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3β-Corner Stability by Comparative Molecular Dynamics Simulations

This study explored the mechanisms by which the stability of super-secondary structures of the 3β-corner type autonomously outside the protein globule are maintained in an aqueous environment. A molecular dynamic (MD) study determined the behavioral diversity of a large set of non-homologous 3β-corn...

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Autores principales: Rudnev, Vladimir R., Nikolsky, Kirill S., Petrovsky, Denis V., Kulikova, Liudmila I., Kargatov, Anton M., Malsagova, Kristina A., Stepanov, Alexander A., Kopylov, Arthur T., Kaysheva, Anna L., Efimov, Alexander V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9570037/
https://www.ncbi.nlm.nih.gov/pubmed/36232976
http://dx.doi.org/10.3390/ijms231911674
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author Rudnev, Vladimir R.
Nikolsky, Kirill S.
Petrovsky, Denis V.
Kulikova, Liudmila I.
Kargatov, Anton M.
Malsagova, Kristina A.
Stepanov, Alexander A.
Kopylov, Arthur T.
Kaysheva, Anna L.
Efimov, Alexander V.
author_facet Rudnev, Vladimir R.
Nikolsky, Kirill S.
Petrovsky, Denis V.
Kulikova, Liudmila I.
Kargatov, Anton M.
Malsagova, Kristina A.
Stepanov, Alexander A.
Kopylov, Arthur T.
Kaysheva, Anna L.
Efimov, Alexander V.
author_sort Rudnev, Vladimir R.
collection PubMed
description This study explored the mechanisms by which the stability of super-secondary structures of the 3β-corner type autonomously outside the protein globule are maintained in an aqueous environment. A molecular dynamic (MD) study determined the behavioral diversity of a large set of non-homologous 3β-corner structures of various origins. We focused on geometric parameters such as change in gyration radius, solvent-accessible area, major conformer lifetime and torsion angles, and the number of hydrogen bonds. Ultimately, a set of 3β-corners from 330 structures was characterized by a root mean square deviation (RMSD) of less than 5 Å, a change in the gyration radius of no more than 5%, and the preservation of amino acid residues positioned within the allowed regions on the Ramachandran map. The studied structures retained their topologies throughout the MD experiments. Thus, the 3β-corner structure was found to be rather stable per se in a water environment, i.e., without the rest of a protein molecule, and can act as the nucleus or “ready-made” building block in protein folding. The 3β-corner can also be considered as an independent object for study in field of structural biology.
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spelling pubmed-95700372022-10-17 3β-Corner Stability by Comparative Molecular Dynamics Simulations Rudnev, Vladimir R. Nikolsky, Kirill S. Petrovsky, Denis V. Kulikova, Liudmila I. Kargatov, Anton M. Malsagova, Kristina A. Stepanov, Alexander A. Kopylov, Arthur T. Kaysheva, Anna L. Efimov, Alexander V. Int J Mol Sci Article This study explored the mechanisms by which the stability of super-secondary structures of the 3β-corner type autonomously outside the protein globule are maintained in an aqueous environment. A molecular dynamic (MD) study determined the behavioral diversity of a large set of non-homologous 3β-corner structures of various origins. We focused on geometric parameters such as change in gyration radius, solvent-accessible area, major conformer lifetime and torsion angles, and the number of hydrogen bonds. Ultimately, a set of 3β-corners from 330 structures was characterized by a root mean square deviation (RMSD) of less than 5 Å, a change in the gyration radius of no more than 5%, and the preservation of amino acid residues positioned within the allowed regions on the Ramachandran map. The studied structures retained their topologies throughout the MD experiments. Thus, the 3β-corner structure was found to be rather stable per se in a water environment, i.e., without the rest of a protein molecule, and can act as the nucleus or “ready-made” building block in protein folding. The 3β-corner can also be considered as an independent object for study in field of structural biology. MDPI 2022-10-02 /pmc/articles/PMC9570037/ /pubmed/36232976 http://dx.doi.org/10.3390/ijms231911674 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Rudnev, Vladimir R.
Nikolsky, Kirill S.
Petrovsky, Denis V.
Kulikova, Liudmila I.
Kargatov, Anton M.
Malsagova, Kristina A.
Stepanov, Alexander A.
Kopylov, Arthur T.
Kaysheva, Anna L.
Efimov, Alexander V.
3β-Corner Stability by Comparative Molecular Dynamics Simulations
title 3β-Corner Stability by Comparative Molecular Dynamics Simulations
title_full 3β-Corner Stability by Comparative Molecular Dynamics Simulations
title_fullStr 3β-Corner Stability by Comparative Molecular Dynamics Simulations
title_full_unstemmed 3β-Corner Stability by Comparative Molecular Dynamics Simulations
title_short 3β-Corner Stability by Comparative Molecular Dynamics Simulations
title_sort 3β-corner stability by comparative molecular dynamics simulations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9570037/
https://www.ncbi.nlm.nih.gov/pubmed/36232976
http://dx.doi.org/10.3390/ijms231911674
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