1
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Mitin D, Bullinger F, Dobrynin S, Engelmann J, Scheffler K, Kolokolov M, Krumkacheva O, Buckenmaier K, Kirilyuk I, Chubarov A. Contrast Agents Based on Human Serum Albumin and Nitroxides for 1H-MRI and Overhauser-Enhanced MRI. Int J Mol Sci 2024; 25:4041. [PMID: 38612851 PMCID: PMC11012161 DOI: 10.3390/ijms25074041] [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: 02/27/2024] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
In cancer diagnostics, magnetic resonance imaging (MRI) uses contrast agents to enhance the distinction between the target tissue and background. Several promising approaches have been developed to increase MRI sensitivity, one of which is Overhauser dynamic nuclear polarization (ODNP)-enhanced MRI (OMRI). In this study, a macromolecular construct based on human serum albumin and nitroxyl radicals (HSA-NIT) was developed using a new synthesis method that significantly increased the modification to 21 nitroxide residues per protein. This was confirmed by electron paramagnetic resonance (EPR) spectroscopy and matrix-assisted laser desorption/ionization time-of-flight (MALDI ToF) mass spectrometry. Gel electrophoresis and circular dichroism showed no significant changes in the structure of HSA-NITs, and no oligomers were formed during modification. The cytotoxicity of HSA-NITs was comparable to that of native albumin. HSA-NITs were evaluated as potential "metal-free" organic radical relaxation-based contrast agents for 1H-MRI and as hyperpolarizing contrast agents for OMRI. Relaxivities (longitudinal and transversal relaxation rates r1 and r2) for HSA-NITs were measured at different magnetic field strengths (1.88, 3, 7, and 14 T). Phantoms were used to demonstrate the potential use of HSA-NIT as a T1- and T2-weighted relaxation-based contrast agent at 3 T and 14 T. The efficacy of 1H Overhauser dynamic nuclear polarization (ODNP) in liquids at an ultralow magnetic field (ULF, B0 = 92 ± 0.8 μT) was investigated for HSA-NIT conjugates. The HSA-NITs themselves did not show ODNP enhancement; however, under the proteolysis conditions simulating cancer tissue, HSA-NIT conjugates were cleaved into lower-molecular-weight (MW) protein fragments that activate ODNP capabilities, resulting in a maximum achievable enhancement |Emax| of 40-50 and a radiofrequency power required to achieve half of Emax, P1/2, of 21-27 W. The HSA-NIT with a higher degree of modification released increased the number of spin probes upon biodegradation, which significantly enhanced the Overhauser effect. Thus, HSA-NITs may represent a new class of MRI relaxation-based contrast agents as well as novel cleavable conjugates for use as hyperpolarizing contrast agents (HCAs) in OMRI.
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Affiliation(s)
- Dmitry Mitin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia;
| | - Friedemann Bullinger
- High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, 72076 Tuebingen, Germany; (F.B.); (J.E.); (K.S.); (K.B.)
| | - Sergey Dobrynin
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia;
| | - Jörn Engelmann
- High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, 72076 Tuebingen, Germany; (F.B.); (J.E.); (K.S.); (K.B.)
| | - Klaus Scheffler
- High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, 72076 Tuebingen, Germany; (F.B.); (J.E.); (K.S.); (K.B.)
- Department of Biomedical Magnetic Resonance, Eberhard-Karls University, 72076 Tuebingen, Germany
| | - Mikhail Kolokolov
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia; (M.K.); (O.K.)
| | - Olesya Krumkacheva
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia; (M.K.); (O.K.)
| | - Kai Buckenmaier
- High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, 72076 Tuebingen, Germany; (F.B.); (J.E.); (K.S.); (K.B.)
| | - Igor Kirilyuk
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia;
| | - Alexey Chubarov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia;
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2
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Ben‐Ishay Y, Barak Y, Feintuch A, Ouari O, Pierro A, Mileo E, Su X, Goldfarb D. Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy. Protein Sci 2024; 33:e4903. [PMID: 38358137 PMCID: PMC10868451 DOI: 10.1002/pro.4903] [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: 11/14/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
The combined effects of the cellular environment on proteins led to the definition of a fifth level of protein structural organization termed quinary structure. To explore the implication of potential quinary structure for globular proteins, we studied the dynamics and conformations of Escherichia coli (E. coli) peptidyl-prolyl cis/trans isomerase B (PpiB) in E. coli cells. PpiB plays a major role in maturation and regulation of folded proteins by catalyzing the cis/trans isomerization of the proline imidic peptide bond. We applied electron paramagnetic resonance (EPR) techniques, utilizing both Gadolinium (Gd(III)) and nitroxide spin labels. In addition to using standard spin labeling approaches with genetically engineered cysteines, we incorporated an unnatural amino acid to achieve Gd(III)-nitroxide orthogonal labeling. We probed PpiB's residue-specific dynamics by X-band continuous wave EPR at ambient temperatures and its structure by double electron-electron resonance (DEER) on frozen samples. PpiB was delivered to E. coli cells by electroporation. We report a significant decrease in the dynamics induced by the cellular environment for two chosen labeling positions. These changes could not be reproduced by adding crowding agents and cell extracts. Concomitantly, we report a broadening of the distance distribution in E. coli, determined by Gd(III)-Gd(III) DEER measurements, as compared with solution and human HeLa cells. This suggests an increase in the number of PpiB conformations present in E. coli cells, possibly due to interactions with other cell components, which also contributes to the reduction in mobility and suggests the presence of a quinary structure.
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Affiliation(s)
- Yasmin Ben‐Ishay
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Yoav Barak
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovotIsrael
| | - Akiva Feintuch
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Olivier Ouari
- CNRS, ICR, Institut de Chimie RadicalaireAix‐Marseille UniversitéMarseilleFrance
| | - Annalisa Pierro
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
- Present address:
Konstanz Research School Chemical Biology, Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Elisabetta Mileo
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
| | - Xun‐Cheng Su
- State Key Laboratory of Elemento‐organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular RecognitionCollege of Chemistry, Nankai UniversityTianjinChina
| | - Daniella Goldfarb
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
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3
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Usatov MS, Dobrynin SA, Polienko YF, Morozov DA, Glazachev YI, An’kov SV, Tolstikova TG, Gatilov YV, Bagryanskaya IY, Raizvikh AE, Bagryanskaya EG, Kirilyuk IA. Hydrophilic Reduction-Resistant Spin Labels of Pyrrolidine and Pyrroline Series from 3,4-Bis-hydroxymethyl-2,2,5,5-tetraethylpyrrolidine-1-oxyl. Int J Mol Sci 2024; 25:1550. [PMID: 38338825 PMCID: PMC10855552 DOI: 10.3390/ijms25031550] [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: 11/28/2023] [Revised: 12/18/2023] [Accepted: 12/24/2023] [Indexed: 02/12/2024] Open
Abstract
Highly resistant to reduction nitroxides open new opportunities for structural studies of biological macromolecules in their native environment inside living cells and for functional imaging of pH and thiols, enzymatic activity and redox status in living animals. 3,4-Disubstituted nitroxides of 2,2,5,5-tetraethylpyrrolidine and pyrroline series with a functional group for binding to biomolecules and a polar moiety for higher solubility in water and for more rigid attachment via additional coordination to polar sites were designed and synthesized. The EPR spectra, lipophilicities, kinetics of the reduction in ascorbate-containing systems and the decay rates in liver homogenates were measured. The EPR spectra of all 3,4-disubstituted pyrrolidine nitroxides showed additional large splitting on methylene hydrogens of the ethyl groups, while the spectra of similar pyrroline nitroxides were represented with a simple triplet with narrow lines and hyperfine structure of the nitrogen manifolds resolved in oxygen-free conditions. Both pyrrolidine and pyrroline nitroxides demonstrated low rates of reduction with ascorbate, pyrrolidines being a bit more stable than similar pyrrolines. The decay of positively charged nitroxides in the rat liver homogenate was faster than that of neutral and negatively charged radicals, with lipophilicity, rate of reduction with ascorbate and the ring type playing minor role. The EPR spectra of N,N-dimethyl-3,4-bis-(aminomethyl)-2,2,5,5-tetraethylpyrrolidine-1-oxyl showed dependence on pH with pKa = 3, ΔaN = 0.055 mT and ΔaH = 0.075 mT.
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Affiliation(s)
- Mikhail S. Usatov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (M.S.U.); (S.A.D.); (Y.F.P.); (D.A.M.); (S.V.A.); (T.G.T.); (Y.V.G.); (I.Y.B.); (A.E.R.); (E.G.B.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 1, Novosibirsk 630090, Russia
| | - Sergey A. Dobrynin
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (M.S.U.); (S.A.D.); (Y.F.P.); (D.A.M.); (S.V.A.); (T.G.T.); (Y.V.G.); (I.Y.B.); (A.E.R.); (E.G.B.)
| | - Yuliya F. Polienko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (M.S.U.); (S.A.D.); (Y.F.P.); (D.A.M.); (S.V.A.); (T.G.T.); (Y.V.G.); (I.Y.B.); (A.E.R.); (E.G.B.)
| | - Denis A. Morozov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (M.S.U.); (S.A.D.); (Y.F.P.); (D.A.M.); (S.V.A.); (T.G.T.); (Y.V.G.); (I.Y.B.); (A.E.R.); (E.G.B.)
| | - Yurii I. Glazachev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3, Novosibirsk 630090, Russia;
| | - Sergey V. An’kov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (M.S.U.); (S.A.D.); (Y.F.P.); (D.A.M.); (S.V.A.); (T.G.T.); (Y.V.G.); (I.Y.B.); (A.E.R.); (E.G.B.)
| | - Tatiana G. Tolstikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (M.S.U.); (S.A.D.); (Y.F.P.); (D.A.M.); (S.V.A.); (T.G.T.); (Y.V.G.); (I.Y.B.); (A.E.R.); (E.G.B.)
| | - Yuri V. Gatilov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (M.S.U.); (S.A.D.); (Y.F.P.); (D.A.M.); (S.V.A.); (T.G.T.); (Y.V.G.); (I.Y.B.); (A.E.R.); (E.G.B.)
| | - Irina Yu. Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (M.S.U.); (S.A.D.); (Y.F.P.); (D.A.M.); (S.V.A.); (T.G.T.); (Y.V.G.); (I.Y.B.); (A.E.R.); (E.G.B.)
| | - Arthur E. Raizvikh
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (M.S.U.); (S.A.D.); (Y.F.P.); (D.A.M.); (S.V.A.); (T.G.T.); (Y.V.G.); (I.Y.B.); (A.E.R.); (E.G.B.)
- Department of Physics, Novosibirsk State University, Pirogova Str. 1, Novosibirsk 630090, Russia
| | - Elena G. Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (M.S.U.); (S.A.D.); (Y.F.P.); (D.A.M.); (S.V.A.); (T.G.T.); (Y.V.G.); (I.Y.B.); (A.E.R.); (E.G.B.)
| | - Igor A. Kirilyuk
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, Novosibirsk 630090, Russia; (M.S.U.); (S.A.D.); (Y.F.P.); (D.A.M.); (S.V.A.); (T.G.T.); (Y.V.G.); (I.Y.B.); (A.E.R.); (E.G.B.)
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4
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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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5
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Bertran A, De Zotti M, Timmel CR, Di Valentin M, Bowen AM. Determining and controlling conformational information from orientationally selective light-induced triplet-triplet electron resonance spectroscopy for a set of bis-porphyrin rulers. Phys Chem Chem Phys 2024; 26:2589-2602. [PMID: 38170870 PMCID: PMC10793979 DOI: 10.1039/d3cp03454b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/31/2023] [Indexed: 01/05/2024]
Abstract
We recently reported a new technique, light-induced triplet-triplet electron resonance (LITTER) spectroscopy, which allows quantification of the dipolar interaction between the photogenerated triplet states of two chromophores. Here we carry out a systematic LITTER study, considering orientation selection by the detection pulses, of a series of bis-porphyrin model peptides with different porphyrin-porphyrin distances and relative orientations. Orientation-dependent analysis of the dipolar datasets yields conformational information of the molecules in frozen solution which is in good agreement with density functional theory predictions. Additionally, a fast partial orientational-averaging treatment produces distance distributions with minimized orientational artefacts. Finally, by direct comparison of LITTER data to double electron-electron resonance (DEER) measured on a system with Cu(II) coordinated into the porphyrins, we demonstrate the advantages of the LITTER technique over the standard DEER methodology. This is due to the remarkable spectroscopic properties of the photogenerated porphyrin triplet state. This work sets the basis for the use of LITTER in structural investigations of unmodified complex biological macromolecules, which could be combined with Förster resonance energy transfer and microscopy inside cells.
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Affiliation(s)
- Arnau Bertran
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK.
| | - Marta De Zotti
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- Centro Interdipartimentale di Ricerca "Centro Studi di Economia e Tecnica dell'energia Giorgio Levi Cases", 35131 Padova, Italy.
| | - Christiane R Timmel
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK.
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 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 and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
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6
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Bogetti X, Saxena S. Integrating Electron Paramagnetic Resonance Spectroscopy and Computational Modeling to Measure Protein Structure and Dynamics. Chempluschem 2024; 89:e202300506. [PMID: 37801003 DOI: 10.1002/cplu.202300506] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/07/2023]
Abstract
Electron paramagnetic resonance (EPR) has become a powerful probe of conformational heterogeneity and dynamics of biomolecules. In this Review, we discuss different computational modeling techniques that enrich the interpretation of EPR measurements of dynamics or distance restraints. A variety of spin labels are surveyed to provide a background for the discussion of modeling tools. Molecular dynamics (MD) simulations of models containing spin labels provide dynamical properties of biomolecules and their labels. These simulations can be used to predict EPR spectra, sample stable conformations and sample rotameric preferences of label sidechains. For molecular motions longer than milliseconds, enhanced sampling strategies and de novo prediction software incorporating or validated by EPR measurements are able to efficiently refine or predict protein conformations, respectively. To sample large-amplitude conformational transition, a coarse-grained or an atomistic weighted ensemble (WE) strategy can be guided with EPR insights. Looking forward, we anticipate an integrative strategy for efficient sampling of alternate conformations by de novo predictions, followed by validations by systematic EPR measurements and MD simulations. Continuous pathways between alternate states can be further sampled by WE-MD including all intermediate states.
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Affiliation(s)
- Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
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7
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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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8
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Shu C, Yang Z, Rajca A. From Stable Radicals to Thermally Robust High-Spin Diradicals and Triradicals. Chem Rev 2023; 123:11954-12003. [PMID: 37831948 DOI: 10.1021/acs.chemrev.3c00406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Stable radicals and thermally robust high-spin di- and triradicals have emerged as important organic materials due to their promising applications in diverse fields. New fundamental properties, such as SOMO/HOMO inversion of orbital energies, are explored for the design of new stable radicals, including highly luminescent ones with good photostability. A relation with the singlet-triplet energy gap in the corresponding diradicals is proposed. Thermally robust high-spin di- and triradicals, with energy gaps that are comparable to or greater than a thermal energy at room temperature, are more challenging to synthesize but more rewarding. We summarize a number of high-spin di- and triradicals, based on nitronyl nitroxides that provide a relation between the experimental pairwise exchange coupling constant J/k in the high-spin species vs experimental hyperfine coupling constants in the corresponding monoradicals. This relation allows us to identify outliers, which may correspond to radicals where J/k is not measured with sufficient accuracy. Double helical high-spin diradicals, in which spin density is delocalized over the chiral π-system, have been barely explored, with the sole example of such high-spin diradical possessing alternant π-system with Kekulé resonance form. Finally, we discuss a high-spin diradical with electrical conductivity and derivatives of triangulene diradicals.
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Affiliation(s)
- Chan Shu
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Zhimin Yang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
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9
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Pierro A, Tamburrini KC, Leguenno H, Gerbaud G, Etienne E, Guigliarelli B, Belle V, Zambelli B, Mileo E. In-cell investigation of the conformational landscape of the GTPase UreG by SDSL-EPR. iScience 2023; 26:107855. [PMID: 37766968 PMCID: PMC10520941 DOI: 10.1016/j.isci.2023.107855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/07/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
UreG is a cytosolic GTPase involved in the maturation network of urease, an Ni-containing bacterial enzyme. Previous investigations in vitro showed that UreG features a flexible tertiary organization, making this protein the first enzyme discovered to be intrinsically disordered. To determine whether this heterogeneous behavior is maintained in the protein natural environment, UreG structural dynamics was investigated directly in intact bacteria by in-cell EPR. This approach, based on site-directed spin labeling coupled to electron paramagnetic resonance (SDSL-EPR) spectroscopy, enables the study of proteins in their native environment. The results show that UreG maintains heterogeneous structural landscape in-cell, existing in a conformational ensemble of two major conformers, showing either random coil-like or compact properties. These data support the physiological relevance of the intrinsically disordered nature of UreG and indicates a role of protein flexibility for this specific enzyme, possibly related to the regulation of promiscuous protein interactions for metal ion delivery.
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Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ, CNRS, BIP, IMM, 13009 Marseille, France
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Ketty Concetta Tamburrini
- Aix Marseille Univ, CNRS, AFMB, 13009 Marseille, France
- INRAE, Aix Marseille Univ, BBF, 13009 Marseille, France
| | - Hugo Leguenno
- Aix Marseille Univ, CNRS, IMM, Microscopy Core Facility, 13009 Marseille, France
| | | | | | | | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP, IMM, 13009 Marseille, France
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
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10
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Polienko YF, Dobrynin SA, Lomanovich KA, Brovko AO, Bagryanskaya EG, Kirilyuk IA. Origin of Long-Range Hyperfine Couplings in the EPR Spectra of 2,2,5,5-Tetraethylpyrrolidine-1-oxyls. ACS OMEGA 2023; 8:38723-38732. [PMID: 37867656 PMCID: PMC10586448 DOI: 10.1021/acsomega.3c06090] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/08/2023] [Indexed: 10/24/2023]
Abstract
Cyclic nitroxides with several bulky alkyl substituents adjacent to the nitroxide group are known to demonstrate a much higher stability to bioreduction than their tetramethyl analogues. Among these so-called "sterically shielded" nitroxides, the pyrrolidine derivatives are the most stable. The EPR spectra of some sterically shielded pyrrolidine-1-oxyls were reported to show one or two large additional doublet splittings with a hyperfine coupling (hfc) constant (ca. 0.2-0.4 mT). To determine the origin of these hfc, a series of 2-R-2,5,5-triethyl-3,4-bis(hydroxymethyl)-pyrrolidine-1-oxyls with methylene groups stereospecifically enriched with deuterium were prepared, and their CW EPR spectra were studied. In addition, these nitroxides were investigated using quantum chemical calculations on the UB3LYP/def2-TZVP level and NBO analysis. The apparent constants were assigned to hfc with γ-hydrogen in the side chain, with the contribution of the NBO orbital βπ*(N-O) to the natural localized molecular orbital βσ(C-H) playing the major role. This interaction is efficient if the ethyl substituent is in the pseudoaxial position of the ring and the CH2-CH3 bond is codirected with (parallel to) N-O. The apparent constant aH increases with the Boltzmann population of this conformation.
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Affiliation(s)
- Yuliya F. Polienko
- N.N.
Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Sergey A. Dobrynin
- N.N.
Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | | | - Anastasiya O. Brovko
- N.N.
Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
- Department
of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena G. Bagryanskaya
- N.N.
Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Igor A. Kirilyuk
- N.N.
Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
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11
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Wang XW, Zhang X, Cui CY, Li B, Goldfarb D, Yang Y, Su XC. Stabilizing Nitroxide Spin Labels for Structural and Conformational Studies of Biomolecules by Maleimide Treatment. Chemistry 2023; 29:e202301350. [PMID: 37354082 DOI: 10.1002/chem.202301350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 06/26/2023]
Abstract
Nitroxide (NO) spin radicals are effective in characterizing structures, interactions and dynamics of biomolecules. The EPR applications in cell lysates or intracellular milieu require stable spin labels, but NO radicals are unstable in such conditions. We showed that the destabilization of NO radicals in cell lysates or even in cells is caused by NADPH/NADH related enzymes, but not by the commonly believed reducing reagents such as GSH. Maleimide stabilizes the NO radicals in the cell lysates by consumption of the NADPH/NADH that are essential for the enzymes involved in destabilizing NO radicals, instead of serving as the solo thiol scavenger. The maleimide treatment retains the crowding properties of the intracellular components and allows to perform long-time EPR measurements of NO labeled biomolecules close to the intracellular conditions. The strategy of maleimide treatment on cell lysates for the EPR applications has been demonstrated on double electron-electron resonance (DEER) measurements on a number of NO labeled protein samples. The method opens a broad application range for the NO labeled biomolecules by EPR in conditions that resemble the intracellular milieu.
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Affiliation(s)
- Xi-Wei Wang
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xing Zhang
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chao-Yu Cui
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bin Li
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yin Yang
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
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12
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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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13
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Sowiński MP, Gahlawat S, Lund BA, Warnke AL, Hopmann KH, Lovett JE, Haugland MM. Conformational tuning improves the stability of spirocyclic nitroxides with long paramagnetic relaxation times. Commun Chem 2023; 6:111. [PMID: 37277501 DOI: 10.1038/s42004-023-00912-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/24/2023] [Indexed: 06/07/2023] Open
Abstract
Nitroxides are widely used as probes and polarization transfer agents in spectroscopy and imaging. These applications require high stability towards reducing biological environments, as well as beneficial relaxation properties. While the latter is provided by spirocyclic groups on the nitroxide scaffold, such systems are not in themselves robust under reducing conditions. In this work, we introduce a strategy for stability enhancement through conformational tuning, where incorporating additional substituents on the nitroxide ring effects a shift towards highly stable closed spirocyclic conformations, as indicated by X-ray crystallography and density functional theory (DFT) calculations. Closed spirocyclohexyl nitroxides exhibit dramatically improved stability towards reduction by ascorbate, while maintaining long relaxation times in electron paramagnetic resonance (EPR) spectroscopy. These findings have important implications for the future design of new nitroxide-based spin labels and imaging agents.
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Affiliation(s)
- Mateusz P Sowiński
- Department of Chemistry, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Sahil Gahlawat
- Department of Chemistry, UiT The Arctic University of Norway, 9037, Tromsø, Norway
- Hylleraas Center for Quantum Molecular Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Bjarte A Lund
- Department of Chemistry, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Anna-Luisa Warnke
- Department of Chemistry, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Kathrin H Hopmann
- Department of Chemistry, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Janet E Lovett
- SUPA, School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9SS, UK
| | - Marius M Haugland
- Department of Chemistry, UiT The Arctic University of Norway, 9037, Tromsø, Norway.
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14
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Tessmer MH, Stoll S. chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling. PLoS Comput Biol 2023; 19:e1010834. [PMID: 37000838 PMCID: PMC10096462 DOI: 10.1371/journal.pcbi.1010834] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/12/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Abstract
Here we introduce chiLife, a Python package for site-directed spin label (SDSL) modeling for electron paramagnetic resonance (EPR) spectroscopy, in particular double electron-electron resonance (DEER). It is based on in silico attachment of rotamer ensemble representations of spin labels to protein structures. chiLife enables the development of custom protein analysis and modeling pipelines using SDSL EPR experimental data. It allows the user to add custom spin labels, scoring functions and spin label modeling methods. chiLife is designed with integration into third-party software in mind, to take advantage of the diverse and rapidly expanding set of molecular modeling tools available with a Python interface. This article describes the main design principles of chiLife and presents a series of examples.
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Affiliation(s)
- Maxx H. Tessmer
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
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15
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Rančić A, Babić N, Orio M, Peyrot F. Structural Features Governing the Metabolic Stability of Tetraethyl-Substituted Nitroxides in Rat Liver Microsomes. Antioxidants (Basel) 2023; 12:antiox12020402. [PMID: 36829960 PMCID: PMC9952648 DOI: 10.3390/antiox12020402] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Nitroxides are potent tools for studying biological systems by electron paramagnetic resonance (EPR). Whatever the application, a certain stability is necessary for successful detection. Since conventional tetramethyl-substituted cyclic nitroxides have insufficient in vivo stability, efforts have recently been made to synthesize more stable, tetraethyl-substituted nitroxides. In our previous study on piperidine nitroxides, the introduction of steric hindrance around the nitroxide moiety successfully increased the resistance to reduction into hydroxylamine. However, it also rendered the carbon backbone susceptible to modifications by xenobiotic metabolism due to increased lipophilicity. Here, we focus on a new series of three nitroxide candidates with tetraethyl substitution, namely with pyrrolidine, pyrroline, and isoindoline cores, to identify which structural features afford increased stability for future probe design and application in in vivo EPR imaging. In the presence of rat liver microsomes, pyrrolidine and pyrroline tetraethyl nitroxides exhibited a higher stability than isoindoline nitroxide, which was studied in detail by HPLC-HRMS. Multiple metabolites suggest that the aerobic transformation of tetraethyl isoindoline nitroxide is initiated by hydrogen abstraction by P450-FeV = O from one of the ethyl groups, followed by rearrangement and further modifications by cytochrome P450, as supported by DFT calculations. Under anaerobic conditions, only reduction by rat liver microsomes was observed with involvement of P450-FeII.
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Affiliation(s)
- Aleksandra Rančić
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS, F-75006 Paris, France
| | - Nikola Babić
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS, F-75006 Paris, France
| | - Maylis Orio
- iSm2, Aix-Marseille University, CNRS, Centrale Marseille, F-13397 Marseille, France
| | - Fabienne Peyrot
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS, F-75006 Paris, France
- Institut National Supérieur du Professorat et de l’Education (INSPE) de l’Académie de Paris, Sorbonne Université, F-75016 Paris, France
- Correspondence:
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16
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Pierro A, Drescher M. Dance with spins: site-directed spin labeling coupled to electron paramagnetic resonance spectroscopy directly inside cells. Chem Commun (Camb) 2023; 59:1274-1284. [PMID: 36633152 PMCID: PMC9890500 DOI: 10.1039/d2cc05907j] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023]
Abstract
Depicting how biomolecules move and interact within their physiological environment is one of the hottest topics of structural biology. This Feature Article gives an overview of the most recent advances in Site-directed Spin Labeling coupled to Electron Paramagnetic Resonance spectroscopy (SDSL-EPR) to study biomolecules in living cells. The high sensitivity, the virtual absence of background, and the versatility of spin-labeling strategies make this approach one of the most promising techniques for the study of biomolecules in physiologically relevant environments. After presenting the milestones achieved in this field, we present a summary of the future goals and ambitions of this community.
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Affiliation(s)
- Annalisa Pierro
- Department of Chemistry, University of Konstanz, and Konstanz Research School Chemical Biology, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Malte Drescher
- Department of Chemistry, University of Konstanz, and Konstanz Research School Chemical Biology, Universitätsstraße 10, 78457 Konstanz, Germany.
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17
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Ackermann BE, Lim BJ, Elathram N, Narayanan S, Debelouchina GT. A Comparative Study of Nitroxide-Based Biradicals for Dynamic Nuclear Polarization in Cellular Environments. Chembiochem 2022; 23:e202200577. [PMID: 36250276 PMCID: PMC9856215 DOI: 10.1002/cbic.202200577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/15/2022] [Indexed: 01/25/2023]
Abstract
Dynamic nuclear polarization (DNP) is a powerful tool to enhance the NMR signals of molecules by transferring polarization from unpaired electron spins to nuclei through microwave irradiation. The resulting signal enhancements can enable the analysis of samples that have previously been intractable by NMR spectroscopy, including proteins, nucleic acids, and metabolites in cells. To carry out DNP, the sample is doped with a polarization agent, a biradical containing two nitroxide moieties. DNP applications in cells, however, present significant challenges as nitroxides are often susceptible to the reducing cellular environment. Here, we introduce a novel polarization agent, POPAPOL, that exhibits increased lifetimes under reducing conditions. We also compare its bioresistance and DNP performance with three popular, commercially available polarization agents. Our work indicates that pyrrolidine-based nitroxides can outperform piperidine-based nitroxides in cellular environments, and that future polarization agent designs must carefully balance DNP performance and stability for cellular applications.
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Affiliation(s)
- Bryce E. Ackermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Byung Joon Lim
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nesreen Elathram
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sirish Narayanan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA,Corresponding author: , http://debelouchinalab.ucsd.edu/
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18
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Yao R, Beriashvili D, Zhang W, Li S, Safeer A, Gurinov A, Rockenbauer A, Yang Y, Song Y, Baldus M, Liu Y. Highly bioresistant, hydrophilic and rigidly linked trityl-nitroxide biradicals for cellular high-field dynamic nuclear polarization. Chem Sci 2022; 13:14157-14164. [PMID: 36540821 PMCID: PMC9728575 DOI: 10.1039/d2sc04668g] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/16/2022] [Indexed: 09/23/2023] Open
Abstract
Cellular dynamic nuclear polarization (DNP) has been an effective means of overcoming the intrinsic sensitivity limitations of solid-state nuclear magnetic resonance (ssNMR) spectroscopy, thus enabling atomic-level biomolecular characterization in native environments. Achieving DNP signal enhancement relies on doping biological preparations with biradical polarizing agents (PAs). Unfortunately, PA performance within cells is often limited by their sensitivity to the reductive nature of the cellular lumen. Herein, we report the synthesis and characterization of a highly bioresistant and hydrophilic PA (StaPol-1) comprising the trityl radical OX063 ligated to a gem-diethyl pyrroline nitroxide via a rigid piperazine linker. EPR experiments in the presence of reducing agents such as ascorbate and in HeLa cell lysates demonstrate the reduction resistance of StaPol-1. High DNP enhancements seen in small molecules, proteins and cell lysates at 18.8 T confirm that StaPol-1 is an excellent PA for DNP ssNMR investigations of biomolecular systems at high magnetic fields in reductive environments.
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Affiliation(s)
- Ru Yao
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - David Beriashvili
- NMR Spectroscopy Group, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Wenxiao Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Shuai Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Adil Safeer
- NMR Spectroscopy Group, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Andrei Gurinov
- NMR Spectroscopy Group, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry, Hungarian Academy of Sciences And, Department of Physics, Budapest University of Technology and Economics Budafoki Ut 8 1111 Budapest Hungary
| | - Yin Yang
- State Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University Tianjin 300071 China
| | - Yuguang Song
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Marc Baldus
- NMR Spectroscopy Group, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Yangping Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, 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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19
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Dobrynin SA, Gulman MM, Morozov DA, Zhurko IF, Taratayko AI, Sotnikova YS, Glazachev YI, Gatilov YV, Kirilyuk IA. Synthesis of Sterically Shielded Nitroxides Using the Reaction of Nitrones with Alkynylmagnesium Bromides. Molecules 2022; 27:molecules27217626. [PMID: 36364453 PMCID: PMC9654931 DOI: 10.3390/molecules27217626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Sterically shielded nitroxides, which demonstrate high resistance to bioreduction, are the spin labels of choice for structural studies inside living cells using pulsed EPR and functional MRI and EPRI in vivo. To prepare new sterically shielded nitroxides, a reaction of cyclic nitrones, including various 1-pyrroline-1-oxides, 2,5-dihydroimidazole-3-oxide and 4H-imidazole-3-oxide with alkynylmagnesium bromide wereused. The reaction gave corresponding nitroxides with an alkynyl group adjacent to the N-O moiety. The hydrogenation of resulting 2-ethynyl-substituted nitroxides with subsequent re-oxidation of the N-OH group produced the corresponding sterically shielded tetraalkylnitroxides of pyrrolidine, imidazolidine and 2,5-dihydroimidazole series. EPR studies revealed large additional couplings up to 4 G in the spectra of pyrrolidine and imidazolidine nitroxides with substituents in 3- and/or 4-positions of the ring.
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Affiliation(s)
- Sergey A. Dobrynin
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
- Correspondence: (S.A.D.); (D.A.M.)
| | - Mark M. Gulman
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 2, 630090 Novosibirsk, Russia
| | - Denis A. Morozov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
- Correspondence: (S.A.D.); (D.A.M.)
| | - Irina F. Zhurko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Andrey I. Taratayko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 2, 630090 Novosibirsk, Russia
| | - Yulia S. Sotnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Yurii I. Glazachev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3, 630090 Novosibirsk, Russia
| | - Yuri V. Gatilov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Igor A. Kirilyuk
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
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20
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Pierro A, Bonucci A, Normanno D, Ansaldi M, Pilet E, Ouari O, Guigliarelli B, Etienne E, Gerbaud G, Magalon A, Belle V, Mileo E. Probing the Structural Dynamics of a Bacterial Chaperone in Its Native Environment by Nitroxide‐Based EPR Spectroscopy. Chemistry 2022; 28:e202202249. [DOI: 10.1002/chem.202202249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
- Department of Chemistry University of Konstanz, and Konstanz Research School Chemical Biology 78457 Konstanz Germany
| | - Alessio Bonucci
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Davide Normanno
- Aix Marseille Univ CNRS, Inserm Institut Paoli-Calmettes, CRCM Centre de Recherche en Cancérologie de Marseille 13273 Marseille France
- Univ Montpellier CNRS, IGH Institut de Génétique Humaine 34396 Montpellier France
| | - Mireille Ansaldi
- Aix Marseille Univ CNRS, LCB Laboratoire de Chimie Bacterienne, IMM 13009 Marseille France
| | - Eric Pilet
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Olivier Ouari
- Aix Marseille Univ CNRS, ICR Institut de Chimie Radicalaire 13397 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Emilien Etienne
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Guillaume Gerbaud
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Axel Magalon
- Aix Marseille Univ CNRS, LCB Laboratoire de Chimie Bacterienne, IMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
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21
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Carnahan SL, Chen Y, Wishart JF, Lubach JW, Rossini AJ. Magic angle spinning dynamic nuclear polarization solid-state NMR spectroscopy of γ-irradiated molecular organic solids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 119:101785. [PMID: 35405629 DOI: 10.1016/j.ssnmr.2022.101785] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 02/22/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
In the past 15 years, magic angle spinning (MAS) dynamic nuclear polarization (DNP) has emerged as a method to increase the sensitivity of high-resolution solid-state NMR spectroscopy experiments. Recently, γ-irradiation has been used to generate significant concentrations of homogeneously distributed free radicals in a variety of solids, including quartz, glucose, and cellulose. Both γ-irradiated quartz and glucose previously showed significant MAS DNP enhancements. Here, γ-irradiation is applied to twelve small organic molecules to test the applicability of γ-irradiation as a general method of creating stable free radicals for MAS DNP experiments on organic solids and pharmaceuticals. Radical concentrations in the range of 0.25 mM-10 mM were observed in irradiated glucose, histidine, malic acid, and malonic acid, and significant 1H DNP enhancements of 32, 130, 19, and 11 were obtained, respectively, as measured by 1H→13C CPMAS experiments. However, concentrations of free radicals below 0.05 mM were generally observed in organic molecules containing aromatic rings, preventing sizeable DNP enhancements. DNP sensitivity gains for several of the irradiated compounds exceed that which can be obtained with the relayed DNP approach that uses exogeneous polarizing agent solutions and impregnation procedures. In several cases, significant 1H DNP enhancements were realized at room temperature. This study demonstrates that in many cases γ-irradiation is a viable alternative to addition of stable exogenous radicals for DNP experiments on organic solids.
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Affiliation(s)
- Scott L Carnahan
- US DOE Ames Laboratory, Ames, IA, 50011, USA; Iowa State University, Department of Chemistry, Ames, IA, 50011, USA
| | - Yunhua Chen
- US DOE Ames Laboratory, Ames, IA, 50011, USA; Iowa State University, Department of Chemistry, Ames, IA, 50011, USA
| | - James F Wishart
- Brookhaven National Laboratory, Chemistry Division, Upton, NY, 11973, United States
| | - Joseph W Lubach
- Genentech Inc., South San Francisco, CA, 94080, United States
| | - Aaron J Rossini
- US DOE Ames Laboratory, Ames, IA, 50011, USA; Iowa State University, Department of Chemistry, Ames, IA, 50011, USA.
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22
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Abstract
Different types of spin labels are currently available for structural studies of biomolecules both in vitro and in cells using Electron Paramagnetic Resonance (EPR) and pulse dipolar spectroscopy (PDS). Each type of label has its own advantages and disadvantages, that will be addressed in this chapter. The spectroscopically distinct properties of the labels have fostered new applications of PDS aimed to simultaneously extract multiple inter-label distances on the same sample. In fact, combining different labels and choosing the optimal strategy to address their inter-label distances can increase the information content per sample, and this is pivotal to better characterize complex multi-component biomolecular systems. In this review, we provide a brief background of the spectroscopic properties of the four most common orthogonal spin labels for PDS measurements and focus on the various methods at disposal to extract homo- and hetero-label distances in proteins. We also devote a section to possible artifacts arising from channel crosstalk and provide few examples of applications in structural biology.
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23
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Taratayko AI, Glazachev YI, Eltsov IV, Chernyak EI, Kirilyuk IA. 3,4-Unsubstituted 2- tert-Butyl-pyrrolidine-1-oxyls with Hydrophilic Functional Groups in the Side Chains. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27061922. [PMID: 35335285 PMCID: PMC8948954 DOI: 10.3390/molecules27061922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/30/2022]
Abstract
Pyrrolidine nitroxides with four bulky alkyl substituents adjacent to N–O group are known for their high resistance to bioreduction. The 3,4-unsubstituted 2-tert-butyl-2-ethylpyrrolidine-1-oxyls were prepared from the corresponding 2-tert-butyl-1-pyrroline-1-oxides via either the addition of ethinylmagnesium bromide with subsequent hydrogenation or via treatment with ethyllithium. The new nitroxides showed excellent stability to reduction with ascorbate with no evidence for additional large hyperfine couplings in the EPR spectra.
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Affiliation(s)
- Andrey I. Taratayko
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia; (E.I.C.); (I.A.K.)
- Correspondence:
| | - Yurii I. Glazachev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3, 630090 Novosibirsk, Russia;
| | - Ilia V. Eltsov
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia;
| | - Elena I. Chernyak
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia; (E.I.C.); (I.A.K.)
| | - Igor A. Kirilyuk
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia; (E.I.C.); (I.A.K.)
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24
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Ghosh R, Dumarieh R, Xiao Y, Frederick KK. Stability of the nitroxide biradical AMUPol in intact and lysed mammalian cells. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 336:107150. [PMID: 35151975 PMCID: PMC8961433 DOI: 10.1016/j.jmr.2022.107150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Dynamic Nuclear Polarization (DNP) enhanced solid state NMR increases experimental sensitivity, potentially enabling detection of biomolecules at their physiological concentrations. The sensitivity of DNP experiments is due to the transfer of polarization from electron spins of free radicals to the nuclear spins of interest. Here, we investigate the reduction of AMUPol in both lysed and intact HEK293 cells. We find that nitroxide radicals are reduced with first order reduction kinetics by cell lysates at a rate of ∼ 12% of the added nitroxide radical concentration per hour. We also found that electroporation delivered a consistent amount of AMUPol to intact cells and that nitroxide radicals are reduced just slightly more rapidly (∼15% per hour) by intact cells than by cell lysates. The two nitroxide radicals of AMUPol are reduced independently and this leads to considerable accumulation of the DNP-silent monoradical form of AMUPol, particularly in preparations of intact cells where nearly half of the AMUPol is already reduced to the DNP silent monoradical form at the earliest experimental time points. This confirms that the loss of the DNP-active biradical form of AMUPol is faster than the nitroxide reduction rate. Finally, we investigate the effect of adding N-ethyl maleimide, a well-known inhibitor of thiol (-SH) group-based reduction of nitroxide biradicals in cells, on AMUPol reduction, cellular viability, and DNP performance. Although pre-treatment of cells with NEM effectively inhibited the reduction of AMUPol, exposure to NEM compromised cellular viability and, surprisingly, did not improve DNP performance. Collectively, these results indicate that, currently, the most effective strategy to obtain high DNP enhancements for DNP-assisted in-cell NMR is to minimize room temperature contact times with cellular constituents and suggest that the development of bio-resistant polarization agents for DNP could considerably increase the sensitivity of DNP-assisted in-cell NMR experiments.
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Affiliation(s)
- Rupam Ghosh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, 75390-8816, United States
| | - Rania Dumarieh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, 75390-8816, United States
| | - Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, 75390-8816, United States
| | - Kendra K Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, 75390-8816, United States; Center for Neurodegenerative and Alzheimer's Disease, UT Southwestern Medical Center, Dallas 75390, United States.
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25
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Xiao Y, Ghosh R, Frederick KK. In-Cell NMR of Intact Mammalian Cells Preserved with the Cryoprotectants DMSO and Glycerol Have Similar DNP Performance. Front Mol Biosci 2022; 8:789478. [PMID: 35145995 PMCID: PMC8824258 DOI: 10.3389/fmolb.2021.789478] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/31/2021] [Indexed: 11/26/2022] Open
Abstract
NMR has the resolution and specificity to determine atomic-level protein structures of isotopically-labeled proteins in complex environments and, with the sensitivity gains conferred by dynamic nuclear polarization (DNP), NMR has the sensitivity to detect proteins at their endogenous concentrations. Prior work established that DNP MAS NMR is compatible with cellular viability. However, in that work, 15% glycerol, rather than the more commonly used 10% DMSO, was used as the cellular cryoprotectant. Moreover, incubation of cells cryoprotected 15% glycerol with the polarization agent, AMUPol, resulted in an inhomogeneous distribution of AMUPol through the cellular biomass, which resulted in a spatial bias of the NMR peak intensities. Because 10% DMSO is not only the most used cryoprotectant for mammalian cells, but also because DMSO is often used to improve delivery of molecules to cells, we sought to characterize the DNP performance of cells that were incubated with AMUPol and cryoprotected with 10% DMSO. We found that, like cells preserved with 15% glycerol, cells preserved with 10% DMSO retain high viability during DNP MAS NMR experiments if they are frozen at a controlled rate. However, DMSO did not improve the dispersion of AMUPol throughout the cellular biomass. Cells preserved with 15% glycerol and with 10% DMSO had similar DNP performance for both the maximal DNP enhancements as well as the inhomogeneous dispersion of AMUPol throughout the cellular biomass. Therefore, 10% DMSO and 15% glycerol are both appropriate cryoprotectant systems for DNP-assisted MAS NMR of intact viable mammalian cells.
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Affiliation(s)
- Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, United States
| | - Rupam Ghosh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, United States
| | - Kendra K. Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, United States
- Center for Alzheimer’s and Neurodegenerative Disease, UT Southwestern Medical Center, Dallas, TX, United States
- *Correspondence: Kendra K. Frederick,
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26
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Gopinath A, Joseph B. Conformational Flexibility of the Protein Insertase BamA in the Native Asymmetric Bilayer Elucidated by ESR Spectroscopy. Angew Chem Int Ed Engl 2022; 61:e202113448. [PMID: 34761852 PMCID: PMC9299766 DOI: 10.1002/anie.202113448] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Indexed: 12/15/2022]
Abstract
The β-barrel assembly machinery (BAM) consisting of the central β-barrel BamA and four other lipoproteins mediates the folding of the majority of the outer membrane proteins. BamA is placed in an asymmetric bilayer and its lateral gate is suggested to be the functional hotspot. Here we used in situ pulsed electron-electron double resonance spectroscopy to characterize BamA in the native outer membrane. In the detergent micelles, the data is consistent with mainly an inward-open conformation of BamA. The native membrane considerably enhanced the conformational heterogeneity. The lateral gate and the extracellular loop 3 exist in an equilibrium between different conformations. The outer membrane provides a favorable environment for occupying multiple conformational states independent of the lipoproteins. Our results reveal a highly dynamic behavior of the lateral gate and other key structural elements and provide direct evidence for the conformational modulation of a membrane protein in situ.
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Affiliation(s)
- Aathira Gopinath
- Institute of BiophysicsDepartment of PhysicsCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
| | - Benesh Joseph
- Institute of BiophysicsDepartment of PhysicsCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
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27
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Gopinath A, Joseph B. Conformational Flexibility of the Protein Insertase BamA in the Native Asymmetric Bilayer Elucidated by ESR Spectroscopy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202113448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Aathira Gopinath
- Institute of Biophysics Department of Physics Center for Biomolecular Magnetic Resonance (BMRZ) Goethe University Frankfurt Max-von-Laue-Str. 1 60438 Frankfurt/Main Germany
| | - Benesh Joseph
- Institute of Biophysics Department of Physics Center for Biomolecular Magnetic Resonance (BMRZ) Goethe University Frankfurt Max-von-Laue-Str. 1 60438 Frankfurt/Main Germany
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28
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A Simple Method of Synthesis of 3-Carboxy-2,2,5,5-Tetraethylpyrrolidine-1-oxyl and Preparation of Reduction-Resistant Spin Labels and Probes of Pyrrolidine Series. Molecules 2021; 26:molecules26195761. [PMID: 34641310 PMCID: PMC8510269 DOI: 10.3390/molecules26195761] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 01/31/2023] Open
Abstract
Stable free radicals are widely used as molecular probes and labels in various biophysical and biomedical research applications of magnetic resonance spectroscopy and imaging. Among these radicals, sterically shielded nitroxides of pyrrolidine series demonstrate the highest stability in biological systems. Here, we suggest new convenient procedure for preparation of 3-carboxy-2,2,5,5-tetraethylpyrrolidine-1-oxyl, a reduction-resistant analog of widely used carboxy-Proxyl, from cheap commercially available reagents with the yield exceeding the most optimistic literature data. Several new spin labels and probes of 2,2,5,5-tetraethylpyrrolidine-1-oxyl series were prepared and reduction of these radicals in ascorbate solutions, mice blood and tissue homogenates was studied.
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29
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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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30
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Torricella F, Bonucci A, Polykretis P, Cencetti F, Banci L. Rapid protein delivery to living cells for biomolecular investigation. Biochem Biophys Res Commun 2021; 570:82-88. [PMID: 34274850 DOI: 10.1016/j.bbrc.2021.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 12/24/2022]
Abstract
The lack of a simple, fast and efficient method for protein delivery is limiting the widespread application of in-cell experiments, which are crucial for understanding the cellular function. We present here an innovative strategy to deliver proteins into both prokaryotic and eukaryotic cells, exploiting thermal vesiculation. This method allows to internalize substantial amounts of proteins, with different molecular weight and conformation, without compromising the structural properties and cell viability. Characterizing proteins in a physiological environment is essential as the environment can dramatically affect the conformation and dynamics of biomolecules as shown by in-cell EPR spectra vs those acquired in buffer solution. Considering its versatility, this method opens the possibility to scientists to study proteins directly in living cells through a wide range of techniques.
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Affiliation(s)
- Francesco Torricella
- Magnetic Resonance Center - CERM, University of Florence, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Alessio Bonucci
- Aix Marseille, Univ, CNRS, BIP, Laboratoire de Bioénergétique et Ingégnerie des protéines, Marseille, France
| | - Panagis Polykretis
- Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Francesca Cencetti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, v.le GB Morgagni 50, 50134, Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy.
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31
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Herr K, Fleckenstein M, Brodrecht M, Höfler MV, Heise H, Aussenac F, Gutmann T, Reggelin M, Buntkowsky G. A novel strategy for site selective spin-labeling to investigate bioactive entities by DNP and EPR spectroscopy. Sci Rep 2021; 11:13714. [PMID: 34211027 PMCID: PMC8249612 DOI: 10.1038/s41598-021-92975-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/18/2021] [Indexed: 11/09/2022] Open
Abstract
A novel specific spin-labeling strategy for bioactive molecules is presented for eptifibatide (integrilin) an antiplatelet aggregation inhibitor, which derives from the venom of certain rattlesnakes. By specifically labeling the disulfide bridge this molecule becomes accessible for analytical techniques such as Electron Paramagnetic Resonance (EPR) and solid state Dynamic Nuclear Polarization (DNP). The necessary spin-label was synthesized and inserted into the disulfide bridge of eptifibatide via reductive followed by insertion by a double Michael addition under physiological conditions. This procedure is universally applicable for disulfide containing biomolecules and is expected to preserve their tertiary structure with minimal change due to the small size of the label and restoring of the previous disulfide connection. HPLC and MS analysis show the successful introduction of the spin label and EPR spectroscopy confirms its activity. DNP-enhanced solid state NMR experiments show signal enhancement factors of up to 19 in 13C CP MAS experiments which corresponds to time saving factors of up to 361. This clearly shows the high potential of our new spin labeling strategy for the introduction of site selective radical spin labels into biomolecules and biosolids without compromising its conformational integrity for structural investigations employing solid-state DNP or advanced EPR techniques.
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Affiliation(s)
- Kevin Herr
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Max Fleckenstein
- Institute of Organic Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Martin Brodrecht
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Mark V Höfler
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Henrike Heise
- Structural Biochemistry (ICS-6), Institute of Complex Systems, Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Fabien Aussenac
- Bruker France SAS, 34 rue de l'industrie, 67160, Wissembourg, France
| | - Torsten Gutmann
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Michael Reggelin
- Institute of Organic Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany.
| | - Gerd Buntkowsky
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany.
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32
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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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33
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Bowen AM, Bertran A, Henbest KB, Gobbo M, Timmel CR, Di Valentin M. Orientation-Selective and Frequency-Correlated Light-Induced Pulsed Dipolar Spectroscopy. J Phys Chem Lett 2021; 12:3819-3826. [PMID: 33856805 PMCID: PMC8154851 DOI: 10.1021/acs.jpclett.1c00595] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
We explore the potential of orientation-resolved pulsed dipolar spectroscopy (PDS) in light-induced versions of the experiment. The use of triplets as spin-active moieties for PDS offers an attractive tool for studying biochemical systems containing optically active cofactors. Cofactors are often rigidly bound within the protein structure, providing an accurate positional marker. The rigidity leads to orientation selection effects in PDS, which can be analyzed to give both distance and mutual orientation information. Herein we present a comprehensive analysis of the orientation selection of a full set of light-induced PDS experiments. We exploit the complementary information provided by the different light-induced techniques to yield atomic-level structural information. For the first time, we measure a 2D frequency-correlated laser-induced magnetic dipolar spectrum, and we are able to monitor the complete orientation dependence of the system in a single experiment. Alternatively, the summed spectrum enables an orientation-independent analysis to determine the distance distribution.
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Affiliation(s)
- Alice M. Bowen
- Department
of Chemistry, Photon Science Institute and The National EPR Research
Facility, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Arnau Bertran
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Kevin B. Henbest
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Marina Gobbo
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Christiane R. Timmel
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Marilena Di Valentin
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
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34
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Kucher S, Elsner C, Safonova M, Maffini S, Bordignon E. In-Cell Double Electron-Electron Resonance at Nanomolar Protein Concentrations. J Phys Chem Lett 2021; 12:3679-3684. [PMID: 33829785 DOI: 10.1021/acs.jpclett.1c00048] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is an established technique to site-specifically monitor conformational changes of spin-labeled biomolecules. Emerging in-cell EPR approaches aiming to address spin-labeled proteins in their native environment still struggle to reach a broad applicability and to target physiologically relevant protein concentrations. Here, we present a comparative in vitro and in-cell double electron-electron resonance (DEER) study demonstrating that nanomolar protein concentrations are at reach to measure distances up to 4.5 nm between protein sites carrying commercial gadolinium spin labels.
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Affiliation(s)
- Svetlana Kucher
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Universitaetsstr. 150, 44801 Bochum, Germany
| | - Christina Elsner
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Universitaetsstr. 150, 44801 Bochum, Germany
| | - Mariya Safonova
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Universitaetsstr. 150, 44801 Bochum, Germany
| | - Stefano Maffini
- Max Planck Institute of Molecular Physiology, Department of Mechanistic Cell Biology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Enrica Bordignon
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Universitaetsstr. 150, 44801 Bochum, Germany
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35
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Priya P, Aneesh B, Harikrishnan K. Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health. J Microbiol Methods 2021; 185:106215. [PMID: 33839214 DOI: 10.1016/j.mimet.2021.106215] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022]
Abstract
Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.
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Affiliation(s)
- P Priya
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
| | - B Aneesh
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences Cochin University of Science and Technology, Cochin, Kerala, India.
| | - K Harikrishnan
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
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36
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Torricella F, Pierro A, Mileo E, Belle V, Bonucci A. Nitroxide spin labels and EPR spectroscopy: A powerful association for protein dynamics studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140653. [PMID: 33757896 DOI: 10.1016/j.bbapap.2021.140653] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/01/2023]
Abstract
Site-Directed Spin Labelling (SDSL) technique is based on the attachment of a paramagnetic label onto a specific position of a protein (or other bio-molecules) and the subsequent study by Electron Paramagnetic Resonance (EPR) spectroscopy. In particular, continuous-wave EPR (cw-EPR) spectra can detect the local conformational dynamics for proteins under various conditions. Moreover, pulse-EPR experiments on doubly spin-labelled proteins allow measuring distances between spin centres in the 1.5-8 nm range, providing information about structures and functions. This review focuses on SDSL-EPR spectroscopy as a structural biology tool to investigate proteins using nitroxide labels. The versatility of this spectroscopic approach for protein structural characterization has been demonstrated through the choice of recent studies. The main aim is to provide a general overview of the technique, particularly for non-experts, to spread the applicability of this technique in various fields of structural biology.
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Affiliation(s)
- F Torricella
- CERM-Magnetic Resonance Center, Department of Chemistry, University of Florence, via L.Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - A Pierro
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - E Mileo
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - V Belle
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - A Bonucci
- CERM-Magnetic Resonance Center, Department of Chemistry, University of Florence, via L.Sacconi 6, 50019 Sesto Fiorentino, Italy; Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France.
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37
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Braun T, Stehle J, Kacprzak S, Carl P, Höfer P, Subramaniam V, Drescher M. Intracellular Protein-Lipid Interactions Studied by Rapid-Scan Electron Paramagnetic Resonance Spectroscopy. J Phys Chem Lett 2021; 12:2471-2475. [PMID: 33663214 PMCID: PMC7957861 DOI: 10.1021/acs.jpclett.0c03583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
Protein-membrane interactions play key roles in essential cellular processes; studying these interactions in the cell is a challenging task of modern biophysical chemistry. A prominent example is the interaction of human α-synuclein (αS) with negatively charged membranes. It has been well-studied in vitro, but in spite of the huge amount of lipid membranes in the crowded environment of biological cells, to date, no interactions have been detected in cells. Here, we use rapid-scan (RS) electron paramagnetic resonance (EPR) spectroscopy to study αS interactions with negatively charged vesicles in vitro and upon transfection of the protein and lipid vesicles into model cells, i.e., oocytes of Xenopus laevis. We show that protein-vesicle interactions are reflected in RS spectra in vitro and in cells, which enables time-resolved monitoring of protein-membrane interaction upon transfection into cells. Our data suggest binding of a small fraction of αS to endogenous membranes.
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Affiliation(s)
- Theresa
S. Braun
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Juliane Stehle
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Sylwia Kacprzak
- Bruker BioSpin
GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Patrick Carl
- Bruker BioSpin
GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Peter Höfer
- Bruker BioSpin
GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Vinod Subramaniam
- Vrije
Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - Malte Drescher
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
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38
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Sen' VD, Golubev VA, Shilov GV, Chernyak AV, Kurmaz VA, Luzhkov VB. Oxygen Atom Transfer in the Oxidation of Dimethyl Sulfoxide by Oxoammonium Cations. J Org Chem 2021; 86:3176-3185. [PMID: 33449678 DOI: 10.1021/acs.joc.0c02526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclic oxoammonium salts and DMSO are known as important reagents for their diverse and unique reactivity. In the present work, we have studied the reaction of six- and five-membered oxoammonium salts with DMSO. The reaction includes ∼100% selective transfer of the O atom from the >N+═O group to the S atom of DMSO and structural rearrangement of the remaining cationic framework, leading to the formation of hydrolytically unstable iminium salts. The logarithms of the bimolecular rate constants k of the reaction correlated linearly with the reduction potentials E>N+═O/>N-O•, a relationship known for other electrophile-nucleophile combinations. The kinetic data and results of the DFT calculations allow for the suggestion that the studied process proceeds via the prereactive charge-transfer complex >N+═O···S (O)Me2 and its direct concerted rearrangement to the iminium salts. An alternative mechanism that includes intermediate steps with discrete nitrenium cations can be ruled out on the basis of product analysis and DFT computations. The obtained results allow a deeper understanding of the redox chemistry of a pair of nitroxide radicals-oxoammonium cations.
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Affiliation(s)
- Vasily D Sen'
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka 142432, Russian Federation
| | - Valery A Golubev
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka 142432, Russian Federation
| | - Gennadii V Shilov
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka 142432, Russian Federation
| | - Alexander V Chernyak
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka 142432, Russian Federation
| | - Vladimir A Kurmaz
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka 142432, Russian Federation
| | - Victor B Luzhkov
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka 142432, Russian Federation.,Department of Fundamental Physico-Chemical Engineering, Lomonosov Moscow State University, Moscow 119991, Russia Federation
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39
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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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40
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Bertran A, Henbest KB, De Zotti M, Gobbo M, Timmel CR, Di Valentin M, Bowen AM. Light-Induced Triplet-Triplet Electron Resonance Spectroscopy. J Phys Chem Lett 2021; 12:80-85. [PMID: 33306382 PMCID: PMC8016185 DOI: 10.1021/acs.jpclett.0c02884] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
We present a new technique, light-induced triplet-triplet electron resonance spectroscopy (LITTER), which measures the dipolar interaction between two photoexcited triplet states, enabling both the distance and angular distributions between the two triplet moieties to be determined on a nanometer scale. This is demonstrated for a model bis-porphyrin peptide that renders dipolar traces with strong orientation selection effects. Using simulations and density functional theory calculations, we extract distance distributions and relative orientations of the porphyrin moieties, allowing the dominant conformation of the peptide in a frozen solution to be identified. LITTER removes the requirement of current light-induced electron spin resonance pulse dipolar spectroscopy techniques to have a permanent paramagnetic moiety, becoming more suitable for in-cell applications and facilitating access to distance determination in unmodified macromolecular systems containing photoexcitable moieties. LITTER also has the potential to enable direct comparison with Förster resonance energy transfer and combination with microscopy inside cells.
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Affiliation(s)
- Arnau Bertran
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Kevin B. Henbest
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Marta De Zotti
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Marina Gobbo
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Christiane R. Timmel
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Marilena Di Valentin
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Alice M. Bowen
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
- Department
of Chemistry and Photon Science Institute, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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41
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New Insight into the Mechanism of Drug Release from Poly(d,l-lactide) Film by Electron Paramagnetic Resonance. Polymers (Basel) 2020; 12:polym12123046. [PMID: 33353203 PMCID: PMC7767321 DOI: 10.3390/polym12123046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 12/31/2022] Open
Abstract
A novel approach based on convolution of the electron paramagnetic resonance (EPR) spectra was used for quantitative study of the release kinetics of paramagnetic dopants from poly(d,l-lactide) films. A non-monotonic dependence of the release rate on time was reliably recorded. The release regularities were compared with the dynamics of polymer structure changes determined by EPR, SEM, and optic microscopy. The data obtained allow for the conclusion that the main factor governing dopant release is the formation of pores connected with the surface. In contrast, the contribution of the dopant diffusion through the polymer matrix is negligible. The dopant release can be divided into two phases: release through surface pores, which are partially closed with time, and release through pores initially formed inside the polymer matrix due to autocatalytic hydrolysis of the polymer and gradually connected to the surface of the sample. For some time, these processes co-occur. The mathematical model of the release kinetics based on pore formation is presented, describing the kinetics of release of various dopants from the polymer films of different thicknesses.
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42
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Collauto A, Bülow S, Gophane DB, Saha S, Stelzl LS, Hummer G, Sigurdsson ST, Prisner TF. Compaction of RNA Duplexes in the Cell**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alberto Collauto
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Sören Bülow
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
| | - Dnyaneshwar B. Gophane
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Subham Saha
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Lukas S. Stelzl
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
- Institute for Biophysics Goethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
| | - Snorri T. Sigurdsson
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
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43
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Collauto A, von Bülow S, Gophane DB, Saha S, Stelzl LS, Hummer G, Sigurdsson ST, Prisner TF. Compaction of RNA Duplexes in the Cell*. Angew Chem Int Ed Engl 2020; 59:23025-23029. [PMID: 32804430 PMCID: PMC7756485 DOI: 10.1002/anie.202009800] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Indexed: 11/15/2022]
Abstract
The structure and flexibility of RNA depends sensitively on the microenvironment. Using pulsed electron-electron double-resonance (PELDOR)/double electron-electron resonance (DEER) spectroscopy combined with advanced labeling techniques, we show that the structure of double-stranded RNA (dsRNA) changes upon internalization into Xenopus laevis oocytes. Compared to dilute solution, the dsRNA A-helix is more compact in cells. We recapitulate this compaction in a densely crowded protein solution. Atomic-resolution molecular dynamics simulations of dsRNA semi-quantitatively capture the compaction, and identify non-specific electrostatic interactions between proteins and dsRNA as a possible driver of this effect.
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Affiliation(s)
- Alberto Collauto
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Str. 760438Frankfurt am MainGermany
| | - Sören von Bülow
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
| | - Dnyaneshwar B. Gophane
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Subham Saha
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Lukas S. Stelzl
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
| | - Gerhard Hummer
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
- Institute for BiophysicsGoethe University FrankfurtMax-von-Laue-Str. 960438Frankfurt am MainGermany
| | - Snorri T. Sigurdsson
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Str. 760438Frankfurt am MainGermany
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44
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Bordignon E, Seeger MA, Galazzo L, Meier G. From in vitro towards in situ: structure-based investigation of ABC exporters by electron paramagnetic resonance spectroscopy. FEBS Lett 2020; 594:3839-3856. [PMID: 33219535 DOI: 10.1002/1873-3468.14004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/30/2020] [Accepted: 11/15/2020] [Indexed: 12/12/2022]
Abstract
ATP-binding cassette (ABC) exporters have been studied now for more than four decades, and recent structural investigation has produced a large number of protein database entries. Yet, important questions about how ABC exporters function at the molecular level remain debated, such as which are the molecular recognition hotspots and the allosteric couplings dynamically regulating the communication between the catalytic cycle and the export of substrates. This conundrum mainly arises from technical limitations confining all research to in vitro analysis of ABC transporters in detergent solutions or embedded in membrane-mimicking environments. Therefore, a largely unanswered question is how ABC exporters operate in situ, namely in the native membrane context of a metabolically active cell. This review focuses on novel mechanistic insights into type I ABC exporters gained through a unique combination of structure determination, biochemical characterization, generation of conformation-specific nanobodies/sybodies and double electron-electron resonance.
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Affiliation(s)
- Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Switzerland
| | - Laura Galazzo
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Gianmarco Meier
- Institute of Medical Microbiology, University of Zurich, Switzerland
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45
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Juliusson HY, Sigurdsson ST. Nitroxide-Derived N-Oxide Phenazines for Noncovalent Spin-Labeling of DNA. Chembiochem 2020; 21:2635-2642. [PMID: 32353177 DOI: 10.1002/cbic.202000128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/28/2020] [Indexed: 12/11/2022]
Abstract
Two o-benzoquinone derivatives of isoindoline were synthesized for use as building blocks to incorporate isoindoline nitroxides into different compounds and materials. These o-quinones were condensed with a number of o-phenylenediamines to form isoindoline-phenazines in high yields. Subsequent oxidation gave phenazine-di-N-oxide isoindoline nitroxides that were evaluated for noncovalent and site-directed spin-labeling of duplex DNA and RNA that contained abasic sites. Although only minor binding was observed for RNA, the unsubstituted phenazine-N,N-dioxide tetramethyl isoindoline nitroxide showed high binding affinity and selectivity towards abasic sites in duplex DNA that contained cytosine as the orphan base.
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Affiliation(s)
- Haraldur Y Juliusson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavik, Iceland
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavik, Iceland
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Babić N, Orio M, Peyrot F. Unexpected rapid aerobic transformation of 2,2,6,6-tetraethyl-4-oxo(piperidin-1-yloxyl) radical by cytochrome P450 in the presence of NADPH: Evidence against a simple reduction of the nitroxide moiety to the hydroxylamine. Free Radic Biol Med 2020; 156:144-156. [PMID: 32561320 DOI: 10.1016/j.freeradbiomed.2020.05.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/29/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022]
Abstract
Aminoxyl radicals (nitroxides) are a class of compounds with important biomedical applications, serving as antioxidants, spin labels for proteins, spin probes of oximetry, pH, or redox status in electron paramagnetic resonance (EPR), or as contrast agents in magnetic resonance imaging (MRI). However, the fast reduction of the radical moiety in common tetramethyl-substituted cyclic nitroxides within cells, yielding diamagnetic hydroxylamines, limits their use in spectroscopic and imaging studies. In vivo half-lives of commonly used tetramethyl-substituted nitroxides span no more than a few minutes. Therefore, synthetic efforts have focused on enhancing the nitroxide stability towards reduction by varying the electronic and steric environment of the radical. Tetraethyl-substitution at alpha position to the aminoxyl function proved efficient in vitro against reduction by ascorbate or cytosolic extracts. Moreover, 2,2,6,6-tetraethyl-4-oxo(piperidin-1-yloxyl) radical (TEEPONE) was used successfully for tridimensional EPR and MRI in vivo imaging of mouse head, with a reported half-life of over 80 min. We decided to investigate the stability of tetraethyl-substituted piperidine nitroxides in the presence of hepatic microsomal fractions, since no detailed study of their "metabolic stability" at the molecular level had been reported despite examples of the use of these nitroxides in vivo. In this context, the rapid aerobic transformation of TEEPONE observed in the presence of rat liver microsomal fractions and NADPH was unexpected. Combining EPR, HPLC-HRMS, and DFT studies on a series of piperidine nitroxides - TEEPONE, 4-oxo-2,2,6,6-tetramethyl(piperidin-1-yloxyl) (TEMPONE), and 2,2,6,6-tetraethyl-4-hydroxy(piperidin-1-yloxyl) (TEEPOL), we propose that the rapid loss in paramagnetic character of TEEPONE is not due to reduction to hydroxylamine but is a consequence of carbon backbone modification initiated by hydrogen radical abstraction in alpha position to the carbonyl by the P450-Fe(V)=O species. Besides, hydrogen radical abstraction by P450 on ethyl substituents, leading to dehydrogenation or hydroxylation products, leaves the aminoxyl function intact but could alter the linewidth of the EPR signal and thus interfere with methods relying on measurement of this parameter (EPR oximetry).
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Affiliation(s)
- Nikola Babić
- Université de Paris, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, F-75006, Paris, France
| | - Maylis Orio
- Aix-Marseille Univ., CNRS, Centrale Marseille, ISm2, Marseille, France
| | - Fabienne Peyrot
- Université de Paris, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, F-75006, Paris, France; Sorbonne Université, Institut National Supérieur Du Professorat et de L'Éducation (INSPE) de L'Académie de Paris, F-75016, Paris, France.
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Fleck N, Heubach CA, Hett T, Haege FR, Bawol PP, Baltruschat H, Schiemann O. SLIM: A Short-Linked, Highly Redox-Stable Trityl Label for High-Sensitivity In-Cell EPR Distance Measurements. Angew Chem Int Ed Engl 2020; 59:9767-9772. [PMID: 32329172 PMCID: PMC7318235 DOI: 10.1002/anie.202004452] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Indexed: 12/15/2022]
Abstract
The understanding of biomolecular function is coupled to knowledge about the structure and dynamics of these biomolecules, preferably acquired under native conditions. In this regard, pulsed dipolar EPR spectroscopy (PDS) in conjunction with site-directed spin labeling (SDSL) is an important method in the toolbox of biophysical chemistry. However, the currently available spin labels have diverse deficiencies for in-cell applications, for example, low radical stability or long bioconjugation linkers. In this work, a synthesis strategy is introduced for the derivatization of trityl radicals with a maleimide-functionalized methylene group. The resulting trityl spin label, called SLIM, yields narrow distance distributions, enables highly sensitive distance measurements down to concentrations of 90 nm, and shows high stability against reduction. Using this label, the guanine-nucleotide dissociation inhibitor (GDI) domain of Yersinia outer protein O (YopO) is shown to change its conformation within eukaryotic cells.
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Affiliation(s)
- Nico Fleck
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Caspar A. Heubach
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Tobias Hett
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Florian R. Haege
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Pawel P. Bawol
- Institute of Physical and Theoretical ChemistryUniversity of BonnRömerstr. 16453117BonnGermany
| | - Helmut Baltruschat
- Institute of Physical and Theoretical ChemistryUniversity of BonnRömerstr. 16453117BonnGermany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
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48
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Fleck N, Heubach CA, Hett T, Haege FR, Bawol PP, Baltruschat H, Schiemann O. SLIM: A Short‐Linked, Highly Redox‐Stable Trityl Label for High‐Sensitivity In‐Cell EPR Distance Measurements. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004452] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Nico Fleck
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Caspar A. Heubach
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Tobias Hett
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Florian R. Haege
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Pawel P. Bawol
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Römerstr. 164 53117 Bonn Germany
| | - Helmut Baltruschat
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Römerstr. 164 53117 Bonn Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
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Narasimhan S, Folkers GE, Baldus M. When Small becomes Too Big: Expanding the Use of In‐Cell Solid‐State NMR Spectroscopy. Chempluschem 2020; 85:760-768. [DOI: 10.1002/cplu.202000167] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/31/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular ResearchUtrecht University Padualaan 8 3584 CH Utrecht (The Netherlands
| | - Gert E. Folkers
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular ResearchUtrecht University Padualaan 8 3584 CH Utrecht (The Netherlands
| | - Marc Baldus
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular ResearchUtrecht University Padualaan 8 3584 CH Utrecht (The Netherlands
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50
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Human Serum Albumin Labelled with Sterically-Hindered Nitroxides as Potential MRI Contrast Agents. Molecules 2020; 25:molecules25071709. [PMID: 32276437 PMCID: PMC7180620 DOI: 10.3390/molecules25071709] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 11/29/2022] Open
Abstract
Four albumin-nitroxide conjugates were prepared and tested as metal-free organic radical contrast agents (ORCAs) for magnetic resonance imaging (MRI). Each human serum albumin (HSA) carrier bears multiple nitroxides conjugated via homocysteine thiolactones. These molecular conjugates retain important physical and biological properties of their HSA component, and the resistance of their nitroxide groups to bioreduction was retained or enhanced. The relaxivities are similar for these four conjugates and are much greater than those of their individual components: the HSA or the small nitroxide molecules. This new family of conjugates has excellent prospects for optimization as ORCAs.
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