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The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins
Intrinsically disordered proteins are frequently involved in important regulatory processes in the cell thanks to their ability to bind several different targets performing sometimes even opposite functions. The PentUnFOLD algorithm is a physicochemical method that is based on new propensity scales...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Vienna
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8924573/ https://www.ncbi.nlm.nih.gov/pubmed/35294674 http://dx.doi.org/10.1007/s00726-022-03153-5 |
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author | Poboinev, Victor Vitoldovich Khrustalev, Vladislav Victorovich Khrustaleva, Tatyana Aleksandrovna Kasko, Tihon Evgenyevich Popkov, Vadim Dmitrievich |
author_facet | Poboinev, Victor Vitoldovich Khrustalev, Vladislav Victorovich Khrustaleva, Tatyana Aleksandrovna Kasko, Tihon Evgenyevich Popkov, Vadim Dmitrievich |
author_sort | Poboinev, Victor Vitoldovich |
collection | PubMed |
description | Intrinsically disordered proteins are frequently involved in important regulatory processes in the cell thanks to their ability to bind several different targets performing sometimes even opposite functions. The PentUnFOLD algorithm is a physicochemical method that is based on new propensity scales for disordered, nonstable and stable elements of secondary structure and on the counting of stabilizing and destabilizing intraprotein contacts. Unlike other methods, it works with a PDB file, and it can determine not only those fragments of alpha helices, beta strands, and random coils that can turn into disordered state (the “dark” side of the disorder), but also nonstable regions of alpha helices and beta strands which are able to turn into random coils (the “light” side), and vice versa (H ↔ C, E ↔ C). The scales have been obtained from structural data on disordered regions from the middle parts of amino acid sequences only, and not on their expectedly disordered N- and C-termini. Among other tendencies we have found that regions of both alpha helices and beta strands that can turn into the disordered state are relatively enriched in residues of Ala, Met, Asp, and Lys, while regions of both alpha helices and beta strands that can turn into random coil are relatively enriched in hydrophilic residues, and Cys, Pro, and Gly. Moreover, PentUnFOLD has the option to determine the effect of secondary structure transitions on the stability of a given region of a protein. The PentUnFOLD algorithm is freely available at http://3.17.12.213/pent-un-fold and http://chemres.bsmu.by/PentUnFOLD.htm. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00726-022-03153-5. |
format | Online Article Text |
id | pubmed-8924573 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Springer Vienna |
record_format | MEDLINE/PubMed |
spelling | pubmed-89245732022-03-16 The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins Poboinev, Victor Vitoldovich Khrustalev, Vladislav Victorovich Khrustaleva, Tatyana Aleksandrovna Kasko, Tihon Evgenyevich Popkov, Vadim Dmitrievich Amino Acids Original Article Intrinsically disordered proteins are frequently involved in important regulatory processes in the cell thanks to their ability to bind several different targets performing sometimes even opposite functions. The PentUnFOLD algorithm is a physicochemical method that is based on new propensity scales for disordered, nonstable and stable elements of secondary structure and on the counting of stabilizing and destabilizing intraprotein contacts. Unlike other methods, it works with a PDB file, and it can determine not only those fragments of alpha helices, beta strands, and random coils that can turn into disordered state (the “dark” side of the disorder), but also nonstable regions of alpha helices and beta strands which are able to turn into random coils (the “light” side), and vice versa (H ↔ C, E ↔ C). The scales have been obtained from structural data on disordered regions from the middle parts of amino acid sequences only, and not on their expectedly disordered N- and C-termini. Among other tendencies we have found that regions of both alpha helices and beta strands that can turn into the disordered state are relatively enriched in residues of Ala, Met, Asp, and Lys, while regions of both alpha helices and beta strands that can turn into random coil are relatively enriched in hydrophilic residues, and Cys, Pro, and Gly. Moreover, PentUnFOLD has the option to determine the effect of secondary structure transitions on the stability of a given region of a protein. The PentUnFOLD algorithm is freely available at http://3.17.12.213/pent-un-fold and http://chemres.bsmu.by/PentUnFOLD.htm. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00726-022-03153-5. Springer Vienna 2022-03-16 2022 /pmc/articles/PMC8924573/ /pubmed/35294674 http://dx.doi.org/10.1007/s00726-022-03153-5 Text en © The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature 2022 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic. |
spellingShingle | Original Article Poboinev, Victor Vitoldovich Khrustalev, Vladislav Victorovich Khrustaleva, Tatyana Aleksandrovna Kasko, Tihon Evgenyevich Popkov, Vadim Dmitrievich The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins |
title | The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins |
title_full | The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins |
title_fullStr | The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins |
title_full_unstemmed | The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins |
title_short | The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins |
title_sort | pentunfold algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8924573/ https://www.ncbi.nlm.nih.gov/pubmed/35294674 http://dx.doi.org/10.1007/s00726-022-03153-5 |
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