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Thiol redox biochemistry: insights from computer simulations

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Abstract

Thiol redox chemical reactions play a key role in a variety of physiological processes, mainly due to the presence of low-molecular-weight thiols and cysteine residues in proteins involved in catalysis and regulation. Specifically, the subtle sensitivity of thiol reactivity to the environment makes the use of simulation techniques extremely valuable for obtaining microscopic insights. In this work we review the application of classical and quantum–mechanical atomistic simulation tools to the investigation of selected relevant issues in thiol redox biochemistry, such as investigations on (1) the protonation state of cysteine in protein, (2) two-electron oxidation of thiols by hydroperoxides, chloramines, and hypochlorous acid, (3) mechanistic and kinetics aspects of the de novo formation of disulfide bonds and thiol−disulfide exchange, (4) formation of sulfenamides, (5) formation of nitrosothiols and transnitrosation reactions, and (6) one-electron oxidation pathways.

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Abbreviations

Cys:

L-cysteine

CysS- :

Cysteinate

CysSOH:

Cysteine sulfenic acid

DFT:

Density functional theory

GPx:

Glutathione peroxidase

GSH:

Glutathione

MD:

Molecular dynamics

MM:

Molecular mechanics

Prx:

Peroxiredoxin

QM:

Quantum mechanics

ROS:

Reactive oxygen species

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Acknowledgments

This work was supported in part by the University of Buenos Aires, ANPCyT (PICT-25667), and Consejo Nacional de Investigaciones Científicas y Tecnicas (CONICET). DAE and AT are CONICET staff researchers. AZ, CMG, and LAD acknowledge a CONICET fellowship. RR and MT acknowledge the financial support of the Howard Hughes Medical Institute, National Institutes of Health, Agencia Nacional de Investigación e Innovación (ANII, Uruguay) and Comisión Sectorial de Investigación Científica (CSIC), Universidad de la República.

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This article does not contain any studies with human or animal subjects performed by any of the authors.

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  1. Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina

    Ari Zeida, Carlos M. Guardia, Pablo Lichtig & Darío A. Estrin

  2. Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB, Canada, T2N 2N4

    Laura L. Perissinotti

  3. Departamento de Química Biológica and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina

    Lucas A. Defelipe & Adrián Turjanski

  4. Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay

    Rafael Radi & Madia Trujillo

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  1. Ari Zeida
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Correspondence to Darío A. Estrin.

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Zeida, A., Guardia, C.M., Lichtig, P. et al. Thiol redox biochemistry: insights from computer simulations. Biophys Rev 6, 27–46 (2014). https://doi.org/10.1007/s12551-013-0127-x

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