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Grosskopf JD, Sidabras JW, Altenbach C, Anderson JR, Mett RR, Strangeway RA, Hyde JS, Hubbell WL, Lerch MT. A pressure-jump EPR system to monitor millisecond conformational exchange rates of spin-labeled proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.593074. [PMID: 38766191 PMCID: PMC11100676 DOI: 10.1101/2024.05.07.593074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) using nitroxide spin labels is a well-established technology for mapping site-specific secondary and tertiary structure and for monitoring conformational changes in proteins of any degree of complexity, including membrane proteins, with high sensitivity. SDSL-EPR also provides information on protein dynamics in the time scale of ps-µs using continuous wave lineshape analysis and spin lattice relaxation time methods. However, the functionally important time domain of µs-ms, corresponding to large-scale protein motions, is inaccessible to those methods. To extend SDSL-EPR to the longer time domain, the perturbation method of pressure-jump relaxation is implemented. Here, we describe a complete high-pressure EPR system at Q-band for both static pressure and millisecond-timescale pressure-jump measurements on spin-labeled proteins. The instrument enables pressure jumps both up and down from any holding pressure, ranging from atmospheric pressure to the maximum pressure capacity of the system components (~3500 bar). To demonstrate the utility of the system, we characterize a local folding-unfolding equilibrium of T4 lysozyme. The results illustrate the ability of the system to measure thermodynamic and kinetic parameters of protein conformational exchange on the millisecond timescale.
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Affiliation(s)
- Julian D Grosskopf
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jason W Sidabras
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Christian Altenbach
- Department of Chemistry and Biochemistry and Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - Jim R Anderson
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Richard R Mett
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Robert A Strangeway
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - James S Hyde
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wayne L Hubbell
- Department of Chemistry and Biochemistry and Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - Michael T Lerch
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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2
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Bizet M, Byrne D, Biaso F, Gerbaud G, Etienne E, Briola G, Guigliarelli B, Urban P, Dorlet P, Kalai T, Truan G, Martinho M. Structural insights into the semiquinone form of human Cytochrome P450 reductase by DEER distance measurements between a native flavin and a spin labelled non-canonical amino acid. Chemistry 2024; 30:e202304307. [PMID: 38277424 DOI: 10.1002/chem.202304307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/28/2024]
Abstract
The flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a "locked/closed" to an "unlocked/open" state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site-Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non-canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH• and the nitroxide. The DEER data revealed a salt concentration-dependent distance distribution, evidence of an "open" CPR conformation at high salt concentrations exceeding previous reports. We also conducted molecular dynamics simulations which unveiled a diverse ensemble of conformations for the "open" semiquinone state of the CPR at high salt concentration. This study unravels the conformational landscape of the one electron reduced state of CPR, which had never been studied before.
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Affiliation(s)
- Maxime Bizet
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Deborah Byrne
- Protein Expression Facility, Aix Marseille Univ, CNRS, IMM, 13402, Marseille, France
| | - Frédéric Biaso
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Emilien Etienne
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Giuseppina Briola
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Philippe Urban
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Pierre Dorlet
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Tamas Kalai
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Pécs, PO Box 99 Szigeti st. 12, H-7602 7624, Pécs, Hungary
| | - Gilles Truan
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Marlène Martinho
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
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3
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Ackermann K, Heubach CA, Schiemann O, Bode BE. Pulse Dipolar Electron Paramagnetic Resonance Spectroscopy Distance Measurements at Low Nanomolar Concentrations: The Cu II-Trityl Case. J Phys Chem Lett 2024; 15:1455-1461. [PMID: 38294197 PMCID: PMC10860127 DOI: 10.1021/acs.jpclett.3c03311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 02/01/2024]
Abstract
Recent sensitivity enhancements in pulse dipolar electron paramagnetic resonance spectroscopy (PDS) have afforded distance measurements at submicromolar spin concentrations. This development opens the path for new science as more biomolecular systems can be investigated at their respective physiological concentrations. Here, we demonstrate that the combination of orthogonal spin-labeling using CuII ions and trityl yields a >3-fold increase in sensitivity compared to that of the established CuII-nitroxide labeling strategy. Application of the recently developed variable-time relaxation-induced dipolar modulation enhancement (RIDME) method yields a further ∼2.5-fold increase compared to the commonly used constant-time RIDME. This overall increase in sensitivity of almost an order of magnitude makes distance measurements in the range of 3 nm with protein concentrations as low as 10 nM feasible, >2 times lower than the previously reported concentration. We expect that experiments at single-digit nanomolar concentrations are imminent, which have the potential to transform biological PDS applications.
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Affiliation(s)
- Katrin Ackermann
- EaStCHEM
School of Chemistry and Biomedical Sciences Research Complex, Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St Andrews KY16 9ST, U.K.
| | - Caspar A. Heubach
- Clausius-Institute
of Physical and Theoretical Chemistry, University
of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Olav Schiemann
- Clausius-Institute
of Physical and Theoretical Chemistry, University
of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Bela E. Bode
- EaStCHEM
School of Chemistry and Biomedical Sciences Research Complex, Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St Andrews KY16 9ST, U.K.
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4
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Gopinath A, Rath T, Morgner N, Joseph B. Lateral gating mechanism and plasticity of the β-barrel assembly machinery complex in micelles and Escherichia coli. PNAS NEXUS 2024; 3:pgae019. [PMID: 38312222 PMCID: PMC10833450 DOI: 10.1093/pnasnexus/pgae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024]
Abstract
The β-barrel assembly machinery (BAM) mediates the folding and insertion of the majority of outer membrane proteins (OMPs) in gram-negative bacteria. BAM is a penta-heterooligomeric complex consisting of the central β-barrel BamA and four interacting lipoproteins BamB, C, D, and E. The conformational switching of BamA between inward-open (IO) and lateral-open (LO) conformations is required for substrate recognition and folding. However, the mechanism for the lateral gating or how the structural details observed in vitro correspond with the cellular environment remains elusive. In this study, we addressed these questions by characterizing the conformational heterogeneity of BamAB, BamACDE, and BamABCDE complexes in detergent micelles and/or Escherichia coli using pulsed dipolar electron spin resonance spectroscopy (PDS). We show that the binding of BamB does not induce any visible changes in BamA, and the BamAB complex exists in the IO conformation. The BamCDE complex induces an IO to LO transition through a coordinated movement along the BamA barrel. However, the extracellular loop 6 (L6) is unaffected by the presence of lipoproteins and exhibits large segmental dynamics extending to the exit pore. PDS experiments with the BamABCDE complex in intact E. coli confirmed the dynamic behavior of both the lateral gate and the L6 in the native environment. Our results demonstrate that the BamCDE complex plays a key role in the function by regulating lateral gating in BamA.
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Affiliation(s)
- Aathira Gopinath
- Department of Physics, Freie Universität Berlin, Berlin, 14195, Germany
- Institute of Biophysics, Goethe Universität Frankfurt, Frankfurt, 60438, Germany
| | - Tobias Rath
- Institute of Physical and Theoretical Chemistry, Goethe Universität Frankfurt, Frankfurt, 60438, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe Universität Frankfurt, Frankfurt, 60438, Germany
| | - Benesh Joseph
- Department of Physics, Freie Universität Berlin, Berlin, 14195, Germany
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5
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Zhurko IF, Dobrynin SA, Glazachev YI, Gatilov YV, Kirilyuk IA. 2,5-Di-tert-butyl-2,5-diethylpyrrolidine-1-oxyls: Where Is a Reasonable Limit of Sterical Loading for Higher Resistance to Reduction? Molecules 2024; 29:599. [PMID: 38338344 PMCID: PMC10856307 DOI: 10.3390/molecules29030599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 02/12/2024] Open
Abstract
The pyrrolidine nitroxides with four bulky alkyl substituents adjacent to the N-O∙ group demonstrate very high resistance to reduction with biogenic antioxidants and enzymatic systems. This makes them valuable molecular tools for studying the structure and functions of biomolecules directly in a living cell and for functional EPR and NMR tomography in vivo. The first example of highly strained pyrrolidine nitroxides with both ethyl and tert-butyl groups at each of the α-carbon atoms of the nitroxide moiety with cis-configuration of the tert-butyl groups was prepared using a three-component domino reaction of tert-leucine and 2,2-dimethylpentan-3-one with dimethyl fumarate with subsequent conversion of the resulting strained pyrrolidine into 1-pyrroline-1-oxide and addition of EtLi. The nitroxide has demonstrated unexpectedly fast reduction with ascorbate, the rate constant k2 = (2.0 ± 0.1) × 10-3 M-1s-1. This effect was explained by destabilization of the planar nitroxide moiety due to repulsion with the two neighboring tert-butyl groups cis to each other.
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Affiliation(s)
- Irina F. Zhurko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (I.F.Z.); (S.A.D.); (Y.V.G.)
| | - Sergey A. Dobrynin
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (I.F.Z.); (S.A.D.); (Y.V.G.)
| | - Yurii I. Glazachev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3, Novosibirsk 630090, Russia;
| | - Yuri V. Gatilov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (I.F.Z.); (S.A.D.); (Y.V.G.)
| | - Igor A. Kirilyuk
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (I.F.Z.); (S.A.D.); (Y.V.G.)
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6
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Bertran A, Morbiato L, Sawyer J, Dalla Torre C, Heyes DJ, Hay S, Timmel CR, Di Valentin M, De Zotti M, Bowen AM. Direct Comparison between Förster Resonance Energy Transfer and Light-Induced Triplet-Triplet Electron Resonance Spectroscopy. J Am Chem Soc 2023; 145:22859-22865. [PMID: 37839071 PMCID: PMC10603778 DOI: 10.1021/jacs.3c04685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Indexed: 10/17/2023]
Abstract
To carry out reliable and comprehensive structural investigations, the exploitation of different complementary techniques is required. Here, we report that dual triplet-spin/fluorescent labels enable the first parallel distance measurements by electron spin resonance (ESR) and Förster resonance energy transfer (FRET) on exactly the same molecules with orthogonal chromophores, allowing for direct comparison. An improved light-induced triplet-triplet electron resonance method with 2-color excitation is used, improving the signal-to-noise ratio of the data and yielding a distance distribution that provides greater insight than the single distance resulting from FRET.
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Affiliation(s)
- Arnau Bertran
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Laura Morbiato
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Jack Sawyer
- The
National Research Facility for Electron Paramagnetic Resonance, Department
of Chemistry, Manchester Institute of Biotechnology and Photon Science
Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Chiara Dalla Torre
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Derren J. Heyes
- The
National Research Facility for Electron Paramagnetic Resonance, Department
of Chemistry, Manchester Institute of Biotechnology and Photon Science
Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam Hay
- The
National Research Facility for Electron Paramagnetic Resonance, Department
of Chemistry, Manchester Institute of Biotechnology and Photon Science
Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Christiane R. Timmel
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Marilena Di Valentin
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
- Centro
Interdipartimentale di Ricerca “Centro Studi di Economia e
Tecnica dell’energia Giorgio Levi Cases”, 35131 Padova, Italy
| | - Marta De Zotti
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
- Centro
Interdipartimentale di Ricerca “Centro Studi di Economia e
Tecnica dell’energia Giorgio Levi Cases”, 35131 Padova, Italy
| | - Alice M. Bowen
- The
National Research Facility for Electron Paramagnetic Resonance, Department
of Chemistry, Manchester Institute of Biotechnology and Photon Science
Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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7
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Stehle J, Fleming JR, Bauer PM, Mayans O, Drescher M. Titin UN2A Acts as a Stable, Non-Polymorphic Scaffold in its Binding to CARP. Chembiochem 2023; 24:e202300408. [PMID: 37503755 DOI: 10.1002/cbic.202300408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023]
Abstract
The N2A segment of titin functions as a pivotal hub for signal transduction and interacts with various proteins involved in structural support, chaperone activities, and transcriptional regulation. Notably, the "unique N2A" (UN2A) subdomain has been shown to interact with the stress-regulated cardiac ankyrin repeat protein (CARP), which contributes to the regulation of sarcomeric stiffness. Previously, the UN2A domain's three-dimensional structure was modelled based on its secondary structure content identified by NMR spectroscopy, considering the domain in isolation. In this study, we report experimental long-range distance distributions by electron paramagnetic resonance (EPR) spectroscopy between the three helixes within the UN2A domain linked to the immunoglobulin domain I81 in the presence and absence of CARP. The data confirm the central three-helix bundle fold of UN2A and show that this adopts a compact and stable conformation in absence of CARP. After binding to CARP, no significant conformational change was observed, suggesting that the UN2A domain retains its structure upon binding to CARP thereby, mediating the interaction approximately as a rigid-body.
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Affiliation(s)
- Juliane Stehle
- Department of Chemistry and Konstanz Research School of Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Jennifer R Fleming
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Piera-Maria Bauer
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Olga Mayans
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School of Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
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8
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Asanbaeva NB, Novopashina DS, Rogozhnikova OY, Tormyshev VM, Kehl A, Sukhanov AA, Shernyukov AV, Genaev AM, Lomzov AA, Bennati M, Meyer A, Bagryanskaya EG. 19F electron nuclear double resonance (ENDOR) spectroscopy for distance measurements using trityl spin labels in DNA duplexes. Phys Chem Chem Phys 2023; 25:23454-23466. [PMID: 37609874 DOI: 10.1039/d3cp02969g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The combination of fluorine labeling and pulsed electron-nuclear double resonance (ENDOR) is emerging as a powerful technique for obtaining structural information about proteins and nucleic acids. In this work, we explored the capability of Mims 19F ENDOR experiments on reporting intermolecular distances in trityl- and 19F-labeled DNA duplexes at three electron paramagnetic resonance (EPR) frequencies (34, 94, and 263 GHz). For spin labeling, we used the hydrophobic Finland trityl radical and hydrophilic OX063 trityl radical. Fluorine labels were introduced into two positions of a DNA oligonucleotide. The results indicated that hyperfine splittings visible in the ENDOR spectra are consistent with the most populated interspin distances between 19F and the trityl radical predicted from molecular dynamic (MD) simulations. Moreover, for some cases, ENDOR spectral simulations based on MD results were able to reproduce the conformational distribution reflected in the experimental ENDOR line broadening. Additionally, MD simulations provided more detailed information about the melting of terminal base pairs of the oligonucleotides and about the configuration of the trityls relative to a DNA end.
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Affiliation(s)
- N B Asanbaeva
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia.
| | - D S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia
| | - O Yu Rogozhnikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia.
| | - V M Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia.
| | - A Kehl
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - A A Sukhanov
- Zavoisky Physical-Technical Institute, FRC Kazan Scientific Center of RAS, 10/7 Sibirsky Tract, Kazan 420029, Russia
| | - A V Shernyukov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia.
| | - A M Genaev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia.
| | - A A Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia
| | - M Bennati
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
- Institute of Physical Chemistry, Department of Chemistry, Georg August University of Göttingen, Tammannstr.6, Göttingen, Germany
| | - A Meyer
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
- Institute of Physical Chemistry, Department of Chemistry, Georg August University of Göttingen, Tammannstr.6, Göttingen, Germany
| | - E G Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia.
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9
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Khoroshunova YV, Morozov DA, Kuznetsov DA, Rybalova TV, Glazachev YI, Bagryanskaya EG, Kirilyuk IA. Synthesis and Properties of (1 R( S),5 R( S),7 R( S),8 R( S))-1,8-Bis(hydroxymethyl)-6-azadispiro[4.1.4.2]tridecane-6-oxyl: Reduction-Resistant Spin Labels with High Spin Relaxation Times. Int J Mol Sci 2023; 24:11498. [PMID: 37511257 PMCID: PMC10380268 DOI: 10.3390/ijms241411498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Site-directed spin labeling followed by investigation using Electron Paramagnetic Resonance spectroscopy is a rapidly expanding powerful biophysical technique to study structure, local dynamics and functions of biomolecules using pulsed EPR techniques and nitroxides are the most widely used spin labels. Modern trends of this method include measurements directly inside a living cell, as well as measurements without deep freezing (below 70 K), which provide information that is more consistent with the behavior of the molecules under study in natural conditions. Such studies require nitroxides, which are resistant to the action of biogenic reductants and have high spin relaxation (dephasing) times, Tm. (1R(S),5R(S),7R(S),8R(S))-1,8-bis(hydroxymethyl)-6-azadispiro[4.1.4.2]tridecane-6-oxyl is a unique nitroxide that combines these features. We have developed a convenient method for the synthesis of this radical and studied the ways of its functionalization. Promising spin labels have been obtained, the parameters of their spin relaxation T1 and Tm have been measured, and the kinetics of reduction with ascorbate have been studied.
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Affiliation(s)
- Yulia V Khoroshunova
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia
| | - Denis A Morozov
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Danil A Kuznetsov
- Department of Physics, Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia
| | - Tatyana V Rybalova
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Yurii I Glazachev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3, 630090 Novosibirsk, Russia
| | - Elena G Bagryanskaya
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Igor A Kirilyuk
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
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