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Transient binding sites at the surface of haloalkane dehalogenase LinB as locations for fine-tuning enzymatic activity
The haloalkane dehalogenase LinB is a well-known enzyme that contains buried active site and is used for many modelling studies. Using classical molecular dynamics simulations of enzymes and substrates, we searched for transient binding sites on the surface of the LinB protein by calculating maps of...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9956002/ https://www.ncbi.nlm.nih.gov/pubmed/36827335 http://dx.doi.org/10.1371/journal.pone.0280776 |
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author | Raczyńska, Agata Kapica, Patryk Papaj, Katarzyna Stańczak, Agnieszka Shyntum, Divine Spychalska, Patrycja Byczek-Wyrostek, Anna Góra, Artur |
author_facet | Raczyńska, Agata Kapica, Patryk Papaj, Katarzyna Stańczak, Agnieszka Shyntum, Divine Spychalska, Patrycja Byczek-Wyrostek, Anna Góra, Artur |
author_sort | Raczyńska, Agata |
collection | PubMed |
description | The haloalkane dehalogenase LinB is a well-known enzyme that contains buried active site and is used for many modelling studies. Using classical molecular dynamics simulations of enzymes and substrates, we searched for transient binding sites on the surface of the LinB protein by calculating maps of enzyme-ligand interactions that were then transformed into sparse matrices. All residues considered as functionally important for enzyme performance (e.g., tunnel entrances) were excluded from the analysis to concentrate rather on non-obvious surface residues. From a set of 130 surface residues, twenty-six were proposed as a promising improvement of enzyme performance. Eventually, based on rational selection and filtering out the potentially unstable mutants, a small library of ten mutants was proposed to validate the possibility of fine-tuning the LinB protein. Nearly half of the predicted mutant structures showed improved activity towards the selected substrates, which demonstrates that the proposed approach could be applied to identify non-obvious yet beneficial mutations for enzyme performance especially when obvious locations have already been explored. |
format | Online Article Text |
id | pubmed-9956002 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-99560022023-02-25 Transient binding sites at the surface of haloalkane dehalogenase LinB as locations for fine-tuning enzymatic activity Raczyńska, Agata Kapica, Patryk Papaj, Katarzyna Stańczak, Agnieszka Shyntum, Divine Spychalska, Patrycja Byczek-Wyrostek, Anna Góra, Artur PLoS One Research Article The haloalkane dehalogenase LinB is a well-known enzyme that contains buried active site and is used for many modelling studies. Using classical molecular dynamics simulations of enzymes and substrates, we searched for transient binding sites on the surface of the LinB protein by calculating maps of enzyme-ligand interactions that were then transformed into sparse matrices. All residues considered as functionally important for enzyme performance (e.g., tunnel entrances) were excluded from the analysis to concentrate rather on non-obvious surface residues. From a set of 130 surface residues, twenty-six were proposed as a promising improvement of enzyme performance. Eventually, based on rational selection and filtering out the potentially unstable mutants, a small library of ten mutants was proposed to validate the possibility of fine-tuning the LinB protein. Nearly half of the predicted mutant structures showed improved activity towards the selected substrates, which demonstrates that the proposed approach could be applied to identify non-obvious yet beneficial mutations for enzyme performance especially when obvious locations have already been explored. Public Library of Science 2023-02-24 /pmc/articles/PMC9956002/ /pubmed/36827335 http://dx.doi.org/10.1371/journal.pone.0280776 Text en © 2023 Raczyńska et al 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 use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Raczyńska, Agata Kapica, Patryk Papaj, Katarzyna Stańczak, Agnieszka Shyntum, Divine Spychalska, Patrycja Byczek-Wyrostek, Anna Góra, Artur Transient binding sites at the surface of haloalkane dehalogenase LinB as locations for fine-tuning enzymatic activity |
title | Transient binding sites at the surface of haloalkane dehalogenase LinB as locations for fine-tuning enzymatic activity |
title_full | Transient binding sites at the surface of haloalkane dehalogenase LinB as locations for fine-tuning enzymatic activity |
title_fullStr | Transient binding sites at the surface of haloalkane dehalogenase LinB as locations for fine-tuning enzymatic activity |
title_full_unstemmed | Transient binding sites at the surface of haloalkane dehalogenase LinB as locations for fine-tuning enzymatic activity |
title_short | Transient binding sites at the surface of haloalkane dehalogenase LinB as locations for fine-tuning enzymatic activity |
title_sort | transient binding sites at the surface of haloalkane dehalogenase linb as locations for fine-tuning enzymatic activity |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9956002/ https://www.ncbi.nlm.nih.gov/pubmed/36827335 http://dx.doi.org/10.1371/journal.pone.0280776 |
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