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Kaiser F, Endeward B, Collauto A, Scheffer U, Prisner TF, Göbel MW. Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block. Chemistry 2022; 28:e202201822. [PMID: 35903916 PMCID: PMC9804336 DOI: 10.1002/chem.202201822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Indexed: 01/05/2023]
Abstract
The nitroxide TPA (2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene) is an excellent spin label for EPR studies of RNA. Previous synthetic methods, however, are complicated and require special equipment. Herein, we describe a uridine derived phosphoramidite with a photocaged TPA unit attached. The light sensitive 2-nitrobenzyloxymethyl group can be removed in high yield by short irradiation at 365 nm. Based on this approach, a doubly spin-labeled 27mer neomycin sensing riboswitch was synthesized and studied by PELDOR. The overall thermal stability of the fold is not much reduced by TPA. In-line probing nevertheless detected changes in local mobility.
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Affiliation(s)
- Frank Kaiser
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Burkhard Endeward
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Alberto Collauto
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Ute Scheffer
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Thomas F. Prisner
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Michael W. Göbel
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
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2
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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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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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4
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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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