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patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures
pH regulates protein function and interactions by altering the charge of individual residues causing loss or gain of intramolecular noncovalent bonds, which may lead to structural rearrangements. While tools to analyze residue-specific charge distribution of proteins at a given pH exist, currently n...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252814/ https://www.ncbi.nlm.nih.gov/pubmed/35438792 http://dx.doi.org/10.1093/nar/gkac252 |
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author | Schmitz, Mirko Schultze, Anne Vanags, Raimonds Voigt, Karsten Di Ventura, Barbara Öztürk, Mehmet Ali |
author_facet | Schmitz, Mirko Schultze, Anne Vanags, Raimonds Voigt, Karsten Di Ventura, Barbara Öztürk, Mehmet Ali |
author_sort | Schmitz, Mirko |
collection | PubMed |
description | pH regulates protein function and interactions by altering the charge of individual residues causing loss or gain of intramolecular noncovalent bonds, which may lead to structural rearrangements. While tools to analyze residue-specific charge distribution of proteins at a given pH exist, currently no tool is available to investigate noncovalent bond changes at two different pH values. To make protein pH sensitivity analysis more accessible, we developed patcHwork, a web server that combines the identification of amino acids undergoing a charge shift with the determination of affected noncovalent bonds at two user-defined pH values. At the sequence-only level, patcHwork applies the Henderson–Hasselbalch equation to determine pH-sensitive residues. When the 3D protein structure is available, patcHwork can be employed to gain mechanistic understanding of the effect of pH. This is achieved using the PDB2PQR and PROPKA tools and noncovalent bond determination algorithms. A user-friendly interface allows visualizing pH-sensitive residues, affected salt bridges, hydrogen bonds and aromatic (pi–pi and cation–pi) interactions. patcHwork can be used to identify patches, a new concept we propose of pH-sensitive residues in close proximity on the protein, which may have a major impact on function. We demonstrate the attractiveness of patcHwork studying experimentally investigated pH-sensitive proteins (https://patchwork.biologie.uni-freiburg.de/). |
format | Online Article Text |
id | pubmed-9252814 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-92528142022-07-05 patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures Schmitz, Mirko Schultze, Anne Vanags, Raimonds Voigt, Karsten Di Ventura, Barbara Öztürk, Mehmet Ali Nucleic Acids Res Web Server Issue pH regulates protein function and interactions by altering the charge of individual residues causing loss or gain of intramolecular noncovalent bonds, which may lead to structural rearrangements. While tools to analyze residue-specific charge distribution of proteins at a given pH exist, currently no tool is available to investigate noncovalent bond changes at two different pH values. To make protein pH sensitivity analysis more accessible, we developed patcHwork, a web server that combines the identification of amino acids undergoing a charge shift with the determination of affected noncovalent bonds at two user-defined pH values. At the sequence-only level, patcHwork applies the Henderson–Hasselbalch equation to determine pH-sensitive residues. When the 3D protein structure is available, patcHwork can be employed to gain mechanistic understanding of the effect of pH. This is achieved using the PDB2PQR and PROPKA tools and noncovalent bond determination algorithms. A user-friendly interface allows visualizing pH-sensitive residues, affected salt bridges, hydrogen bonds and aromatic (pi–pi and cation–pi) interactions. patcHwork can be used to identify patches, a new concept we propose of pH-sensitive residues in close proximity on the protein, which may have a major impact on function. We demonstrate the attractiveness of patcHwork studying experimentally investigated pH-sensitive proteins (https://patchwork.biologie.uni-freiburg.de/). Oxford University Press 2022-04-19 /pmc/articles/PMC9252814/ /pubmed/35438792 http://dx.doi.org/10.1093/nar/gkac252 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Web Server Issue Schmitz, Mirko Schultze, Anne Vanags, Raimonds Voigt, Karsten Di Ventura, Barbara Öztürk, Mehmet Ali patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures |
title | patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures |
title_full | patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures |
title_fullStr | patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures |
title_full_unstemmed | patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures |
title_short | patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures |
title_sort | patchwork: a user-friendly ph sensitivity analysis web server for protein sequences and structures |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252814/ https://www.ncbi.nlm.nih.gov/pubmed/35438792 http://dx.doi.org/10.1093/nar/gkac252 |
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