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Analytical Approaches for Deriving Friction Coefficients for Selected α‑Helical Peptides Based Entirely on Molecular Dynamics Simulations
dc.contributor.author | Wosztyl, Aleksandra | |
dc.contributor.author | Kuczera, Krzysztof | |
dc.contributor.author | Szoszkiewicz, Robert | |
dc.date.accessioned | 2023-02-13T17:02:09Z | |
dc.date.available | 2023-02-13T17:02:09Z | |
dc.date.issued | 2022-10-27 | |
dc.identifier.citation | Wosztyl, A., Kuczera, K., & Szoszkiewicz, R. (2022). Analytical Approaches for Deriving Friction Coefficients for Selected α-Helical Peptides Based Entirely on Molecular Dynamics Simulations. The journal of physical chemistry. B, 126(44), 8901–8912. https://doi.org/10.1021/acs.jpcb.2c03076 | en_US |
dc.identifier.uri | http://hdl.handle.net/1808/33782 | |
dc.description.abstract | In this paper we derive analytically from molecular dynamics (MD) simulations the friction coefficients related to conformational transitions within several model peptides with α-helical structures. We study a series of alanine peptides with various length from ALA5 to ALA21 as well as their two derivatives, the (AAQAA)3 peptide and a 13-residue KR1 peptide that is a derivative of the (AAQAA)2 peptide with the formula GN(AAQAA)2G. We use two kinds of approaches to derive their friction coefficients. In the local approach, friction associated with fluctuations of single hydrogen bonds are studied. In the second approach, friction coefficients associated with a folding transitions within the studied peptides are obtained. In both cases, the respective friction coefficients differentiated very well the subtle structural changes between studied peptides and compared favorably to experimentally available data. | en_US |
dc.publisher | American Chemical Society | en_US |
dc.rights | Copyright © 2022 The Authors. Published by American Chemical Society. This article is licensed under a Creative Commons Attribution 4.0 International License. | en_US |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | en_US |
dc.subject | Chemical structure | en_US |
dc.subject | Computational chemistry | en_US |
dc.subject | Friction | en_US |
dc.subject | Noncovalent interactions | en_US |
dc.subject | Peptides and proteins | en_US |
dc.title | Analytical Approaches for Deriving Friction Coefficients for Selected α‑Helical Peptides Based Entirely on Molecular Dynamics Simulations | en_US |
dc.type | Article | en_US |
kusw.kuauthor | Kuczera, Krzysztof | |
kusw.kudepartment | Chemistry | en_US |
kusw.kudepartment | Molecular Biosciences | en_US |
dc.identifier.doi | 10.1021/acs.jpcb.2c03076 | en_US |
dc.identifier.orcid | https://orcid.org/0000-0003-1994-9040 | en_US |
dc.identifier.orcid | https://orcid.org/0000-0003-2358-1349 | en_US |
dc.identifier.orcid | https://orcid.org/0000-0002-2770-8848 | en_US |
kusw.oaversion | Scholarly/refereed, publisher version | en_US |
kusw.oapolicy | This item meets KU Open Access policy criteria. | en_US |
dc.identifier.pmid | PMC9661531 | en_US |
dc.rights.accessrights | openAccess | en_US |