australia
| | - J Shin
- Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , VIC 3052 , Australia . ;
| | - S Chhabra
- Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , VIC 3052 , Australia . ;
| | - M L Dennis
- Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , VIC 3052 , Australia . ;
| | - G Otting
- Research School of Chemistry , Australian National University , Canberra , ACT 0200 , Australia
| | - J D Swarbrick
- Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , VIC 3052 , Australia . ;
| | - B Graham
- Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , VIC 3052 , Australia . ;
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47
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Martorana A, Yang Y, Zhao Y, Li QF, Su XC, Goldfarb D. Mn(ii) tags for DEER distance measurements in proteins via C–S attachment. Dalton Trans 2015; 44:20812-6. [DOI: 10.1039/c5dt04123f] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tags for Mn2+–Mn2+ distance measurements in proteins with a short and stable linker that generate narrow distance distributions were developed.
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Affiliation(s)
- Andrea Martorana
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yin Yang
- State Key Laboratory of Elemento-organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Yu Zhao
- State Key Laboratory of Elemento-organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Qing-Feng Li
- State Key Laboratory of Elemento-organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
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48
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Vincent Ching HY, Demay-Drouhard P, Bertrand HC, Policar C, Tabares LC, Un S. Nanometric distance measurements between Mn(ii)DOTA centers. Phys Chem Chem Phys 2015; 17:23368-77. [DOI: 10.1039/c5cp03487f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The distance between two Mn(ii)DOTA complexes attached to the ends of polyproline helices of varying lengths was measured by 94 GHz PELDOR spectroscopy with good accuracy demonstrating their effectiveness as spin-labels.
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Affiliation(s)
- H. Y. Vincent Ching
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
| | - Paul Demay-Drouhard
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Hélène C. Bertrand
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Clotilde Policar
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Leandro C. Tabares
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
| | - Sun Un
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
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49
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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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50
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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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