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Early Stage of Structural Changes and Molecular Dynamics of Cytochrome C in an Aqueous Solution Caused by the Addition of Methanol

  • STRUCTURE OF MACROMOLECULAR COMPOUNDS
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Abstract

Molecular dynamics simulations of horse heart cytochrome C were performed in an aqueous solution and in a 50 : 50 water–methanol mixture. Three independent 100-ns trajectories were run for each system. It was shown that the addition of methanol significantly affects the mobility of atoms in the cytochrome C molecule in the region from valine 20 to proline 30, which belongs to one of the known cardiolipin-binding sites. During 100-ns MD simulations, the coordination bond between the heme iron atom and the sulfur atom of the nearest methionine is not cleaved, its length is not significantly changed, and the distances from the heme to the residues responsible for fluorescence remain unchanged, as opposed to other studies, in which such changes were observed upon the addition of methanol to cytochrome C.

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Funding

The study was supported by the Russian Science Foundation (project no. 19-14-00244; molecular dynamics simulations) and the Ministry of Science and Higher Education of the Russian Federation within the framework of the state assignment for the Federal Scientific Research Centre “Crystallography and Photonics” of the Russian Academy of Sciences (analysis of the results of molecular modeling).

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Authors and Affiliations

  1. Lomonosov Moscow State University, 119992, Moscow, Russia

    P. D. Korotkova, A. B. Shumm & Y. A. Vladimirov

  2. Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, 117997, Moscow, Russia

    A. A. Yurchenko, A. R. Gusel’nikova & Y. A. Vladimirov

  3. Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, 119333, Moscow, Russia

    V. I. Timofeev & Y. A. Vladimirov

  4. Kurchatov Complex of NBICS Nature-Like Technologies, National Research Centre “Kurchatov Institute”, 123098, Moscow, Russia

    V. I. Timofeev

  5. Lebedev Physical Institute, Russian Academy of Sciences, 119991, Moscow, Russia

    A. B. Shumm

  6. Institute for Regenerative Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991, Moscow, Russia

    G. K. Vladimirov & Y. A. Vladimirov

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  1. P. D. Korotkova
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  2. A. A. Yurchenko
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  3. V. I. Timofeev
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  4. A. R. Gusel’nikova
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  5. G. K. Vladimirov
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  7. Y. A. Vladimirov
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Correspondence to P. D. Korotkova.

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Translated by T. Safonova

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Korotkova, P.D., Yurchenko, A.A., Timofeev, V.I. et al. Early Stage of Structural Changes and Molecular Dynamics of Cytochrome C in an Aqueous Solution Caused by the Addition of Methanol. Crystallogr. Rep. 67, 229–232 (2022). https://doi.org/10.1134/S1063774522020079

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  • DOI: https://doi.org/10.1134/S1063774522020079

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