Topological data analysis gives two folding paths in HP35(nle-nle), double mutant of villin headpiece subdomain

The folding dynamics of proteins is a primary area of interest in protein science. We carried out topological data analysis (TDA) of the folding process of HP35(nle-nle), a double-mutant of the villin headpiece subdomain. Using persistent homology and non-negative matrix factorization, we reduced th...

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Autor principal: Ichinomiya, Takashi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8854739/
https://www.ncbi.nlm.nih.gov/pubmed/35177744
http://dx.doi.org/10.1038/s41598-022-06682-x
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author Ichinomiya, Takashi
author_facet Ichinomiya, Takashi
author_sort Ichinomiya, Takashi
collection PubMed
description The folding dynamics of proteins is a primary area of interest in protein science. We carried out topological data analysis (TDA) of the folding process of HP35(nle-nle), a double-mutant of the villin headpiece subdomain. Using persistent homology and non-negative matrix factorization, we reduced the dimension of protein structure and investigated the flow in the reduced space. We found this protein has two folding paths, distinguished by the pairings of inter-helix residues. Our analysis showed the excellent performance of TDA in capturing the formation of tertiary structure.
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spelling pubmed-88547392022-02-22 Topological data analysis gives two folding paths in HP35(nle-nle), double mutant of villin headpiece subdomain Ichinomiya, Takashi Sci Rep Article The folding dynamics of proteins is a primary area of interest in protein science. We carried out topological data analysis (TDA) of the folding process of HP35(nle-nle), a double-mutant of the villin headpiece subdomain. Using persistent homology and non-negative matrix factorization, we reduced the dimension of protein structure and investigated the flow in the reduced space. We found this protein has two folding paths, distinguished by the pairings of inter-helix residues. Our analysis showed the excellent performance of TDA in capturing the formation of tertiary structure. Nature Publishing Group UK 2022-02-17 /pmc/articles/PMC8854739/ /pubmed/35177744 http://dx.doi.org/10.1038/s41598-022-06682-x Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Ichinomiya, Takashi
Topological data analysis gives two folding paths in HP35(nle-nle), double mutant of villin headpiece subdomain
title Topological data analysis gives two folding paths in HP35(nle-nle), double mutant of villin headpiece subdomain
title_full Topological data analysis gives two folding paths in HP35(nle-nle), double mutant of villin headpiece subdomain
title_fullStr Topological data analysis gives two folding paths in HP35(nle-nle), double mutant of villin headpiece subdomain
title_full_unstemmed Topological data analysis gives two folding paths in HP35(nle-nle), double mutant of villin headpiece subdomain
title_short Topological data analysis gives two folding paths in HP35(nle-nle), double mutant of villin headpiece subdomain
title_sort topological data analysis gives two folding paths in hp35(nle-nle), double mutant of villin headpiece subdomain
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8854739/
https://www.ncbi.nlm.nih.gov/pubmed/35177744
http://dx.doi.org/10.1038/s41598-022-06682-x
work_keys_str_mv AT ichinomiyatakashi topologicaldataanalysisgivestwofoldingpathsinhp35nlenledoublemutantofvillinheadpiecesubdomain

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