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Modeling Coil–Globule–Helix Transition in Polymers by Self-Interacting Random Walks

Random walks (RWs) have been important in statistical physics and can describe the statistical properties of various processes in physical, chemical, and biological systems. In this study, we have proposed a self-interacting random walk model in a continuous three-dimensional space, where the walker...

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Autores principales: Huang, Eddie, Tan, Zhi-Jie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10537616/
https://www.ncbi.nlm.nih.gov/pubmed/37765542
http://dx.doi.org/10.3390/polym15183688
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author Huang, Eddie
Tan, Zhi-Jie
author_facet Huang, Eddie
Tan, Zhi-Jie
author_sort Huang, Eddie
collection PubMed
description Random walks (RWs) have been important in statistical physics and can describe the statistical properties of various processes in physical, chemical, and biological systems. In this study, we have proposed a self-interacting random walk model in a continuous three-dimensional space, where the walker and its previous visits interact according to a realistic Lennard-Jones (LJ) potential [Formula: see text]. It is revealed that the model shows a novel globule-to-helix transition in addition to the well-known coil-to-globule collapse in its trajectory when the temperature decreases. The dependence of the structural transitions on the equilibrium distance [Formula: see text] of the LJ potential and the temperature T were extensively investigated. The system showed many different structural properties, including globule–coil, helix–globule–coil, and line–coil transitions depending on the equilibrium distance [Formula: see text] when the temperature T increases from low to high. We also obtained a correlation form of k(B)T(c) = λε for the relationship between the transition temperature T(c) and the well depth [Formula: see text] , which is consistent with our numerical simulations. The implications of the random walk model on protein folding are also discussed. The present model provides a new way towards understanding the mechanism of helix formation in polymers like proteins.
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spelling pubmed-105376162023-09-29 Modeling Coil–Globule–Helix Transition in Polymers by Self-Interacting Random Walks Huang, Eddie Tan, Zhi-Jie Polymers (Basel) Article Random walks (RWs) have been important in statistical physics and can describe the statistical properties of various processes in physical, chemical, and biological systems. In this study, we have proposed a self-interacting random walk model in a continuous three-dimensional space, where the walker and its previous visits interact according to a realistic Lennard-Jones (LJ) potential [Formula: see text]. It is revealed that the model shows a novel globule-to-helix transition in addition to the well-known coil-to-globule collapse in its trajectory when the temperature decreases. The dependence of the structural transitions on the equilibrium distance [Formula: see text] of the LJ potential and the temperature T were extensively investigated. The system showed many different structural properties, including globule–coil, helix–globule–coil, and line–coil transitions depending on the equilibrium distance [Formula: see text] when the temperature T increases from low to high. We also obtained a correlation form of k(B)T(c) = λε for the relationship between the transition temperature T(c) and the well depth [Formula: see text] , which is consistent with our numerical simulations. The implications of the random walk model on protein folding are also discussed. The present model provides a new way towards understanding the mechanism of helix formation in polymers like proteins. MDPI 2023-09-07 /pmc/articles/PMC10537616/ /pubmed/37765542 http://dx.doi.org/10.3390/polym15183688 Text en © 2023 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
Huang, Eddie
Tan, Zhi-Jie
Modeling Coil–Globule–Helix Transition in Polymers by Self-Interacting Random Walks
title Modeling Coil–Globule–Helix Transition in Polymers by Self-Interacting Random Walks
title_full Modeling Coil–Globule–Helix Transition in Polymers by Self-Interacting Random Walks
title_fullStr Modeling Coil–Globule–Helix Transition in Polymers by Self-Interacting Random Walks
title_full_unstemmed Modeling Coil–Globule–Helix Transition in Polymers by Self-Interacting Random Walks
title_short Modeling Coil–Globule–Helix Transition in Polymers by Self-Interacting Random Walks
title_sort modeling coil–globule–helix transition in polymers by self-interacting random walks
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10537616/
https://www.ncbi.nlm.nih.gov/pubmed/37765542
http://dx.doi.org/10.3390/polym15183688
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