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The “Beacon” Structural Model of Protein Folding: Application for Trp-Cage in Water

Protein folding is a process in which a polypeptide must undergo folding process to obtain its three-dimensional structure. Thermodynamically, it is a process of enthalpy to overcome the loss of conformational entropy in folding. Folding is primarily related to hydrophobic interactions and intramole...

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Autores principales: Sun, Qiang, He, Xian, Fu, Yanfang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10343236/
https://www.ncbi.nlm.nih.gov/pubmed/37446826
http://dx.doi.org/10.3390/molecules28135164
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author Sun, Qiang
He, Xian
Fu, Yanfang
author_facet Sun, Qiang
He, Xian
Fu, Yanfang
author_sort Sun, Qiang
collection PubMed
description Protein folding is a process in which a polypeptide must undergo folding process to obtain its three-dimensional structure. Thermodynamically, it is a process of enthalpy to overcome the loss of conformational entropy in folding. Folding is primarily related to hydrophobic interactions and intramolecular hydrogen bondings. During folding, hydrophobic interactions are regarded to be the driving forces, especially in the initial structural collapse of a protein. Additionally, folding is guided by the strong interactions within proteins, such as intramolecular hydrogen bondings related to the α-helices and β-sheets of proteins. Therefore, a protein is divided into the folding key (FK) regions related to intramolecular hydrogen bondings and the non-folding key (non-FK) regions. Various conformations are expected for FK and non-FK regions. Different from non-FK regions, it is necessary for FK regions to form the specific conformations in folding, which are regarded as the necessary folding pathways (or “beacons”). Additionally, sequential folding is expected for the FK regions, and the intermediate state is found during folding. They are reflected on the local basins in the free energy landscape (FEL) of folding. To demonstrate the structural model, molecular dynamics (MD) simulations are conducted on the folding pathway of the TRP-cage in water.
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spelling pubmed-103432362023-07-14 The “Beacon” Structural Model of Protein Folding: Application for Trp-Cage in Water Sun, Qiang He, Xian Fu, Yanfang Molecules Article Protein folding is a process in which a polypeptide must undergo folding process to obtain its three-dimensional structure. Thermodynamically, it is a process of enthalpy to overcome the loss of conformational entropy in folding. Folding is primarily related to hydrophobic interactions and intramolecular hydrogen bondings. During folding, hydrophobic interactions are regarded to be the driving forces, especially in the initial structural collapse of a protein. Additionally, folding is guided by the strong interactions within proteins, such as intramolecular hydrogen bondings related to the α-helices and β-sheets of proteins. Therefore, a protein is divided into the folding key (FK) regions related to intramolecular hydrogen bondings and the non-folding key (non-FK) regions. Various conformations are expected for FK and non-FK regions. Different from non-FK regions, it is necessary for FK regions to form the specific conformations in folding, which are regarded as the necessary folding pathways (or “beacons”). Additionally, sequential folding is expected for the FK regions, and the intermediate state is found during folding. They are reflected on the local basins in the free energy landscape (FEL) of folding. To demonstrate the structural model, molecular dynamics (MD) simulations are conducted on the folding pathway of the TRP-cage in water. MDPI 2023-07-02 /pmc/articles/PMC10343236/ /pubmed/37446826 http://dx.doi.org/10.3390/molecules28135164 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
Sun, Qiang
He, Xian
Fu, Yanfang
The “Beacon” Structural Model of Protein Folding: Application for Trp-Cage in Water
title The “Beacon” Structural Model of Protein Folding: Application for Trp-Cage in Water
title_full The “Beacon” Structural Model of Protein Folding: Application for Trp-Cage in Water
title_fullStr The “Beacon” Structural Model of Protein Folding: Application for Trp-Cage in Water
title_full_unstemmed The “Beacon” Structural Model of Protein Folding: Application for Trp-Cage in Water
title_short The “Beacon” Structural Model of Protein Folding: Application for Trp-Cage in Water
title_sort “beacon” structural model of protein folding: application for trp-cage in water
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10343236/
https://www.ncbi.nlm.nih.gov/pubmed/37446826
http://dx.doi.org/10.3390/molecules28135164
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