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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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2
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Krumkacheva OA, Timofeev IO, Politanskaya LV, Polienko YF, Tretyakov EV, Rogozhnikova OY, Trukhin DV, Tormyshev VM, Chubarov AS, Bagryanskaya EG, Fedin MV. Triplet Fullerenes as Prospective Spin Labels for Nanoscale Distance Measurements by Pulsed Dipolar EPR Spectroscopy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Olesya A. Krumkacheva
- International Tomography Center SB RAS Novosibirsk 630090 Russia
- Novosibirsk State University Novosibirsk 630090 Russia
| | - Ivan O. Timofeev
- International Tomography Center SB RAS Novosibirsk 630090 Russia
- Novosibirsk State University Novosibirsk 630090 Russia
| | - Larisa V. Politanskaya
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS Novosibirsk 630090 Russia
- Novosibirsk State University Novosibirsk 630090 Russia
| | - Yuliya F. Polienko
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS Novosibirsk 630090 Russia
- Novosibirsk State University Novosibirsk 630090 Russia
| | - Evgeny V. Tretyakov
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS Novosibirsk 630090 Russia
- Novosibirsk State University Novosibirsk 630090 Russia
| | - Olga Yu. Rogozhnikova
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS Novosibirsk 630090 Russia
- Novosibirsk State University Novosibirsk 630090 Russia
| | - Dmitry V. Trukhin
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS Novosibirsk 630090 Russia
- Novosibirsk State University Novosibirsk 630090 Russia
| | - Victor M. Tormyshev
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS Novosibirsk 630090 Russia
- Novosibirsk State University Novosibirsk 630090 Russia
| | - Alexey S. Chubarov
- Institute of Chemical Biology and Fundamental Medicine SB RAS Novosibirsk 630090 Russia
- Novosibirsk State University Novosibirsk 630090 Russia
| | - Elena G. Bagryanskaya
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS Novosibirsk 630090 Russia
- Novosibirsk State University Novosibirsk 630090 Russia
| | - Matvey V. Fedin
- International Tomography Center SB RAS Novosibirsk 630090 Russia
- Novosibirsk State University Novosibirsk 630090 Russia
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3
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Krumkacheva OA, Timofeev IO, Politanskaya LV, Polienko YF, Tretyakov EV, Rogozhnikova OY, Trukhin DV, Tormyshev VM, Chubarov AS, Bagryanskaya EG, Fedin MV. Triplet Fullerenes as Prospective Spin Labels for Nanoscale Distance Measurements by Pulsed Dipolar EPR Spectroscopy. Angew Chem Int Ed Engl 2019; 58:13271-13275. [PMID: 31322814 DOI: 10.1002/anie.201904152] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/11/2019] [Indexed: 11/11/2022]
Abstract
Precise nanoscale distance measurements by pulsed electron paramagnetic resonance (EPR) spectroscopy play a crucial role in structural studies of biomolecules. The properties of the spin labels used in this approach determine the sensitivity limits, attainable distances, and proximity to biological conditions. Herein, we propose and validate the use of photoexcited fullerenes as spin labels for pulsed dipolar (PD) EPR distance measurements. Hyperpolarization and the narrower spectrum of fullerenes compared to other triplets (e.g., porphyrins) boost the sensitivity, and superior relaxation properties allow PD EPR measurements up to a near-room temperature. This approach is demonstrated using fullerene-nitroxide and fullerene-triarylmethyl pairs, as well as a supramolecular complex of fullerene with nitroxide-labeled protein. Photoexcited triplet fullerenes can be considered as new spin labels with outstanding spectroscopic properties for future structural studies of biomolecules.
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Affiliation(s)
- Olesya A Krumkacheva
- International Tomography Center SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Ivan O Timofeev
- International Tomography Center SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Larisa V Politanskaya
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Yuliya F Polienko
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Evgeny V Tretyakov
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Olga Yu Rogozhnikova
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Dmitry V Trukhin
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Victor M Tormyshev
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Alexey S Chubarov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Elena G Bagryanskaya
- N.N.Vorozhtsov Institute of Organic Chemistry SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Matvey V Fedin
- International Tomography Center SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
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4
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Wegner J, Valora G, Halbmair K, Kehl A, Worbs B, Bennati M, Diederichsen U. Semi-Rigid Nitroxide Spin Label for Long-Range EPR Distance Measurements of Lipid Bilayer Embedded β-Peptides. Chemistry 2019; 25:2203-2207. [DOI: 10.1002/chem.201805880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Janine Wegner
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
| | - Gabriele Valora
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
- Dipartimento di Scienze Chimiche; University of Catania; Italy
| | - Karin Halbmair
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
| | - Annemarie Kehl
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
| | - Brigitte Worbs
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
| | - Marina Bennati
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
| | - Ulf Diederichsen
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
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5
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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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6
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Preise der israelischen chemischen Gesellschaft 2016: D. Milstein, I. Willner, D. Goldfarb, D. Margulies, D. Pappo / Gottfried-Wilhelm-Leibniz-Preis: L. Ackermann und J. P. Spatz / Adolf-Lieben-Vorlesung: A. Fürstner. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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7
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Israel Chemical Society Prizes 2016: D. Milstein, I. Willner, D. Goldfarb, D. Margulies, D. Pappo / Gottfried Wilhelm Leibniz Prize: L. Ackermann and J. P. Spatz / Adolf Lieben Lectureship: A. Fürstner. Angew Chem Int Ed Engl 2017; 56:1957-1958. [DOI: 10.1002/anie.201700079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Lawless MJ, Ghosh S, Cunningham TF, Shimshi A, Saxena S. On the use of the Cu2+–iminodiacetic acid complex for double histidine based distance measurements by pulsed ESR. Phys Chem Chem Phys 2017; 19:20959-20967. [DOI: 10.1039/c7cp02564e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Cu2+-based DEER signal of the double histidine motif was increased by a factor of two by understanding optimal loading conditions.
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Affiliation(s)
- M. J. Lawless
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
| | - S. Ghosh
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
| | - T. F. Cunningham
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
| | - A. Shimshi
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
| | - S. Saxena
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
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9
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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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10
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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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11
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12
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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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13
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Di Valentin M, Albertini M, Zurlo E, Gobbo M, Carbonera D. Porphyrin triplet state as a potential spin label for nanometer distance measurements by PELDOR spectroscopy. J Am Chem Soc 2014; 136:6582-5. [PMID: 24735449 DOI: 10.1021/ja502615n] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This work demonstrates, for the first time, the feasibility of applying pulsed electron-electron double resonance (PELDOR/DEER) to determine the interspin distance between a photoexcited porphyrin triplet state (S = 1) and a nitroxide spin label chemically incorporated into a small helical peptide. The PELDOR trace shows deep envelope modulation induced by electron-electron dipole interaction between the partners in the pair, providing an accurate distance measurement. This new labeling approach has a high potential for measuring nanometer distances in more complex biological systems due to the sensitivity acquired from the spin polarization of the photoexcited triplet state spectrum.
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Affiliation(s)
- Marilena Di Valentin
- Dipartimento di Scienze Chimiche, Università di Padova , via Marzolo 1, 35131 Padova, Italy
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