1
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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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2
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Hasanbasri Z, Poncelet M, Hunter H, Driesschaert B, Saxena S. A new 13C trityl-based spin label enables the use of DEER for distance measurements. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 347:107363. [PMID: 36620971 PMCID: PMC9928843 DOI: 10.1016/j.jmr.2022.107363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Triarylmethyl (TAM)-based labels, while still underutilized, are a powerful class of labels for pulsed-Electron Spin Resonance (ESR) distance measurements. They feature slow relaxation rates for long-lasting signals, high stability for cellular experiments, and narrow spectral features for efficient excitation of the spins. However, the typical narrow line shape limits the available distance measurements to only single-frequency experiments, such as Double Quantum Coherence (DQC) and Relaxation Induced Dipolar Modulation Enhancement (RIDME), which can be complicated to perform or hard to process. Therefore, widespread usage of TAM labels can be enhanced by the use of Double Electron-Electron Resonance (DEER) distance measurements. In this work, we developed a new spin label, 13C1-mOX063-d24, with a 13C isotope as the radical center. Due to the resolved hyperfine splitting, the spectrum is sufficiently broadened to permit DEER-based experiments at Q-band spectrometers. Additionally, this new label can be incorporated orthogonally with Cu(II)-based protein label. The orthogonal labeling scheme enables DEER distance measurement at X-band frequencies. Overall, the new trityl label allows for DEER-based distance measurements that complement existing TAM-label DQC and RIDME experiments.
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Affiliation(s)
- Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Martin Poncelet
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, WV 26506, United States
| | - Hannah Hunter
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, WV 26506, United States; C. Eugene Bennett Department of Chemistry West Virginia University, Morgantown, WV 26506, United States.
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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3
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Vanas A, Soetbeer J, Breitgoff FD, Hintz H, Sajid M, Polyhach Y, Godt A, Jeschke G, Yulikov M, Klose D. Intermolecular contributions, filtration effects and signal composition of SIFTER (single-frequency technique for refocusing). MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2023; 4:1-18. [PMID: 38269110 PMCID: PMC10807728 DOI: 10.5194/mr-4-1-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/14/2022] [Indexed: 01/26/2024]
Abstract
To characterize structure and molecular order in the nanometre range, distances between electron spins and their distributions can be measured via dipolar spin-spin interactions by different pulsed electron paramagnetic resonance experiments. Here, for the single-frequency technique for refocusing dipolar couplings (SIFTER), the buildup of dipolar modulation signal and intermolecular contributions is analysed for a uniform random distribution of monoradicals and biradicals in frozen glassy solvent by using the product operator formalism for electron spin S = 1 / 2 . A dipolar oscillation artefact appearing at both ends of the SIFTER time trace is predicted, which originates from the weak coherence transfer between biradicals. The relative intensity of this artefact is predicted to be temperature independent but to increase with the spin concentration in the sample. Different compositions of the intermolecular background are predicted in the case of biradicals and in the case of monoradicals. Our theoretical account suggests that the appropriate procedure of extracting the intramolecular dipolar contribution (form factor) requires fitting and subtracting the unmodulated part, followed by division by an intermolecular background function that is different in shape. This scheme differs from the previously used heuristic background division approach. We compare our theoretical derivations to experimental SIFTER traces for nitroxide and trityl monoradicals and biradicals. Our analysis demonstrates a good qualitative match with the proposed theoretical description. The resulting perspectives for a quantitative analysis of SIFTER data are discussed.
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Affiliation(s)
- Agathe Vanas
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Janne Soetbeer
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Frauke Diana Breitgoff
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Henrik Hintz
- Department of Chemistry, Bielefeld University, Universitätsstrasse
25, 33615 Bielefeld, Germany
| | - Muhammad Sajid
- Department of Chemistry, Bielefeld University, Universitätsstrasse
25, 33615 Bielefeld, Germany
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Adelheid Godt
- Department of Chemistry, Bielefeld University, Universitätsstrasse
25, 33615 Bielefeld, Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Daniel Klose
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
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4
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Poncelet M, Ngendahimana T, Gluth TD, Hoblitzell EH, Eubank TD, Eaton GR, Eaton SS, Driesschaert B. Synthesis and characterization of a biocompatible 13C 1 isotopologue of trityl radical OX071 for in vivo EPR viscometry. Analyst 2022; 147:5643-5648. [PMID: 36373434 PMCID: PMC9729415 DOI: 10.1039/d2an01527g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
We describe the synthesis, characterization, and application of an isotopologue of the trityl radical OX071, labeled with 13C at the central carbon (13C1). This spin probe features large anisotropy of the hyperfine coupling with the 13C1 (I = 1/2), leading to an EPR spectrum highly sensitive to molecular tumbling. The high biocompatibility and lack of interaction with blood albumin allow for systemic delivery and in vivo measurement of tissue microviscosity by EPR.
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Affiliation(s)
- Martin Poncelet
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV, 26506, USA
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA.
| | - Thacien Ngendahimana
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Teresa D Gluth
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV, 26506, USA
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA.
| | - Emily H Hoblitzell
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA.
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, School of Medicine, Morgantown, WV, 26506, USA
| | - Timothy D Eubank
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA.
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, School of Medicine, Morgantown, WV, 26506, USA
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV, 26506, USA
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA.
- Eugene Bennett Department of Chemistry, West Virginia University, WV, 26506, USA
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5
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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6
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7
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Asanbaeva N, Sukhanov A, Diveikina AA, Rogozhnikova O, Trukhin DV, Tormyshev VM, Chubarov AS, Maryasov AG, Genaev A, Shernyukov AV, Salnikov GE, Lomzov AA, Pyshnyi DV, Bagryanskaya E. Application of W-band 19F electron nuclear double resonance (ENDOR) spectroscopy to distance measurement using a trityl spin probe and a fluorine label. Phys Chem Chem Phys 2022; 24:5982-6001. [DOI: 10.1039/d1cp05445g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently, Marina Bennati and coworkers (Angew. Chemie - Int. Ed., 2020, 59, 373–379., A. J. Magn. Reson., 2021, 333, 107091) proposed to use electron nuclear double resonance (ENDOR) spectroscopy in...
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8
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Ovcherenko SS, Chinak OA, Chechushkov AV, Dobrynin SA, Kirilyuk IA, Krumkacheva OA, Richter VA, Bagryanskaya EG. Uptake of Cell-Penetrating Peptide RL2 by Human Lung Cancer Cells: Monitoring by Electron Paramagnetic Resonance and Confocal Laser Scanning Microscopy. Molecules 2021; 26:5442. [PMID: 34576913 PMCID: PMC8470091 DOI: 10.3390/molecules26185442] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 11/21/2022] Open
Abstract
RL2 is a recombinant analogue of a human κ-casein fragment, capable of penetrating cells and inducing apoptosis of cancer cells with no toxicity to normal cells. The exact mechanism of RL2 penetration into cells remains unknown. In this study, we investigated the mechanism of RL2 penetration into human lung cancer A549 cells by a combination of electron paramagnetic resonance (EPR) spectroscopy and confocal laser scanning microscopy. EPR spectra of A549 cells incubated with RL2 (sRL2) spin-labeled by a highly stable 3-carboxy-2,2,5,5-tetraethylpyrrolidine-1-oxyl radical were found to contain three components, with their contributions changing with time. The combined EPR and confocal-microscopy data allowed us to assign these three forms of sRL2 to the spin-labeled protein sticking to the membrane of the cell and endosomes, to the spin-labeled protein in the cell interior, and to spin labeled short peptides formed in the cell because of protein digestion. EPR spectroscopy enabled us to follow the kinetics of transformations between different forms of the spin-labeled protein at a minimal spin concentration (3-16 μM) in the cell. The prospects of applications of spin-labeled cell-penetrating peptides to EPR imaging, DNP, and magnetic resonance imaging are discussed, as is possible research on an intrinsically disordered protein in the cell by pulsed dipolar EPR spectroscopy.
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Affiliation(s)
- Sergey S. Ovcherenko
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (S.S.O.); (S.A.D.); (I.A.K.)
| | - Olga A. Chinak
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (O.A.C.); (A.V.C.); (V.A.R.)
| | - Anton V. Chechushkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (O.A.C.); (A.V.C.); (V.A.R.)
| | - Sergey A. Dobrynin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (S.S.O.); (S.A.D.); (I.A.K.)
| | - Igor A. Kirilyuk
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (S.S.O.); (S.A.D.); (I.A.K.)
| | | | - Vladimir A. Richter
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (O.A.C.); (A.V.C.); (V.A.R.)
| | - Elena G. Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (S.S.O.); (S.A.D.); (I.A.K.)
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9
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Rogozhnikova OY, Trukhin DV, Asanbaeva NB, Tormyshev VM. A Simple and Convenient Synthesis of a Multifunctional Spin Probe, Phosphonate Derivative of a Persistent Radical of the Triarylmethyl Series. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [DOI: 10.1134/s107042802106004x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Chen L, Wu L, Tan X, Rockenbauer A, Song Y, Liu Y. Synthesis and Redox Properties of Water-Soluble Asymmetric Trityl Radicals. J Org Chem 2021; 86:8351-8364. [PMID: 34043350 DOI: 10.1021/acs.joc.1c00766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tetrathiatriarylmethyl (trityl) radicals have been recently shown to react with biological oxidoreductants including glutathione (GSH), ascorbic acid (Asc), and superoxide anion radical (O2•-). However, how the substituents affect the reactivity of trityl radicals is still unknown. In this work, five asymmetric trityl radicals were synthesized and their reactivities with GSH, Asc, and O2•- investigated. Under aerobic conditions, GSH induces fast decays for the thioether- (TSA) and N-methyleneglycine-substituted (TGA) derivatives and slow decay for the 4-carboxyphenyl-containing one (TPA). Under anaerobic conditions, the direct reduction of these radicals by GSH also occurs with rate constants (kGSH) from 1.8 × 10-4 M-1 s-1 for TPA to 1.0 × 10-2 M-1 s-1 for TGA. Moreover, these radicals can also react with O2•- with rate constants (kSO) from 1.2 × 103 M-1 s-1 for ET-01 to 1.6 × 104 M-1 s-1 for TGA. Surprisingly, these radicals are completely inert to Asc in both aerobic and anaerobic conditions. Additionally, the substituents exert an important effect on redox potentials of these trityl radicals. This work demonstrates that the redox properties of the trityl radicals strongly depend on their substituents, and TPA with high stability toward GSH shows great potential for intracellular applications.
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Affiliation(s)
- Li Chen
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Medicinal Chemistry, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Lanlan Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Medicinal Chemistry, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Xiaoli Tan
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Medicinal Chemistry, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Hungary.,Department of Physics, Budapest University of Technology and Economics, Budafoki ut 8, 1111 Budapest, Hungary
| | - Yuguang Song
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Medicinal Chemistry, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Medicinal Chemistry, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
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11
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Ketter S, Gopinath A, Rogozhnikova O, Trukhin D, Tormyshev VM, Bagryanskaya EG, Joseph B. In Situ Labeling and Distance Measurements of Membrane Proteins in E. coli Using Finland and OX063 Trityl Labels. Chemistry 2021; 27:2299-2304. [PMID: 33197077 PMCID: PMC7898545 DOI: 10.1002/chem.202004606] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/13/2020] [Indexed: 01/03/2023]
Abstract
In situ investigation of membrane proteins is a challenging task. Previously we demonstrated that nitroxide labels combined with pulsed ESR spectroscopy is a promising tool for this purpose. However, the nitroxide labels suffer from poor stability, high background labeling, and low sensitivity. Here we show that Finland (FTAM) and OX063 based labels enable labeling of the cobalamin transporter BtuB and BamA, the central component of the β-barrel assembly machinery (BAM) complex, in E coli. Compared to the methanethiosulfonate spin label (MTSL), trityl labels eliminated the background signals and enabled specific in situ labeling of the proteins with high efficiency. The OX063 labels show a long phase memory time (TM ) of ≈5 μs. All the trityls enabled distance measurements between BtuB and an orthogonally labeled substrate with high selectivity and sensitivity down to a few μm concentration. Our data corroborate the BtuB and BamA conformations in the cellular environment of E. coli.
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Affiliation(s)
- Sophie Ketter
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
| | - Aathira Gopinath
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
| | - Olga Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Dmitrii Trukhin
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Victor M. Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Elena G. Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Benesh Joseph
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
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12
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Trukhin DV, Rogozhnikova OY, Troitskaya TI, Ovcherenko SS, Amosov EV, Tormyshev VM. Novel Acetylene Derivatives of Stable Tetrathiatriarylmethyl Radicals. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1070428020110032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Poncelet M, Driesschaert B. A 13 C-Labeled Triarylmethyl Radical as an EPR Spin Probe Highly Sensitive to Molecular Tumbling. Angew Chem Int Ed Engl 2020; 59:16451-16454. [PMID: 32542924 PMCID: PMC7901239 DOI: 10.1002/anie.202006591] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 12/21/2022]
Abstract
A stable triarylmethyl spin probe whose electron paramagnetic resonance (EPR) spectrum is highly sensitive to molecular tumbling is reported. The strong anisotropy of the hyperfine coupling tensor with the central carbon of a 13 C1 -labeled triarylmethyl radical enables the measurement of the probe rotational correlation time with applications to measure microviscosity and molecular dynamics.
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Affiliation(s)
- Martin Poncelet
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown WV, 26506, USA
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown WV, 26506, USA
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown WV, 26506, USA
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown WV, 26506, USA
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14
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Poncelet M, Driesschaert B. A
13
C‐Labeled Triarylmethyl Radical as an EPR Spin Probe Highly Sensitive to Molecular Tumbling. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Martin Poncelet
- Department of Pharmaceutical SciencesSchool of PharmacyWest Virginia University Morgantown WV 26506 USA
- In Vivo Multifunctional Magnetic Resonance CenterRobert C. Byrd Health Sciences CenterWest Virginia University Morgantown WV 26506 USA
| | - Benoit Driesschaert
- Department of Pharmaceutical SciencesSchool of PharmacyWest Virginia University Morgantown WV 26506 USA
- In Vivo Multifunctional Magnetic Resonance CenterRobert C. Byrd Health Sciences CenterWest Virginia University Morgantown WV 26506 USA
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15
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Yang Y, Pan BB, Tan X, Yang F, Liu Y, Su XC, Goldfarb D. In-Cell Trityl-Trityl Distance Measurements on Proteins. J Phys Chem Lett 2020; 11:1141-1147. [PMID: 31951412 PMCID: PMC7307952 DOI: 10.1021/acs.jpclett.9b03208] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Double-electron electron resonance (DEER) can be used to track the structural dynamics of proteins in their native environment, the cell. This method provides the distance distribution between two spin labels attached at specific, well-defined positions in a protein. For the method to be viable under in-cell conditions, the spin label and its attachment to the protein should exhibit high chemical stability in the cell. Here we present low-temperature, trityl-trityl DEER distance measurements on two model proteins, PpiB (prolyl cis-trans isomerase from E. coli) and GB1 (immunoglobulin G-binding protein), doubly labeled with the trityl spin label, CT02MA. Both proteins gave in-cell distance distributions similar to those observed in vitro, with maxima at 4.5-5 nm, and the data were further compared with in-cell Gd(III)-Gd(III) DEER obtained for PpiB labeled with BrPSPy-DO3A-Gd(III) at the same positions. These results highlight the challenges of designing trityl tags suitable for in-cell distance determination at ambient temperatures on live cells.
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Affiliation(s)
- Yin Yang
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Bin-Bin Pan
- State
Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation
Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Xiaoli Tan
- Tianjin
Key Laboratory on Technologies Enabling Development of Clinical Therapeutics
and Diagnostics, School of Pharmacy, Tianjin
Medical University, Tianjin 300070, China
| | - Feng Yang
- State
Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation
Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Yangping Liu
- Tianjin
Key Laboratory on Technologies Enabling Development of Clinical Therapeutics
and Diagnostics, School of Pharmacy, Tianjin
Medical University, Tianjin 300070, China
| | - Xun-Cheng Su
- State
Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation
Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Daniella Goldfarb
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
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16
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Kuzhelev AA, Tormyshev VM, Plyusnin VF, Rogozhnikova OY, Edeleva MV, Veber SL, Bagryanskaya EG. Photochemistry of tris(2,3,5,6-tetrathiaaryl)methyl radicals in various solutions. Phys Chem Chem Phys 2020; 22:1019-1026. [DOI: 10.1039/c9cp06213k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A detailed mechanism of TAM photolysis was studied and includes photoionization of the TAM radical with the formation of carbocation and further conversion of the carbocation under aerobic conditions into quinone-methide and under anaerobic conditions supposedly into an aromatic carbene.
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Affiliation(s)
- Andrey A. Kuzhelev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- Novosibirsk 630090
- Russia
| | - Victor M. Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- Novosibirsk 630090
- Russia
- Novosibirsk State University
- Novosibirsk 630090
| | - Victor F. Plyusnin
- Novosibirsk State University
- Novosibirsk 630090
- Russia
- Voevodsky Institute of Chemical Kinetics and Combustion
- SB RAS
| | - Olga Yu. Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- Novosibirsk 630090
- Russia
| | - Mariya V. Edeleva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- Novosibirsk 630090
- Russia
- Novosibirsk State University
- Novosibirsk 630090
| | - Sergey L. Veber
- Novosibirsk State University
- Novosibirsk 630090
- Russia
- International Tomography Center SB RAS
- Novosibirsk 630090
| | - Elena G. Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- Novosibirsk 630090
- Russia
- Novosibirsk State University
- Novosibirsk 630090
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17
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Krumkacheva OA, Shevelev GY, Lomzov AA, Dyrkheeva NS, Kuzhelev AA, Koval VV, Tormyshev VM, Polienko YF, Fedin MV, Pyshnyi DV, Lavrik OI, Bagryanskaya EG. DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling. Nucleic Acids Res 2019; 47:7767-7780. [PMID: 31329919 PMCID: PMC6735896 DOI: 10.1093/nar/gkz620] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/04/2019] [Accepted: 07/11/2019] [Indexed: 12/19/2022] Open
Abstract
A DNA molecule is under continuous influence of endogenous and exogenous damaging factors, which produce a variety of DNA lesions. Apurinic/apyrimidinic sites (abasic or AP sites) are among the most common DNA lesions. In this work, we applied pulse dipolar electron paramagnetic resonance (EPR) spectroscopy in combination with molecular dynamics (MD) simulations to investigate in-depth conformational changes in DNA containing an AP site and in a complex of this DNA with AP endonuclease 1 (APE1). For this purpose, triarylmethyl (TAM)-based spin labels were attached to the 5' ends of an oligonucleotide duplex, and nitroxide spin labels were introduced into APE1. In this way, we created a system that enabled monitoring the conformational changes of the main APE1 substrate by EPR. In addition, we were able to trace substrate-to-product transformation in this system. The use of different (orthogonal) spin labels in the enzyme and in the DNA substrate has a crucial advantage allowing for detailed investigation of local damage and conformational changes in AP-DNA alone and in its complex with APE1.
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Affiliation(s)
- Olesya A Krumkacheva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Georgiy Yu Shevelev
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Andrey A Kuzhelev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Vladimir V Koval
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Victor M Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Yuliya F Polienko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Matvey V Fedin
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
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18
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Meschaninova MI, Novopashina DS, Semikolenova OA, Silnikov VN, Venyaminova AG. Novel Convenient Approach to the Solid-Phase Synthesis of Oligonucleotide Conjugates. Molecules 2019; 24:E4266. [PMID: 31771111 PMCID: PMC6930482 DOI: 10.3390/molecules24234266] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 01/03/2023] Open
Abstract
A novel and convenient approach for the solid-phase 5'-functionalization of oligonucleotides is proposed in this article. The approach is based on the activation of free 5'-hydroxyl of polymer support-bound protected oligonucleotides by N,N'-disuccinimidyl carbonate followed by interaction with amino-containing ligands. Novel amino-containing derivatives of closo-dodecaborate, estrone, cholesterol, and α-tocopherol were specially prepared. A wide range of oligonucleotide conjugates bearing closo-dodecaborate, short peptide, pyrene, lipophilic residues (cholesterol, α-tocopherol, folate, estrone), aliphatic diamines, and propargylamine were synthesized and characterized to demonstrate the versatility of the approach. The developed method is suitable for the conjugate synthesis of oligonucleotides of different types (ribo-, deoxyribo-, 2'-O-methylribo-, and others).
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Affiliation(s)
- Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova str.2, Novosibirsk 630090, Russia;
| | - Olga A. Semikolenova
- Department of Natural Sciences, Novosibirsk State University, Pirogova str.2, Novosibirsk 630090, Russia;
| | - Vladimir N. Silnikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
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19
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Poncelet M, Huffman JL, Khramtsov VV, Dhimitruka I, Driesschaert B. Synthesis of hydroxyethyl tetrathiatriarylmethyl radicals OX063 and OX071. RSC Adv 2019; 9:35073-35076. [PMID: 32483485 PMCID: PMC7263632 DOI: 10.1039/c9ra08633a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We report the synthesis of hydroxyethyl tetrathiatriarylmethyl radical OX063 and its deuterated analogue OX071 for biomedical EPR applications. Synthesis of OX063 and OX063-d24 spin probes and DNP agents.![]()
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Affiliation(s)
- Martin Poncelet
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV, 26506, USA.,In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA
| | - Justin L Huffman
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV, 26506, USA.,In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA
| | - Valery V Khramtsov
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA.,Department of Biochemistry, School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
| | - Ilirian Dhimitruka
- School of Health and Natural Sciences, Mercy College, Dobbs Ferry, NY 10522, USA
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV, 26506, USA.,In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA
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20
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Li Y, Zhai W, Liao Y, Nie J, Han G, Song Y, Li S, Hou J, Liu Y. Synthesis of Central Chirality-Containing Triarylmethanols and Triarylmethyl Radicals with Extraordinarily Stable Configurations. J Org Chem 2019; 84:11774-11782. [PMID: 31454244 DOI: 10.1021/acs.joc.9b01675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Triarylmethanol adopts a propeller-shaped conformation with either right-handed (P) or left-handed (M) configuration. Herein, new triarylmethanols with two chiral centers were obtained via introduction of two cis-hydroxyl groups on the side chains, affording four stereoisomers. These four stereoisomers were easily separated by silica gel column chromatography into two pairs of propeller-shaped enantiomers, as shown by NMR and X-ray crystallographic studies. High-performance liquid chromatography (HPLC) studies showed that the configurations of the hydroxyl-bearing triarylmethanols are much more stable than those of the bulky tert-butyldimethylsilyl-protected precursors, inconsistent with the general strategy in which the steric repulsion is largely responsible for the configurational stability. Similarly, two hydroxyl-bearing tetrathiatriarylmethyl (TAM) radicals also exhibit excellent configurational stability and are thus separable by CS-HPLC into four stereoisomers. Interestingly, both helical chirality from triaryl group (M or P) and central chirality (R and S) on the side chain have little effect on their electron paramagnetic resonance properties. Our present study provides a new strategy to construct configurationally stable triaryl compounds and demonstrates that the side chain on TAM radicals is a new site for their structural modifications.
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Affiliation(s)
- Yingchun Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy , Tianjin Medical University , Tianjin 300070 , P. R. China
| | - Weixiang Zhai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy , Tianjin Medical University , Tianjin 300070 , P. R. China
| | - Yongfang Liao
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy , Tianjin Medical University , Tianjin 300070 , P. R. China
| | - Jiangping Nie
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy , Tianjin Medical University , Tianjin 300070 , P. R. China
| | - Guifang Han
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy , Tianjin Medical University , Tianjin 300070 , P. R. China
| | - Yuguang Song
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy , Tianjin Medical University , Tianjin 300070 , P. R. China
| | - Shaoyong Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy , Tianjin Medical University , Tianjin 300070 , P. R. China
| | - Jingli Hou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy , Tianjin Medical University , Tianjin 300070 , P. R. China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy , Tianjin Medical University , Tianjin 300070 , P. R. China
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21
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Site Selective and Efficient Spin Labeling of Proteins with a Maleimide-Functionalized Trityl Radical for Pulsed Dipolar EPR Spectroscopy. Molecules 2019; 24:molecules24152735. [PMID: 31357628 PMCID: PMC6696014 DOI: 10.3390/molecules24152735] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 01/18/2023] Open
Abstract
Pulsed dipolar electron paramagnetic resonance spectroscopy (PDS) in combination with site-directed spin labeling (SDSL) of proteins and oligonucleotides is a powerful tool in structural biology. Instead of using the commonly employed gem-dimethyl-nitroxide labels, triarylmethyl (trityl) spin labels enable such studies at room temperature, within the cells and with single-frequency electron paramagnetic resonance (EPR) experiments. However, it has been repeatedly reported that labeling of proteins with trityl radicals led to low labeling efficiencies, unspecific labeling and label aggregation. Therefore, this work introduces the synthesis and characterization of a maleimide-functionalized trityl spin label and its corresponding labeling protocol for cysteine residues in proteins. The label is highly cysteine-selective, provides high labeling efficiencies and outperforms the previously employed methanethiosulfonate-functionalized trityl label. Finally, the new label is successfully tested in PDS measurements on a set of doubly labeled Yersinia outer protein O (YopO) mutants.
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22
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Qu Y, Li Y, Tan X, Zhai W, Han G, Hou J, Liu G, Song Y, Liu Y. Synthesis and Characterization of Hydrophilic Trityl Radical TFO for Biomedical and Biophysical Applications. Chemistry 2019; 25:7888-7895. [PMID: 30972843 DOI: 10.1002/chem.201900262] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Indexed: 12/18/2022]
Abstract
Tetrathiatriarylmethyl (TAM, trityl) radicals have found wide applications as spin probes/labels for EPR spectroscopy and imaging, and as polarizing agents for dynamic nuclear polarization. The high hydrophilicity of TAM radicals is essential for their biomedical applications. However, the synthesis of hydrophilic TAM radicals (e.g., OX063) is extremely challenging and has only been reported in the patent literature, to date. Herein, an efficient synthesis of a highly water-soluble TAM radical bis(8-carboxyl-2,2,6,6-tetramethylbenzo[1,2-d:4,5-d']bis([1,3]dithiol-4-yl)-mono-(8-carboxyl-2,2,6,6-tetrakis(2-hydroxyethyl)benzo[1,2-d:4,5-d']bis([1,3]dithiol-4-yl)methyl (TFO), which contains four additional hydroxylethyl groups, relative to the Finland trityl radical CT-03, is reported. Similar to OX063, TFO exhibits excellent properties, including high water solubility in phosphate buffer, low log P, low pKa , long relaxation times, and negligible binding with bovine serum albumin. On the other hand, TFO has a sharper EPR line and higher O2 sensitivity than those of OX063. Therefore, in combination with its facile synthesis, TFO should find wide applications in magnetic resonance related fields and this synthetic approach would shed new light on the synthesis of other hydrophilic TAM radicals.
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Affiliation(s)
- Yuying Qu
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Yingchun Li
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Xiaoli Tan
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Weixiang Zhai
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Guifang Han
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Jingli Hou
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Guoquan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, P.R. China
| | - Yuguang Song
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling, Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P.R. China
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23
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Hintz H, Vanas A, Klose D, Jeschke G, Godt A. Trityl Radicals with a Combination of the Orthogonal Functional Groups Ethyne and Carboxyl: Synthesis without a Statistical Step and EPR Characterization. J Org Chem 2019; 84:3304-3320. [DOI: 10.1021/acs.joc.8b03234] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Henrik Hintz
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Agathe Vanas
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Daniel Klose
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
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24
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Kuzhelev AA, Krumkacheva OA, Ivanov MY, Prikhod'ko SA, Adonin NY, Tormyshev VM, Bowman MK, Fedin MV, Bagryanskaya EG. Pulse EPR of Triarylmethyl Probes: A New Approach for the Investigation of Molecular Motions in Soft Matter. J Phys Chem B 2018; 122:8624-8630. [PMID: 30137993 DOI: 10.1021/acs.jpcb.8b07714] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triarylmethyl (TAM) radicals have become widely used free radicals in the past few years. Their electron spins have long relaxation times and narrow electron paramagnetic resonance (EPR) lines, which make them an important class of probes and tags in biological applications and materials science. In this work, we propose a new approach to characterize librations by means of TAM radicals. The temperature dependence of motional parameter ⟨α2⟩τc, where ⟨α2⟩ is the mean-squared amplitude of librations and τc is their characteristic time, is obtained by comparison of the 1/ Tm phase-relaxation rates at X- and Q-band EPR frequencies. We study three soft matrixes, viz., glassy trehalose and two ionic liquids, using TAMs with optimized relaxation properties OX063D and a dodeca- n-butyl homologue of Finland trityl (DBT). The motional parameters ⟨α2⟩τc obtained using TAMs are in excellent agreement with those obtained by means of nitroxide radicals. At the same time, the new TAM-based approach has (1) greater sensitivity due to the narrower EPR spectrum and (2) greater measuring accuracy and broader temperature range due to longer relaxation times. The developed approach may be fruitfully implemented to probe low-temperature molecular motions of TAM-labeled biopolymers, membrane systems, polymers, molecules in glassy media, and ionic liquids.
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Affiliation(s)
- Andrey A Kuzhelev
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS , Novosibirsk 630090 , Russia.,International Tomography Center SB RAS , Novosibirsk 630090 , Russia.,Novosibirsk State University , Novosibirsk 630090 , Russia
| | - Olesya A Krumkacheva
- International Tomography Center SB RAS , Novosibirsk 630090 , Russia.,Novosibirsk State University , Novosibirsk 630090 , Russia
| | - Mikhail Yu Ivanov
- International Tomography Center SB RAS , Novosibirsk 630090 , Russia.,Novosibirsk State University , Novosibirsk 630090 , Russia
| | | | - Nicolay Yu Adonin
- Boreskov Institute of Catalysis SB RAS , Novosibirsk 630090 , Russia
| | - Victor M Tormyshev
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS , Novosibirsk 630090 , Russia.,Novosibirsk State University , Novosibirsk 630090 , Russia
| | - Michael K Bowman
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS , Novosibirsk 630090 , Russia.,University of Alabama , Tuscaloosa , Alabama 35487-0336 , United States
| | - Matvey V Fedin
- International Tomography Center 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
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25
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Giassa IC, Rynes J, Fessl T, Foldynova-Trantirkova S, Trantirek L. Advances in the cellular structural biology of nucleic acids. FEBS Lett 2018; 592:1997-2011. [PMID: 29679394 DOI: 10.1002/1873-3468.13054] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/31/2018] [Accepted: 04/09/2018] [Indexed: 01/01/2023]
Abstract
Conventional biophysical and chemical biology approaches for delineating relationships between the structure and biological function of nucleic acids (NAs) abstract NAs from their native biological context. However, cumulative experimental observations have revealed that the structure, dynamics and interactions of NAs might be strongly influenced by a broad spectrum of specific and nonspecific physical-chemical environmental factors. This consideration has recently sparked interest in the development of novel tools for structural characterization of NAs in the native cellular context. Here, we review the individual methods currently being employed for structural characterization of NA structure in a native cellular environment with a focus on recent advances and developments in the emerging fields of in-cell NMR and electron paramagnetic resonance spectroscopy and in-cell single-molecule FRET of NAs.
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Affiliation(s)
- Ilektra-Chara Giassa
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jan Rynes
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tomas Fessl
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Silvie Foldynova-Trantirkova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Institute of Biophysics, Academy of Science of the Czech Republic, Brno, Czech Republic
| | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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26
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Kuzhelev AA, Krumkacheva OA, Shevelev GY, Yulikov M, Fedin MV, Bagryanskaya EG. Room-temperature distance measurements using RIDME and the orthogonal spin labels trityl/nitroxide. Phys Chem Chem Phys 2018; 20:10224-10230. [PMID: 29594278 DOI: 10.1039/c8cp01093e] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron paramagnetic resonance (EPR) based nanometer distance measurements at ambient temperatures are of particular interest for structural biology applications. The nitroxide spin labels commonly used in EPR reveal relatively short transverse relaxation under these conditions, which limits their use for detecting static dipolar interactions. At the same time, the longitudinal relaxation of nitroxide spin labels is still long enough to allow using them as 'pumped' species in the relaxation induced dipolar modulation enhancement (RIDME) experiment where the detection is carried out on the slower relaxing triarylmethyl (TAM) spin labels. In the present study, we report the first demonstration of room-temperature RIDME distance measurements in nucleic acids using TAM as the slow-relaxing detected species and traditional nitroxide as the fast-relaxing partner spin. Two types of immobilizers, glassy trehalose and the modified silica gel Nucleosil, were used for immobilization of the spin-labeled biomolecules. The room-temperature RIDME-based distance distributions are in good agreement with those measured at 80 K by other techniques. Room-temperature RIDME on the spin pairs trityl/nitroxide may become a useful method for the structural characterization of biomacromolecules and biomolecular complexes at near physiological temperatures.
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Affiliation(s)
- Andrey A Kuzhelev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.
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27
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Jassoy JJ, Meyer A, Spicher S, Wuebben C, Schiemann O. Synthesis of Nanometer Sized Bis- and Tris-trityl Model Compounds with Different Extent of Spin-Spin Coupling. Molecules 2018; 23:E682. [PMID: 29562622 PMCID: PMC6017437 DOI: 10.3390/molecules23030682] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 12/29/2022] Open
Abstract
Tris(2,3,5,6-tetrathiaaryl)methyl radicals, so-called trityl radicals, are emerging as spin labels for distance measurements in biological systems based on Electron Paramagnetic Resonance (EPR). Here, the synthesis and characterization of rigid model systems carrying either two or three trityl moieties is reported. The monofunctionalized trityl radicals are connected to the molecular bridging scaffold via an esterification reaction employing the Mukaiyama reagent 2-chloro-methylpyridinium iodide. The bis- and tris-trityl compounds exhibit different inter-spin distances, strength of electron-electron exchange and dipolar coupling and can give rise to multi-spin effects. They are to serve as benchmark systems in comparing EPR distance measurement methods.
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Affiliation(s)
- J Jacques Jassoy
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Andreas Meyer
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Sebastian Spicher
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Christine Wuebben
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
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28
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Kuzhelev A, Akhmetzyanov D, Denysenkov V, Shevelev G, Krumkacheva O, Bagryanskaya E, Prisner T. High-frequency pulsed electron–electron double resonance spectroscopy on DNA duplexes using trityl tags and shaped microwave pulses. Phys Chem Chem Phys 2018; 20:26140-26144. [DOI: 10.1039/c8cp03951h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Distances between trityl spin labels attached to DNA duplexes were determined by 180 GHz and 260 GHz PELDOR spectroscopy applying broadband pump pulse at higher frequency.
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Affiliation(s)
- A. Kuzhelev
- Novosibirsk State University
- 630090 Novosibirsk
- Russia
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- 630090 Novosibirsk
| | - D. Akhmetzyanov
- Goethe University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry
- Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
| | - V. Denysenkov
- Goethe University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry
- Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
| | - G. Shevelev
- Novosibirsk State University
- 630090 Novosibirsk
- Russia
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- 630090 Novosibirsk
| | - O. Krumkacheva
- Novosibirsk State University
- 630090 Novosibirsk
- Russia
- International Tomography Center SB RAS
- Novosibirsk
| | - E. Bagryanskaya
- Novosibirsk State University
- 630090 Novosibirsk
- Russia
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS
- 630090 Novosibirsk
| | - T. Prisner
- Goethe University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry
- Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
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