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Journal articles on the topic 'Sdsl-Epr'

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Published: 25 May 2024

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1

Braun, Theresa, Malte Drescher, and Daniel Summerer. "Expanding the Genetic Code for Site-Directed Spin-Labeling." International Journal of Molecular Sciences 20, no. 2 (January 16, 2019): 373. http://dx.doi.org/10.3390/ijms20020373.

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Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy enables studies of the structure, dynamics, and interactions of proteins in the noncrystalline state. The scope and analytical value of SDSL–EPR experiments crucially depends on the employed labeling strategy, with key aspects being labeling chemoselectivity and biocompatibility, as well as stability and spectroscopic properties of the resulting label. The use of genetically encoded noncanonical amino acids (ncAA) is an emerging strategy for SDSL that holds great promise for providing excellent chemoselectivity and potential for experiments in complex biological environments such as living cells. We here give a focused overview of recent advancements in this field and discuss their potentials and challenges for advancing SDSL–EPR studies.

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2

Klare, Johann P. "Site-directed spin labeling EPR spectroscopy in protein research." Biological Chemistry 394, no. 10 (October 1, 2013): 1281–300. http://dx.doi.org/10.1515/hsz-2013-0155.

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Abstract Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy has emerged as an efficient tool to elucidate the structure and the conformational dynamics of proteins under conditions close to the native state. This review article summarizes the basics as well as the recent progress in SDSL and EPR methods, especially for investigations on protein structure, protein function, and interaction of proteins with other proteins or nucleic acids. Labeling techniques as well as EPR methods are introduced and exemplified with applications to systems that have been studied in the author’s laboratory in the past 15 years, headmost the sensory rhodopsin-transducer complex mediating the photophobic response of the halophilic archaeum Natronomonas pharaonis. Further examples underline the application of SDSL EPR spectroscopy to answer specific questions about the system under investigation, such as the nature and influence of interactions of proteins with other proteins or nucleic acids. Finally, it is discussed how SDSL EPR can be combined with other biophysical techniques to combine the strengths of the different methodologies.

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3

Sahu, Indra D., and Gary A. Lorigan. "Site-Directed Spin Labeling EPR for Studying Membrane Proteins." BioMed Research International 2018 (2018): 1–13. http://dx.doi.org/10.1155/2018/3248289.

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Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy is a rapidly expanding powerful biophysical technique to study the structural and dynamic properties of membrane proteins in a native environment. Membrane proteins are responsible for performing important functions in a wide variety of complicated biological systems that are responsible for the survival of living organisms. In this review, a brief introduction of the most popular SDSL EPR techniques and illustrations of recent applications for studying pertinent structural and dynamic properties on membrane proteins will be discussed.

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4

Etienne, Emilien, Annalisa Pierro, Ketty C. Tamburrini, Alessio Bonucci, Elisabetta Mileo, Marlène Martinho, and Valérie Belle. "Guidelines for the Simulations of Nitroxide X-Band cw EPR Spectra from Site-Directed Spin Labeling Experiments Using SimLabel." Molecules 28, no. 3 (January 31, 2023): 1348. http://dx.doi.org/10.3390/molecules28031348.

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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.

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5

Wang, Yan, Venkatesan Kathiresan, Yaoyi Chen, Yanping Hu, Wei Jiang, Guangcan Bai, Guoquan Liu, Peter Z. Qin, and Xianyang Fang. "Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions." Chemical Science 11, no. 35 (2020): 9655–64. http://dx.doi.org/10.1039/d0sc01717e.

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6

Böhme, Sabine, Heinz-Jürgen Steinhoff, and Johann P. Klare. "Accessing the distance range of interest in biomolecules: Site-directed spin labeling and DEER spectroscopy." Spectroscopy 24, no. 3-4 (2010): 283–88. http://dx.doi.org/10.1155/2010/729060.

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Investigations on the structure and function of biomolecules often depend on the availability of topological information to build up structural models or to characterize conformational changes during function. Electron paramagnetic resonance (EPR) spectroscopy in combination with site–directed spin labeling (SDSL) allow to determine intra- and intermolecular distances in the range from 4–70 Å, covering the range of interest for biomolecules. The approach does not require crystalline samples and is well suited also for molecules exhibiting intrinsic flexibility. This article is intended to give an overview on pulsed EPR in conjunction with SDSL to study protein interactions as well as conformational changes, exemplified on the tRNA modifying enzyme MnmE.

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7

Tessmer, Maxx H., and Stefan Stoll. "chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling." PLOS Computational Biology 19, no. 3 (March 31, 2023): e1010834. http://dx.doi.org/10.1371/journal.pcbi.1010834.

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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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8

Roser, P., M. J. Schmidt, M. Drescher, and D. Summerer. "Site-directed spin labeling of proteins for distance measurements in vitro and in cells." Organic & Biomolecular Chemistry 14, no. 24 (2016): 5468–76. http://dx.doi.org/10.1039/c6ob00473c.

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9

Georgieva, Elka R. "Nanoscale lipid membrane mimetics in spin-labeling and electron paramagnetic resonance spectroscopy studies of protein structure and function." Nanotechnology Reviews 6, no. 1 (February 1, 2017): 75–92. http://dx.doi.org/10.1515/ntrev-2016-0080.

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AbstractCellular membranes and associated proteins play critical physiological roles in organisms from all life kingdoms. In many cases, malfunction of biological membranes triggered by changes in the lipid bilayer properties or membrane protein functional abnormalities lead to severe diseases. To understand in detail the processes that govern the life of cells and to control diseases, one of the major tasks in biological sciences is to learn how the membrane proteins function. To do so, a variety of biochemical and biophysical approaches have been used in molecular studies of membrane protein structure and function on the nanoscale. This review focuses on electron paramagnetic resonance with site-directed nitroxide spin-labeling (SDSL EPR), which is a rapidly expanding and powerful technique reporting on the local protein/spin-label dynamics and on large functionally important structural rearrangements. On the other hand, adequate to nanoscale study membrane mimetics have been developed and used in conjunction with SDSL EPR. Primarily, these mimetics include various liposomes, bicelles, and nanodiscs. This review provides a basic description of the EPR methods, continuous-wave and pulse, applied to spin-labeled proteins, and highlights several representative applications of EPR to liposome-, bicelle-, or nanodisc-reconstituted membrane proteins.

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10

Sahu, Indra D., and Gary A. Lorigan. "Electron Paramagnetic Resonance as a Tool for Studying Membrane Proteins." Biomolecules 10, no. 5 (May 13, 2020): 763. http://dx.doi.org/10.3390/biom10050763.

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Membrane proteins possess a variety of functions essential to the survival of organisms. However, due to their inherent hydrophobic nature, it is extremely difficult to probe the structure and dynamic properties of membrane proteins using traditional biophysical techniques, particularly in their native environments. Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling (SDSL) is a very powerful and rapidly growing biophysical technique to study pertinent structural and dynamic properties of membrane proteins with no size restrictions. In this review, we will briefly discuss the most commonly used EPR techniques and their recent applications for answering structure and conformational dynamics related questions of important membrane protein systems.

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11

Hirst, Stephanie, Nathan Alexander, Kristian Kaufmann, Hassane Mchaourab, and Jens Meiler. "Rosettaepr: Developing Protein Structure Prediction Methods using Sparse SDSL-EPR Data." Biophysical Journal 98, no. 3 (January 2010): 461a—462a. http://dx.doi.org/10.1016/j.bpj.2009.12.2508.

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12

Doni, Davide, Leonardo Passerini, Gérard Audran, Sylvain R. A. Marque, Marvin Schulz, Javier Santos, Paola Costantini, Marco Bortolus, and Donatella Carbonera. "Effects of Fe2+/Fe3+ Binding to Human Frataxin and Its D122Y Variant, as Revealed by Site-Directed Spin Labeling (SDSL) EPR Complemented by Fluorescence and Circular Dichroism Spectroscopies." International Journal of Molecular Sciences 21, no. 24 (December 17, 2020): 9619. http://dx.doi.org/10.3390/ijms21249619.

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Frataxin is a highly conserved protein whose deficiency results in the neurodegenerative disease Friederich’s ataxia. Frataxin’s actual physiological function has been debated for a long time without reaching a general agreement; however, it is commonly accepted that the protein is involved in the biosynthetic iron-sulphur cluster (ISC) machinery, and several authors have pointed out that it also participates in iron homeostasis. In this work, we use site-directed spin labeling coupled to electron paramagnetic resonance (SDSL EPR) to add new information on the effects of ferric and ferrous iron binding on the properties of human frataxin in vitro. Using SDSL EPR and relating the results to fluorescence experiments commonly performed to study iron binding to FXN, we produced evidence that ferric iron causes reversible aggregation without preferred interfaces in a concentration-dependent fashion, starting at relatively low concentrations (micromolar range), whereas ferrous iron binds without inducing aggregation. Moreover, our experiments show that the ferrous binding does not lead to changes of protein conformation. The data reported in this study reveal that the currently reported binding stoichiometries should be taken with caution. The use of a spin label resistant to reduction, as well as the comparison of the binding effect of Fe2+ in wild type and in the pathological D122Y variant of frataxin, allowed us to characterize the Fe2+ binding properties of different protein sites and highlight the effect of the D122Y substitution on the surrounding residues. We suggest that both Fe2+ and Fe3+ might play a relevant role in the context of the proposed FXN physiological functions.

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13

Rendon, Julia, Margot Di Cesare, Alexia Godet, Guillaume Gerbaud, Emilien Etienne, Vincent Chaptal, Pierre Falson, et al. "Conformational dynamics of the ABC-transporter BmrA reveals by SDSL-EPR spectroscopy." Biochimica et Biophysica Acta (BBA) - Bioenergetics 1863 (September 2022): 148732. http://dx.doi.org/10.1016/j.bbabio.2022.148732.

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14

Pirman, Natasha L., and Gail E. Fanucci. "Investigation of the Intrinsically Disordered Protein IA3 by Multiple SDSL-EPR Techniques." Biophysical Journal 98, no. 3 (January 2010): 257a. http://dx.doi.org/10.1016/j.bpj.2009.12.1397.

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15

Aziz, Atya, John F. Hess, Madhu S. Budamagunta, John C. Voss, and Paul G. FitzGerald. "To Determine the Structure of Vimentin Head Domain Using SDSL-EPR Approach." Biophysical Journal 98, no. 3 (January 2010): 558a. http://dx.doi.org/10.1016/j.bpj.2009.12.3021.

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16

Sahu, Indra D., and Gary A. Lorigan. "Probing Structural Dynamics of Membrane Proteins Using Electron Paramagnetic Resonance Spectroscopic Techniques." Biophysica 1, no. 2 (March 30, 2021): 106–25. http://dx.doi.org/10.3390/biophysica1020009.

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Membrane proteins are essential for the survival of living organisms. They are involved in important biological functions including transportation of ions and molecules across the cell membrane and triggering the signaling pathways. They are targets of more than half of the modern medical drugs. Despite their biological significance, information about the structural dynamics of membrane proteins is lagging when compared to that of globular proteins. The major challenges with these systems are low expression yields and lack of appropriate solubilizing medium required for biophysical techniques. Electron paramagnetic resonance (EPR) spectroscopy coupled with site directed spin labeling (SDSL) is a rapidly growing powerful biophysical technique that can be used to obtain pertinent structural and dynamic information on membrane proteins. In this brief review, we will focus on the overview of the widely used EPR approaches and their emerging applications to answer structural and conformational dynamics related questions on important membrane protein systems.

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17

Cooke, James A., Jean Chamoun, Michael W. Howell, Paul M. Curmi, Peter G. Fajer, and Louise J. Brown. "Structure and Dynamics of the Mobile Domain of Troponin I by SDSL-EPR." Biophysical Journal 98, no. 3 (January 2010): 148a. http://dx.doi.org/10.1016/j.bpj.2009.12.798.

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18

Stowe, Rebecca, Gunjan Dixit, Indra D. Sahu, Alison Bates, Carole Dabney-Smith, and Gary A. Lorigan. "Protein protein interactions of KCNQ1 and KCNE1 observed via SDSL EPR line shape analysis." Biophysical Journal 121, no. 3 (February 2022): 241a. http://dx.doi.org/10.1016/j.bpj.2021.11.1548.

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19

Pan, Yanxiong, Hui Li, Qiaobin Li, Mary Lenertz, Isabelle Schuster, Drew Jordahl, Xiao Zhu, Bingcan Chen, and Zhongyu Yang. "Protocol for resolving enzyme orientation and dynamics in advanced porous materials via SDSL-EPR." STAR Protocols 2, no. 3 (September 2021): 100676. http://dx.doi.org/10.1016/j.xpro.2021.100676.

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20

Hoofnagle, Andrew N., James W. Stoner, Thomas Lee, Sandra S. Eaton, and Natalie G. Ahn. "Phosphorylation-Dependent Changes in Structure and Dynamics in ERK2 Detected by SDSL and EPR." Biophysical Journal 86, no. 1 (January 2004): 395–403. http://dx.doi.org/10.1016/s0006-3495(04)74115-6.

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21

TANG, Li, LinChao GUO, Hong XIAN, 可. 吴, Yu ZHOU, ZhangBao WU Ke CHEN, Peng CHEN, et al. "Study on motional and conformational changes of BSA in solution using SDSL-EPR technique." Chinese Science Bulletin 55, no. 14 (May 1, 2010): 1365–69. http://dx.doi.org/10.1360/972010-176.

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22

Pirman, Natasha L., Eugene Milshteyn, Luis Galiano, Justin C. Hewlett, and Gail E. Fanucci. "Characterization of the disordered-to-α-helical transition of IA3 by SDSL-EPR spectroscopy." Protein Science 20, no. 1 (December 23, 2010): 150–59. http://dx.doi.org/10.1002/pro.547.

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23

Stowe, Rebecca, Gunjan Dixit, Indra D. Sahu, and Gary A. Lorigan. "Protein-Protein Interactions of KCNQ1 and KCNE1 Observed via SDSL-EPR Line Shape Analysis." Biophysical Journal 118, no. 3 (February 2020): 264a. http://dx.doi.org/10.1016/j.bpj.2019.11.1528.

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24

Kavalenka, Aleh, Iztok Urbančič, Valérie Belle, Sabrina Rouger, Stéphanie Costanzo, Sandra Kure, André Fournel, Sonia Longhi, Bruno Guigliarelli, and Janez Strancar. "Conformational Analysis of the Partially Disordered Measles Virus NTAIL-XD Complex by SDSL EPR Spectroscopy." Biophysical Journal 98, no. 6 (March 2010): 1055–64. http://dx.doi.org/10.1016/j.bpj.2009.11.036.

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25

Lerch, Michael, Carlos López, and Wayne L. Hubbell. "Conformational Flexibility and Structure in High-Pressure Excited States of Apomyoglobin Revealed by SDSL-EPR." Biophysical Journal 106, no. 2 (January 2014): 259a. http://dx.doi.org/10.1016/j.bpj.2013.11.1521.

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26

Pornthep Sompornpisut and Ngoc Lan Le Nguyen. "Structure and dynamics of spin label side chains in KvAP voltage-sensor domain: an all-atom MD simulation study." Science Proceedings Series 2, no. 1 (April 9, 2020): 34–38. http://dx.doi.org/10.31580/sps.v2i1.1239.

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Site-directed spin labeling (SDSL) combined with continuous-wave electron paramagnetic resonance (CW-EPR) spectroscopy has become a useful approach to investigate the structural and dynamical properties of biomolecules, especially membrane protein. In this method, spin label side chains due to their motion highly depending on the local environment were employed as external molecules to probe the structure and dynamics of the membrane protein. The close relationships between the dynamics of the spin label side chain and protein structure have been studied for T4 lysozyme. Besides, molecular dynamics (MD) simulations were widely applied as a powerful tool to study the microscopic behavior of the proteins, completing experimental approaches. Here, we presented an all-atom MD simulation study of the nitroxide spin label (MTSSL) in the X-ray structure of a potassium channel voltage-sensor domain (VSD) from Aeropyrum Pernix (KvAP).

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27

Le Breton, N., S. Longhi, A. Rockenbauer, B. Guigliarelli, S. R. A. Marque, V. Belle, and M. Martinho. "Probing the dynamic properties of two sites simultaneously in a protein–protein interaction process: a SDSL-EPR study." Physical Chemistry Chemical Physics 21, no. 40 (2019): 22584–88. http://dx.doi.org/10.1039/c9cp04660g.

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28

Jassoy, J. Jacques, Caspar A. Heubach, Tobias Hett, Frédéric Bernhard, Florian R. Haege, Gregor Hagelueken, and Olav Schiemann. "Site Selective and Efficient Spin Labeling of Proteins with a Maleimide-Functionalized Trityl Radical for Pulsed Dipolar EPR Spectroscopy." Molecules 24, no. 15 (July 27, 2019): 2735. http://dx.doi.org/10.3390/molecules24152735.

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Pulsed dipolar electron paramagnetic resonance spectroscopy (PDS) in combination with site-directed spin labeling (SDSL) of proteins and oligonucleotides is a powerful tool in structural biology. Instead of using the commonly employed gem-dimethyl-nitroxide labels, triarylmethyl (trityl) spin labels enable such studies at room temperature, within the cells and with single-frequency electron paramagnetic resonance (EPR) experiments. However, it has been repeatedly reported that labeling of proteins with trityl radicals led to low labeling efficiencies, unspecific labeling and label aggregation. Therefore, this work introduces the synthesis and characterization of a maleimide-functionalized trityl spin label and its corresponding labeling protocol for cysteine residues in proteins. The label is highly cysteine-selective, provides high labeling efficiencies and outperforms the previously employed methanethiosulfonate-functionalized trityl label. Finally, the new label is successfully tested in PDS measurements on a set of doubly labeled Yersinia outer protein O (YopO) mutants.

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29

Georgieva, Ekaterina, Vasil Atanasov, Rositsa Kostandieva, Vanya Tsoneva, Mitko Mitev, Georgi Arabadzhiev, Yovcho Yovchev, Yanka Karamalakova, and Galina Nikolova. "Direct Application of 3-Maleimido-PROXYL for Proving Hypoalbuminemia in Cases of SARS-CoV-2 Infection: The Potential Diagnostic Method of Determining Albumin Instability and Oxidized Protein Level in Severe COVID-19." International Journal of Molecular Sciences 24, no. 6 (March 18, 2023): 5807. http://dx.doi.org/10.3390/ijms24065807.

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Oxidative stress and the albumin oxidized form can lead to hypoalbuminemia, which is a predisposing factor for reduced treatment effectiveness and an increased mortality rate in severe COVID-19 patients. The aim of the study is to evaluate the application of free radical 3-Maleimido-PROXYL and SDSL-EPR spectroscopy in the in vitro determination of ox/red HSA in serum samples from patients with SARS-CoV-2 infection. Venous blood was collected from patients intubated (pO2 < 90%) with a positive PCR test for SARS-CoV-2 and controls. At the 120th minute after the incubation of the serum samples from both groups with the 3-Maleimido-PROXYL, the EPR measurement was started. The high levels of free radicals were determined through the nitroxide radical TEMPOL, which probably led to increased oxidation of HSA and hypoalbuminemia in severe COVID-19. The double-integrated spectra of 3-Maleimido-PROXYL radical showed a low degree of connectivity due to high levels of oxidized albumin in COVID-19 patients. The low concentrations of reduced albumin in serum samples partially inhibit spin-label rotation, with Amax values and ΔH0 spectral parameters comparable to those of 3-Maleimido-PROXYL/DMSO. Based on the obtained results, we suggest that the stable nitroxide radical 3-Maleimido-PROXYL can be successfully used as a marker to study oxidized albumin levels in COVID-19.

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30

Homchaudhuri, Lopamudra, Miguel De Avila, Stina B. Nilsson, Vladimir V. Bamm, Abdiwahab A. Musse, Graham S. T. Smith, George Harauz, and Joan M. Boggs. "SDSL-EPR Study of a C-terminal Segment of Myelin Basic Protein in a Myelin Mimetic Environment." Biophysical Journal 98, no. 3 (January 2010): 232a—233a. http://dx.doi.org/10.1016/j.bpj.2009.12.1258.

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31

Wang, Changzhen, Juntao Yang, Yu Zhou, Jianbo Cong, Guofu Dong, Xiangjun Hu, Li Tang, and Ke Wu. "Mobility Study of Individual Residue Sites in the Carbohydrate Recognition Domain of LSECtin Using SDSL–EPR Technique." Applied Biochemistry and Biotechnology 167, no. 8 (June 19, 2012): 2295–304. http://dx.doi.org/10.1007/s12010-012-9766-9.

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32

Nickolaus, Chen, Carolyn Vargas, Jörg Reichenwallner, Mohammed Chakour, Benjamin Selmke, Rusha Chakraborty, Raghavan Varadarajan, Sandro Keller, and Wolfgang E. Trommer. "The Molten Globule State of Maltose-Binding Protein: Structural and Thermodynamic Characterization by EPR Spectroscopy and Isothermal Titration Calorimetry." Applied Magnetic Resonance 51, no. 9-10 (September 22, 2020): 877–86. http://dx.doi.org/10.1007/s00723-020-01232-y.

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Abstract Employing site-directed spin labeling (SDSL), the structure of maltose-binding protein (MBP) had previously been studied in the native state by electron paramagnetic resonance (EPR) spectroscopy. Several spin-labeled double cysteine mutants were distributed all over the structure of this cysteine-free protein and revealed distance information between the nitroxide residues from double electron–electron resonance (DEER). The results were in good agreement with the known X-ray structure. We have now extended these studies to the molten globule (MG) state, a folding intermediate, which can be stabilized around pH 3 and that is characterized by secondary but hardly any tertiary structure. Instead of clearly defined distance features as found in the native state, several additional characteristics indicate that the MG structure of MBP contains different polypeptide chain and domain orientations. MBP is also known to bind its substrate maltose even in MG state although with lower affinity. Additionally, we have now created new mutants allowing for spin labeling at or near the active site. Our data confirm an already preformed ligand site structure in the MG explaining its substrate binding capability and thus most probably serving as a nucleation center for the final native structure.

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Georgieva, Ekaterina, Yanka Karamalakova, Georgi Arabadzhiev, Vasil Atanasov, Rositsa Kostandieva, Mitko Mitev, Vanya Tsoneva, Yovcho Yovchev, and Galina Nikolova. "Site-Directed Spin Labeling EPR Spectroscopy for Determination of Albumin Structural Damage and Hypoalbuminemia in Critical COVID-19." Antioxidants 11, no. 12 (November 22, 2022): 2311. http://dx.doi.org/10.3390/antiox11122311.

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The main factors in the COVID-19 pathology, which can initiate extensive structural changes at the cellular and molecular levels, are the generation of free radicals in abnormal amounts, and oxidative stress. Under “oxidative shock” conditions, the proteins undergo various modifications that affect their function and activity, and as a result distribute malfunctioning protein derivatives in the body. Human serum albumin is a small globular protein characterized by a high overall binding capacity for neutral lipophilic and acidic dosage forms. The albumin concentration is crucial for the maintenance of plasma oncotic pressure, the transport of nutrients, amino acids, and drugs, the effectiveness of drug therapy, and the prevention of drug toxicity. Hypoalbuminemia and structural defects molecule in the protein suggest a risk of changed metabolism and increased plasma concentration of unbound drugs. Therefore, the albumin structural and functional changes accompanied by low protein levels can be a serious prerequisite for ineffective therapy, frequent complications, and high mortality in patients with SARS-CoV-2 infection. The current opinion aims the research community the application of Site-Directed Spin Labeling Electron Paramagnetic Resonance spectroscopy (SDSL-EPR) and 3-Maleimido-PROXYL radical in determining abnormalities of the albumin dynamics and protein concentrations in COVID-19 critical patients.

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34

Li, Hui, Yanxiong Pan, Zhongyu Yang, Jiajia Rao, and Bingcan Chen. "Emerging applications of site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) to study food protein structure, dynamics, and interaction." Trends in Food Science & Technology 109 (March 2021): 37–50. http://dx.doi.org/10.1016/j.tifs.2021.01.022.

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35

Doni, Davide, Marta Meggiolaro, Javier Santos, Gérard Audran, Sylvain R. A. Marque, Paola Costantini, Marco Bortolus, and Donatella Carbonera. "A Combined Spectroscopic and In Silico Approach to Evaluate the Interaction of Human Frataxin with Mitochondrial Superoxide Dismutase." Biomedicines 9, no. 12 (November 25, 2021): 1763. http://dx.doi.org/10.3390/biomedicines9121763.

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Frataxin (FXN) is a highly conserved mitochondrial protein whose deficiency causes Friedreich’s ataxia, a neurodegenerative disease. The precise physiological function of FXN is still unclear; however, there is experimental evidence that the protein is involved in biosynthetic iron–sulfur cluster machinery, redox imbalance, and iron homeostasis. FXN is synthesized in the cytosol and imported into the mitochondria, where it is proteolytically cleaved to the mature form. Its involvement in the redox imbalance suggests that FXN could interact with mitochondrial superoxide dismutase (SOD2), a key enzyme in antioxidant cellular defense. In this work, we use site-directed spin labelling coupled to electron paramagnetic resonance spectroscopy (SDSL-EPR) and fluorescence quenching experiments to investigate the interaction between human FXN and SOD2 in vitro. Spectroscopic data are combined with rigid body protein–protein docking to assess the potential structure of the FXN-SOD2 complex, which leaves the metal binding region of FXN accessible to the solvent. We provide evidence that human FXN interacts with human SOD2 in vitro and that the complex is in fast exchange. This interaction could be relevant during the assembly of iron-sulfur (FeS) clusters and/or their incorporation in proteins when FeS clusters are potentially susceptible to attacks by reactive oxygen species.

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36

Pistolesi, Sara, Elisa Ferro, Annalisa Santucci, Riccardo Basosi, Lorenza Trabalzini, and Rebecca Pogni. "Molecular motion of spin labeled side chains in the C-terminal domain of RGL2 protein: A SDSL-EPR and MD study." Biophysical Chemistry 123, no. 1 (August 2006): 49–57. http://dx.doi.org/10.1016/j.bpc.2006.03.021.

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37

Ehrenberger, Michelle A., Aleida Vieyra, Jackie M. Esquiaqui, and Gail E. Fanucci. "Ion-dependent mobility effects of the Fusobacterium nucleatum glycine riboswitch aptamer II via site-directed spin-labeling (SDSL) electron paramagnetic resonance (EPR)." Biochemical and Biophysical Research Communications 516, no. 3 (August 2019): 839–44. http://dx.doi.org/10.1016/j.bbrc.2019.06.105.

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38

Crouch, Catherine, Margaret Bost, Tae Kim, Bryan Green, D. Arbuckle, Carl Grossman, and Kathleen Howard. "Optimization of Detergent-Mediated Reconstitution of Influenza A M2 Protein into Proteoliposomes." Membranes 8, no. 4 (November 8, 2018): 103. http://dx.doi.org/10.3390/membranes8040103.

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We report the optimization of detergent-mediated reconstitution of an integral membrane-bound protein, full-length influenza M2 protein, by direct insertion into detergent-saturated liposomes. Detergent-mediated reconstitution is an important method for preparing proteoliposomes for studying membrane proteins, and must be optimized for each combination of protein and membrane constituents used. The purpose of the reconstitution was to prepare samples for site-directed spin-labeling electron paramagnetic resonance (SDSL-EPR) studies. Our goals in optimizing the protocol were to minimize the amount of detergent used, reduce overall proteoliposome preparation time, and confirm the removal of all detergent. The liposomes were comprised of (1-palmitoyl-2-oleyl-sn-glycero-phosphocholine (POPC) and 1-palmitoyl-2-oleyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (POPG), and the detergent octylglucoside (OG) was used for reconstitution. Rigorous physical characterization was applied to optimize each step of the reconstitution process. We used dynamic light scattering (DLS) to determine the amount of OG needed to saturate the preformed liposomes. During detergent removal by absorption with Bio-Beads, we quantified the detergent concentration by means of a colorimetric assay, thereby determining the number of Bio-Bead additions needed to remove all detergent from the final proteoliposomes. We found that the overnight Bio-Bead incubation used in previously published protocols can be omitted, reducing the time needed for reconstitution. We also monitored the size distribution of the proteoliposomes with DLS, confirming that the size distribution remains essentially constant throughout the reconstitution process.

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Fischer, Axel W., David M. Anderson, Maxx H. Tessmer, Dara W. Frank, Jimmy B. Feix, and Jens Meiler. "Structure and Dynamics of Type III Secretion Effector Protein ExoU As determined by SDSL-EPR Spectroscopy in Conjunction with De Novo Protein Folding." ACS Omega 2, no. 6 (June 27, 2017): 2977–84. http://dx.doi.org/10.1021/acsomega.7b00349.

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Ueki, Shoji, and Toshiaki Arata. "1P154 SDSL-EPR study of the effect of troponin I phosphorylation on the structure of cardiac troponin C(Muscle-muscle proteins and contraction,Oral Presentations)." Seibutsu Butsuri 47, supplement (2007): S62. http://dx.doi.org/10.2142/biophys.47.s62_1.

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Aziz, Atya, John F. Hess, Madhu S. Budamagunta, John C. Voss, Alexandre P. Kuzin, Yuanpeng J. Huang, Rong Xiao, Gaetano T. Montelione, Paul G. FitzGerald, and John F. Hunt. "The Structure of Vimentin Linker 1 and Rod 1B Domains Characterized by Site-directed Spin-labeling Electron Paramagnetic Resonance (SDSL-EPR) and X-ray Crystallography." Journal of Biological Chemistry 287, no. 34 (June 26, 2012): 28349–61. http://dx.doi.org/10.1074/jbc.m111.334011.

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42

Mileo, Elisabetta, Emilien Etienne, Marlène Martinho, Régine Lebrun, Valérie Roubaud, Paul Tordo, Brigitte Gontero, Bruno Guigliarelli, Sylvain R. A. Marque, and Valérie Belle. "Enlarging the Panoply of Site-Directed Spin Labeling Electron Paramagnetic Resonance (SDSL-EPR): Sensitive and Selective Spin-Labeling of Tyrosine Using an Isoindoline-Based Nitroxide." Bioconjugate Chemistry 24, no. 6 (May 22, 2013): 1110–17. http://dx.doi.org/10.1021/bc4000542.

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Fischer, Axel W., Enrica Bordignon, Stephanie Bleicken, Ana J. García-Sáez, Gunnar Jeschke, and Jens Meiler. "Pushing the size limit of de novo structure ensemble prediction guided by sparse SDSL-EPR restraints to 200 residues: The monomeric and homodimeric forms of BAX." Journal of Structural Biology 195, no. 1 (July 2016): 62–71. http://dx.doi.org/10.1016/j.jsb.2016.04.014.

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44

Ueki, Shoji, Jun Abe, Yasunori Ohba, and Toshiaki Arata. "3P-003 The influence of the spin label mobility on the distance measurement of SDSL EPR in protein structure(Protein:Structure,The 47th Annual Meeting of the Biophysical Society of Japan)." Seibutsu Butsuri 49, supplement (2009): S151. http://dx.doi.org/10.2142/biophys.49.s151_2.

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45

Zhao, Chenchao, Hiroaki Yamashita, Keisuke Ueda, Shoji Ueki, and Toshiaki Arata. "1P143 Structural Dynamics of N-terminal Extension of Cardiac Troponin I by Site Directed Spin Labeling-EPR(10.Muscle,Poster,The 51st Annual Meeting of the Biophysical Society of Japan)." Seibutsu Butsuri 53, supplement1-2 (2013): S129. http://dx.doi.org/10.2142/biophys.53.s129_4.

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Chen, Mengzhen, Tamás Kálai, Duilio Cascio, Michael D. Bridges, Julian P. Whitelegge, Matthias Elgeti, and Wayne L. Hubbell. "A Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in Proteins." Applied Magnetic Resonance, October 14, 2023. http://dx.doi.org/10.1007/s00723-023-01618-8.

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AbstractSite-directed spin labeling electron paramagnetic resonance (SDSL-EPR) is an established tool for exploring protein structure and dynamics. Although nitroxide side chains attached to a single cysteine via a disulfide linkage are commonly employed in SDSL-EPR, their internal flexibility complicates applications to monitor slow internal motions in proteins and to structure determination by distance mapping. Moreover, the labile disulfide linkage prohibits the use of reducing agents often needed for protein stability. To enable the application of SDSL-EPR to the measurement of slow internal dynamics, new spin labels with hindered internal motion are desired. Here, we introduce a highly ordered nitroxide side chain, designated R9, attached at a single cysteine residue via a non-reducible thioether linkage. The reaction to introduce R9 is highly selective for solvent-exposed cysteine residues. Structures of R9 at two helical sites in T4 Lysozyme were determined by X-ray crystallography and the mobility in helical sequences was characterized by EPR spectral lineshape analysis, Saturation Transfer EPR, and Saturation Recovery EPR. In addition, interspin distance measurements between pairs of R9 residues are reported. Collectively, all data indicate that R9 will be useful for monitoring slow internal structural fluctuations, and applications to distance mapping via dipolar spectroscopy and relaxation enhancement methods are anticipated.

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Roopnarine, Osha, and David D. Thomas. "Structural Dynamics of Protein Interactions Using Site-Directed Spin Labeling of Cysteines to Measure Distances and Rotational Dynamics with EPR Spectroscopy." Applied Magnetic Resonance, October 11, 2023. http://dx.doi.org/10.1007/s00723-023-01623-x.

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AbstractHere we review applications of site-directed spin labeling (SDSL) with engineered cysteines in proteins, to study the structural dynamics of muscle and non-muscle proteins, using and developing the electron paramagnetic resonance (EPR) spectroscopic techniques of dipolar EPR, double electron electron resonance (DEER), saturation transfer EPR (STEPR), and orientation measured by EPR. The SDSL technology pioneered by Wayne Hubbell and collaborators has greatly expanded the use of EPR, including the measurement of distances between spin labels covalently attached to proteins and peptides. The Thomas lab and collaborators have applied these techniques to elucidate dynamic interactions in the myosin–actin complex, myosin-binding protein C, calmodulin, ryanodine receptor, phospholamban, utrophin, dystrophin, β-III-spectrin, and Aurora kinase. The ability to design and engineer cysteines in proteins for site-directed covalent labeling has enabled the use of these powerful EPR techniques to measure distances, while showing that they are complementary with optical spectroscopy measurements.

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Fries, Sandra J., Theresa S. Braun, Christoph Globisch, Christine Peter, Malte Drescher, and Elke Deuerling. "Deciphering molecular details of the RAC–ribosome interaction by EPR spectroscopy." Scientific Reports 11, no. 1 (April 21, 2021). http://dx.doi.org/10.1038/s41598-021-87847-y.

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AbstractThe eukaryotic ribosome-associated complex (RAC) plays a significant role in de novo protein folding. Its unique interaction with the ribosome, comprising contacts to both ribosomal subunits, suggests a RAC-mediated coordination between translation elongation and co-translational protein folding. Here, we apply electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labeling (SDSL) to gain deeper insights into a RAC–ribosome contact affecting translational accuracy. We identified a local contact point of RAC to the ribosome. The data provide the first experimental evidence for the existence of a four-helix bundle as well as a long α-helix in full-length RAC, in solution as well as on the ribosome. Additionally, we complemented the structural picture of the region mediating this functionally important contact on the 40S ribosomal subunit. In sum, this study constitutes the first application of SDSL-EPR spectroscopy to elucidate the molecular details of the interaction between the 3.3 MDa translation machinery and a chaperone complex.

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"Recent Developments in Electron Paramagnetic Resonance for Spectroscopic Applications." Biointerface Research in Applied Chemistry 13, no. 1 (January 24, 2022): 45. http://dx.doi.org/10.33263/briac131.045.

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This review investigated the developments of Electron paramagnetic resonance such as SDSL EPR, pulsed/CW ENDOR, high frequency/ high-field EPR, and ESEEM in biological systems such as photosynthesis, metalloproteins, radical enzymes, and phospholipid membranes. EPR spectroscopy act as a powerful tool to calculate the dynamics and structure of the biological systems from the paramagnetic centers. Applying the EPR measurements on the biomolecules like calmodulin, pyruvate kinase, nitrogenase, bromoperoxidase can also help understand their intermolecular behavior. The better insight into the detailed kinetics of the protein in the radical state can be evaluated quickly with the EPR spectroscopy than that of the XRD or NMR techniques. Hence, the specific potentials, principles, technicality, developments, and limitations, of EPR spectroscopy are highlighted here to understand its applications in the research and development of bio-medicine.

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Bonucci, Alessio, Martina Palomino-Schätzlein, Paula Malo de Molina, Arantxa Arbe, Roberta Pierattelli, Bruno Rizzuti, Juan L. Iovanna, and José L. Neira. "Crowding Effects on the Structure and Dynamics of the Intrinsically Disordered Nuclear Chromatin Protein NUPR1." Frontiers in Molecular Biosciences 8 (July 5, 2021). http://dx.doi.org/10.3389/fmolb.2021.684622.

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The intracellular environment is crowded with macromolecules, including sugars, proteins and nucleic acids. In the cytoplasm, crowding effects are capable of excluding up to 40% of the volume available to any macromolecule when compared to dilute conditions. NUPR1 is an intrinsically disordered protein (IDP) involved in cell-cycle regulation, stress-cell response, apoptosis processes, DNA binding and repair, chromatin remodeling and transcription. Simulations of molecular crowding predict that IDPs can adopt compact states, as well as more extended conformations under crowding conditions. In this work, we analyzed the conformation and dynamics of NUPR1 in the presence of two synthetic polymers, Ficoll-70 and Dextran-40, which mimic crowding effects in the cells, at two different concentrations (50 and 150 mg/ml). The study was carried out by using a multi-spectroscopic approach, including: site-directed spin labelling electron paramagnetic resonance spectroscopy (SDSL-EPR), nuclear magnetic resonance spectroscopy (NMR), circular dichroism (CD), small angle X-ray scattering (SAXS) and dynamic light scattering (DLS). SDSL-EPR spectra of two spin-labelled mutants indicate that there was binding with the crowders and that the local dynamics of the C and N termini of NUPR1 were partially affected by the crowders. However, the overall disordered nature of NUPR1 did not change substantially in the presence of the crowders, as shown by circular dichroism CD and NMR, and further confirmed by EPR. The changes in the dynamics of the paramagnetic probes appear to be related to preferred local conformations and thus crowding agents partially affect some specific regions, further pinpointing that NUPR1 flexibility has a key physiological role in its activity.

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