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Application of EPR Spectroscopy in Biophysics and Biochemistry
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Application of EPR Spectroscopy in Biophysics and Biochemistry

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Physical Chemistry".

Deadline for manuscript submissions: closed (15 November 2022) | Viewed by 18904

Special Issue Editors

Dr. Olesya A. Krumkacheva

E-Mail Website
Guest Editor
International Tomography Center, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
Interests: electron paramagnetic resonance; method development; structural biology; nucleic acids; ribosomes; photodynamic treatment
Dr. Matvey Fedin

E-Mail Website
Guest Editor
International Tomography Center, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
Interests: electron paramagnetic resonance; molecular magnetism; metal-organic frameworks; ionic liquids; spin-labelled biomolecules; spin chemistry; photochemistry

Special Issue Information

Dear Colleagues,

Electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for studying the structure and dynamics of a wide variety of biological systems. EPR combined with site-directed spin labeling applies to biopolymers of any size, including multicomponent complexes of ribosomes, large proteins, and their complexes with RNA and DNA. Moreover, EPR is suitable for studying systems with a broad conformational ensemble and following structural changes in different environments, including cells. These features of the EPR have promoted its application to address complex biological problems.

The focus of this Special Issue is the application of EPR spectroscopy in biochemistry and biophysics. Papers can cover the application of EPR methods in different areas of research, such as structural biology (protein, peptide, RNA, DNA, ribosome, etc.), interactions between macromolecules and their ligands, structural bases of folded and unfolded proteins; biomolecular recognition, and features of biomolecules in cells, etc. Studies related to the methodology’s development of biomolecular EPR and works conducted by integrating EPR data with those from other experimental techniques along with computational tools are highly welcome. Articles reporting original research as well as reviews will be considered for publication.

Dr. Olesya A. Krumkacheva
Dr. Matvey Fedin
Guest Editors

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Keywords

  • EPR
  • structural biology
  • DNA
  • RNA
  • proteins
  • biomolecular recognition and interaction
  • novel techniques in biophysics

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Published Papers (7 papers)

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Research

16 pages, 2150 KiB  
Article
Guidelines for the Simulations of Nitroxide X-Band cw EPR Spectra from Site-Directed Spin Labeling Experiments Using SimLabel
by Emilien Etienne, Annalisa Pierro, Ketty C. Tamburrini, Alessio Bonucci, Elisabetta Mileo, Marlène Martinho and Valérie Belle
Molecules 2023, 28(3), 1348; https://doi.org/10.3390/molecules28031348 - 31 Jan 2023
Cited by 6 | Viewed by 3062
Abstract
Site-directed spin labeling (SDSL) combined with continuous wave electron paramagnetic resonance (cw EPR) spectroscopy is a powerful technique to reveal, at the local level, the dynamics of structural transitions in proteins. Here, we consider SDSL-EPR based on the selective grafting of a nitroxide [...] Read more.
Site-directed spin labeling (SDSL) combined with continuous wave electron paramagnetic resonance (cw EPR) spectroscopy is a powerful technique to reveal, at the local level, the dynamics of structural transitions in proteins. Here, we consider SDSL-EPR based on the selective grafting of a nitroxide on the protein under study, followed by X-band cw EPR analysis. To extract valuable quantitative information from SDSL-EPR spectra and thus give a reliable interpretation on biological system dynamics, a numerical simulation of the spectra is required. However, regardless of the numerical tool chosen to perform such simulations, the number of parameters is often too high to provide unambiguous results. In this study, we have chosen SimLabel to perform such simulations. SimLabel is a graphical user interface (GUI) of Matlab, using some functions of Easyspin. An exhaustive review of the parameters used in this GUI has enabled to define the adjustable parameters during the simulation fitting and to fix the others prior to the simulation fitting. Among them, some are set once and for all (gy, gz) and others are determined (Az, gx) thanks to a supplementary X-band spectrum recorded on a frozen solution. Finally, we propose guidelines to perform the simulation of X-band cw-EPR spectra of nitroxide labeled proteins at room temperature, with no need of uncommon higher frequency spectrometry and with the minimal number of variable parameters. Full article
(This article belongs to the Special Issue Application of EPR Spectroscopy in Biophysics and Biochemistry)
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13 pages, 1384 KiB  
Communication
Erythrosin B as a New Photoswitchable Spin Label for Light-Induced Pulsed EPR Dipolar Spectroscopy
by Arnau Bertran, Laura Morbiato, Sara Aquilia, Laura Gabbatore, Marta De Zotti, Christiane R. Timmel, Marilena Di Valentin and Alice M. Bowen
Molecules 2022, 27(21), 7526; https://doi.org/10.3390/molecules27217526 - 3 Nov 2022
Cited by 4 | Viewed by 2077
Abstract
We present a new photoswitchable spin label for light-induced pulsed electron paramagnetic resonance dipolar spectroscopy (LiPDS), the photoexcited triplet state of erythrosin B (EB), which is ideal for biological applications. With this label, we perform an in-depth study of the orientational effects in [...] Read more.
We present a new photoswitchable spin label for light-induced pulsed electron paramagnetic resonance dipolar spectroscopy (LiPDS), the photoexcited triplet state of erythrosin B (EB), which is ideal for biological applications. With this label, we perform an in-depth study of the orientational effects in dipolar traces acquired using the refocused laser-induced magnetic dipole technique to obtain information on the distance and relative orientation between the EB and nitroxide labels in a rigid model peptide, in good agreement with density functional theory predictions. Additionally, we show that these orientational effects can be averaged to enable an orientation-independent analysis to determine the distance distribution. Furthermore, we demonstrate the feasibility of these experiments above liquid nitrogen temperatures, removing the need for expensive liquid helium or cryogen-free cryostats. The variety of choices in photoswitchable spin labels and the affordability of the experiments are critical for LiPDS to become a widespread methodology in structural biology. Full article
(This article belongs to the Special Issue Application of EPR Spectroscopy in Biophysics and Biochemistry)
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13 pages, 1934 KiB  
Article
EPR Investigations to Study the Impact of Mito-Metformin on the Mitochondrial Function of Prostate Cancer Cells
by Donatienne d’Hose, Barbara Mathieu, Lionel Mignion, Micael Hardy, Olivier Ouari, Bénédicte F. Jordan, Pierre Sonveaux and Bernard Gallez
Molecules 2022, 27(18), 5872; https://doi.org/10.3390/molecules27185872 - 10 Sep 2022
Cited by 3 | Viewed by 1937
Abstract
Background: Mito-metformin10 (MM10), synthesized by attaching a triphenylphosphonium cationic moiety via a 10-carbon aliphatic side chain to metformin, is a mitochondria-targeted analog of metformin that was recently demonstrated to alter mitochondrial function and proliferation in pancreatic ductal adenocarcinoma. Here, we hypothesized that this [...] Read more.
Background: Mito-metformin10 (MM10), synthesized by attaching a triphenylphosphonium cationic moiety via a 10-carbon aliphatic side chain to metformin, is a mitochondria-targeted analog of metformin that was recently demonstrated to alter mitochondrial function and proliferation in pancreatic ductal adenocarcinoma. Here, we hypothesized that this compound may decrease the oxygen consumption rate (OCR) in prostate cancer cells, increase the level of mitochondrial ROS, alleviate tumor hypoxia, and radiosensitize tumors. Methods: OCR and mitochondrial superoxide production were assessed by EPR (9 GHz) in vitro in PC-3 and DU-145 prostate cancer cells. Reduced and oxidized glutathione were assessed before and after MM10 exposure. Tumor oxygenation was measured in vivo using 1 GHz EPR oximetry in PC-3 tumor model. Tumors were irradiated at the time of maximal reoxygenation. Results: 24-hours exposure to MM10 significantly decreased the OCR of PC-3 and DU-145 cancer cells. An increase in mitochondrial superoxide levels was observed in PC-3 but not in DU-145 cancer cells, an observation consistent with the differences observed in glutathione levels in both cancer cell lines. In vivo, the tumor oxygenation significantly increased in the PC-3 model (daily injection of 2 mg/kg MM10) 48 and 72 h after initiation of the treatment. Despite the significant effect on tumor hypoxia, MM10 combined to irradiation did not increase the tumor growth delay compared to the irradiation alone. Conclusions: MM10 altered the OCR in prostate cancer cells. The effect of MM10 on the superoxide level was dependent on the antioxidant capacity of cell line. In vivo, MM10 alleviated tumor hypoxia, yet without consequence in terms of response to irradiation. Full article
(This article belongs to the Special Issue Application of EPR Spectroscopy in Biophysics and Biochemistry)
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10 pages, 1506 KiB  
Article
Synthesis of Spin-Labeled Ibuprofen and Its Interaction with Lipid Membranes
by Denis S. Baranov, Anna S. Smorygina and Sergei A. Dzuba
Molecules 2022, 27(13), 4127; https://doi.org/10.3390/molecules27134127 - 27 Jun 2022
Cited by 6 | Viewed by 2068
Abstract
Ibuprofen is a non-steroidal anti-inflammatory drug possessing analgesic and antipyretic activity. Electron paramagnetic resonance (EPR) spectroscopy could be applied to study its interaction with biological membranes and proteins if its spin-labeled analogs were synthesized. Here, a simple sequence of ibuprofen transformations—nitration, esterification, reduction, [...] Read more.
Ibuprofen is a non-steroidal anti-inflammatory drug possessing analgesic and antipyretic activity. Electron paramagnetic resonance (EPR) spectroscopy could be applied to study its interaction with biological membranes and proteins if its spin-labeled analogs were synthesized. Here, a simple sequence of ibuprofen transformations—nitration, esterification, reduction, Sandmeyer reaction, Sonogashira cross-coupling, oxidation and saponification—was developed to attain this goal. The synthesis resulted in spin-labeled ibuprofen (ibuprofen-SL) in which the spin label TEMPOL is attached to the benzene ring. EPR spectra confirmed interaction of ibuprofen-SL with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. Using 2H electron spin echo envelope modulation (ESEEM) spectroscopy, ibuprofen-SL was found to be embedded into the hydrophobic bilayer interior. Full article
(This article belongs to the Special Issue Application of EPR Spectroscopy in Biophysics and Biochemistry)
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16 pages, 2384 KiB  
Article
Magnetophotoselection in the Investigation of Excitonically Coupled Chromophores: The Case of the Water-Soluble Chlorophyll Protein
by Susanna Ciuti, Alessandro Agostini, Antonio Barbon, Marco Bortolus, Harald Paulsen, Marilena Di Valentin and Donatella Carbonera
Molecules 2022, 27(12), 3654; https://doi.org/10.3390/molecules27123654 - 7 Jun 2022
Cited by 6 | Viewed by 2184
Abstract
A magnetophotoselection (MPS) investigation of the photoexcited triplet state of chlorophyll a both in a frozen organic solvent and in a protein environment, provided by the water-soluble chlorophyll protein (WSCP) of Lepidium virginicum, is reported. The MPS experiment combines the photoselection achieved [...] Read more.
A magnetophotoselection (MPS) investigation of the photoexcited triplet state of chlorophyll a both in a frozen organic solvent and in a protein environment, provided by the water-soluble chlorophyll protein (WSCP) of Lepidium virginicum, is reported. The MPS experiment combines the photoselection achieved by exciting with linearly polarized light with the magnetic selection of electron paramagnetic resonance (EPR) spectroscopy, allowing the determination of the relative orientation of the optical transition dipole moment and the zero-field splitting tensor axes in both environments. We demonstrate the robustness of the proposed methodology for a quantitative description of the excitonic interactions among pigments. The orientation of the optical transition dipole moments determined by the EPR analysis in WSCP, identified as an appropriate model system, are in excellent agreement with those calculated in the point-dipole approximation. In addition, MPS provides information on the electronic properties of the triplet state, localized on a single chlorophyll a pigment of the protein cluster, in terms of orientation of the zero-field splitting tensor axes in the molecular frame. Full article
(This article belongs to the Special Issue Application of EPR Spectroscopy in Biophysics and Biochemistry)
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16 pages, 3355 KiB  
Article
Effects of Spiro-Cyclohexane Substitution of Nitroxyl Biradicals on Dynamic Nuclear Polarization
by Nargiz B. Asanbaeva, Larisa Yu. Gurskaya, Yuliya F. Polienko, Tatyana V. Rybalova, Maxim S. Kazantsev, Alexey A. Dmitriev, Nina P. Gritsan, Nadia Haro-Mares, Torsten Gutmann, Gerd Buntkowsky, Evgeny V. Tretyakov and Elena G. Bagryanskaya
Molecules 2022, 27(10), 3252; https://doi.org/10.3390/molecules27103252 - 19 May 2022
Cited by 3 | Viewed by 2066
Abstract
Spiro-substituted nitroxyl biradicals are widely used as reagents for dynamic nuclear polarization (DNP), which is especially important for biopolymer research. The main criterion for their applicability as polarizing agents is the value of the spin–spin exchange interaction parameter (J), which can [...] Read more.
Spiro-substituted nitroxyl biradicals are widely used as reagents for dynamic nuclear polarization (DNP), which is especially important for biopolymer research. The main criterion for their applicability as polarizing agents is the value of the spin–spin exchange interaction parameter (J), which can vary considerably when different couplers are employed that link the radical moieties. This paper describes a study on biradicals, with a ferrocene-1,1′-diyl-substituted 1,3-diazetidine-2,4-diimine coupler, that have never been used before as DNP agents. We observed a substantial difference in the temperature dependence between Electron Paramagnetic Resonance (EPR) spectra of biradicals carrying either methyl or spirocyclohexane substituents and explain the difference using Density Functional Theory (DFT) calculation results. It was shown that the replacement of methyl groups by spirocycles near the N-O group leads to an increase in the contribution of conformers having J ≈ 0. The DNP gain observed for the biradicals with methyl substituents is three times higher than that for the spiro-substituted nitroxyl biradicals and is inversely proportional to the contribution of biradicals manifesting the negligible exchange interaction. The effects of nucleophiles and substituents in the nitroxide biradicals on the ring-opening reaction of 1,3-diazetidine and the influence of the ring opening on the exchange interaction were also investigated. It was found that in contrast to the methyl-substituted nitroxide biradical (where we observed the ring-opening reaction upon the addition of amines), the ring opening does not occur in the spiro-substituted biradical owing to a steric barrier created by the bulky cyclohexyl substituents. Full article
(This article belongs to the Special Issue Application of EPR Spectroscopy in Biophysics and Biochemistry)
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13 pages, 1860 KiB  
Article
Stability of ZIF-8 Nanoparticles in Most Common Cell Culture Media
by Anna S. Spitsyna, Artem S. Poryvaev, Natalya E. Sannikova, Anastasiya A. Yazikova, Igor A. Kirilyuk, Sergey A. Dobrynin, Olga A. Chinak, Matvey V. Fedin and Olesya A. Krumkacheva
Molecules 2022, 27(10), 3240; https://doi.org/10.3390/molecules27103240 - 18 May 2022
Cited by 22 | Viewed by 4247
Abstract
Zeolite imidazolate framework-8 (ZIF-8) is a promising platform for drug delivery, and information regarding the stability of ZIF-8 nanoparticles in cell culture media is essential for proper interpretation of in vitro experimental results. In this work, we report a quantitative investigation of the [...] Read more.
Zeolite imidazolate framework-8 (ZIF-8) is a promising platform for drug delivery, and information regarding the stability of ZIF-8 nanoparticles in cell culture media is essential for proper interpretation of in vitro experimental results. In this work, we report a quantitative investigation of the ZIF-8 nanoparticle’s stability in most common cell culture media. To this purpose, ZIF-8 nanoparticles containing sterically shielded nitroxide probes with high resistance to reduction were synthesized and studied using electron paramagnetic resonance (EPR). The degradation of ZIF-8 in cell media was monitored by tracking the cargo leakage. It was shown that nanoparticles degrade at least partially in all studied media, although the degree of cargo leakage varies widely. We found a strong correlation between the amount of escaped cargo and total concentration of amino acids in the environment. We also established the role of individual amino acids in ZIF-8 degradation. Finally, 2-methylimidazole preliminary dissolved in cell culture media partially inhibits the degradation of ZIF-8 nanoparticles. The guidelines for choosing the proper cell culture medium for the in vitro study of ZIF-8 nanoparticles have been formulated. Full article
(This article belongs to the Special Issue Application of EPR Spectroscopy in Biophysics and Biochemistry)
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