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Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins
Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to includ...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9814862/ https://www.ncbi.nlm.nih.gov/pubmed/36697562 http://dx.doi.org/10.1038/s42004-021-00499-x |
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author | Badasyan, Artem Tonoyan, Shushanik Valant, Matjaz Grdadolnik, Joze |
author_facet | Badasyan, Artem Tonoyan, Shushanik Valant, Matjaz Grdadolnik, Joze |
author_sort | Badasyan, Artem |
collection | PubMed |
description | Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra-molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold denaturation and thus clarifies its absence in some proteins. |
format | Online Article Text |
id | pubmed-9814862 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-98148622023-01-10 Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins Badasyan, Artem Tonoyan, Shushanik Valant, Matjaz Grdadolnik, Joze Commun Chem Article Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra-molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold denaturation and thus clarifies its absence in some proteins. Nature Publishing Group UK 2021-05-04 /pmc/articles/PMC9814862/ /pubmed/36697562 http://dx.doi.org/10.1038/s42004-021-00499-x Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Badasyan, Artem Tonoyan, Shushanik Valant, Matjaz Grdadolnik, Joze Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins |
title | Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins |
title_full | Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins |
title_fullStr | Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins |
title_full_unstemmed | Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins |
title_short | Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins |
title_sort | implicit water model within the zimm-bragg approach to analyze experimental data for heat and cold denaturation of proteins |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9814862/ https://www.ncbi.nlm.nih.gov/pubmed/36697562 http://dx.doi.org/10.1038/s42004-021-00499-x |
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