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Analytical Approaches for Deriving Friction Coefficients for Selected α-Helical Peptides Based Entirely on Molecular Dynamics Simulations
[Image: see text] 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 ALA(5) to ALA(21) as...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9661531/ https://www.ncbi.nlm.nih.gov/pubmed/36300354 http://dx.doi.org/10.1021/acs.jpcb.2c03076 |
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author | Wosztyl, Aleksandra Kuczera, Krzysztof Szoszkiewicz, Robert |
author_facet | Wosztyl, Aleksandra Kuczera, Krzysztof Szoszkiewicz, Robert |
author_sort | Wosztyl, Aleksandra |
collection | PubMed |
description | [Image: see text] 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 ALA(5) to ALA(21) 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)(2)G. 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. |
format | Online Article Text |
id | pubmed-9661531 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-96615312022-11-15 Analytical Approaches for Deriving Friction Coefficients for Selected α-Helical Peptides Based Entirely on Molecular Dynamics Simulations Wosztyl, Aleksandra Kuczera, Krzysztof Szoszkiewicz, Robert J Phys Chem B [Image: see text] 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 ALA(5) to ALA(21) 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)(2)G. 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. American Chemical Society 2022-10-27 2022-11-10 /pmc/articles/PMC9661531/ /pubmed/36300354 http://dx.doi.org/10.1021/acs.jpcb.2c03076 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Wosztyl, Aleksandra Kuczera, Krzysztof Szoszkiewicz, Robert Analytical Approaches for Deriving Friction Coefficients for Selected α-Helical Peptides Based Entirely on Molecular Dynamics Simulations |
title | Analytical Approaches for Deriving Friction Coefficients
for Selected α-Helical Peptides Based Entirely on Molecular
Dynamics Simulations |
title_full | Analytical Approaches for Deriving Friction Coefficients
for Selected α-Helical Peptides Based Entirely on Molecular
Dynamics Simulations |
title_fullStr | Analytical Approaches for Deriving Friction Coefficients
for Selected α-Helical Peptides Based Entirely on Molecular
Dynamics Simulations |
title_full_unstemmed | Analytical Approaches for Deriving Friction Coefficients
for Selected α-Helical Peptides Based Entirely on Molecular
Dynamics Simulations |
title_short | Analytical Approaches for Deriving Friction Coefficients
for Selected α-Helical Peptides Based Entirely on Molecular
Dynamics Simulations |
title_sort | analytical approaches for deriving friction coefficients
for selected α-helical peptides based entirely on molecular
dynamics simulations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9661531/ https://www.ncbi.nlm.nih.gov/pubmed/36300354 http://dx.doi.org/10.1021/acs.jpcb.2c03076 |
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