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Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets

Mutational scanning can be used to probe effects of large numbers of point mutations on protein function. Positions affected by mutation are primarily at either buried or at exposed residues directly involved in function, hereafter designated as active-site residues. In the absence of prior structur...

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Autores principales: Bhasin, Munmun, Varadarajan, Raghavan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7991590/
https://www.ncbi.nlm.nih.gov/pubmed/33778004
http://dx.doi.org/10.3389/fmolb.2021.635425
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author Bhasin, Munmun
Varadarajan, Raghavan
author_facet Bhasin, Munmun
Varadarajan, Raghavan
author_sort Bhasin, Munmun
collection PubMed
description Mutational scanning can be used to probe effects of large numbers of point mutations on protein function. Positions affected by mutation are primarily at either buried or at exposed residues directly involved in function, hereafter designated as active-site residues. In the absence of prior structural information, it has not been easy to distinguish between these two categories of residues. We curated and analyzed a set of twelve published deep mutational scanning datasets. The analysis revealed differential patterns of mutational sensitivity and substitution preferences at buried and exposed positions. Prediction of buried-sites solely from the mutational sensitivity data was facilitated by incorporating predicted sequence-based accessibility values. For active-site residues we observed mean sensitivity, specificity and accuracy of 61, 90 and 88% respectively. For buried residues the corresponding figures were 59, 90 and 84% while for exposed non active-site residues these were 98, 44 and 82% respectively. We also identified positions which did not follow these general trends and might require further experimental re-validation. This analysis highlights the ability of deep mutational scans to provide important structural and functional insights, even in the absence of three-dimensional structures determined using conventional structure determination techniques, and also discuss some limitations of the methodology.
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spelling pubmed-79915902021-03-26 Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets Bhasin, Munmun Varadarajan, Raghavan Front Mol Biosci Molecular Biosciences Mutational scanning can be used to probe effects of large numbers of point mutations on protein function. Positions affected by mutation are primarily at either buried or at exposed residues directly involved in function, hereafter designated as active-site residues. In the absence of prior structural information, it has not been easy to distinguish between these two categories of residues. We curated and analyzed a set of twelve published deep mutational scanning datasets. The analysis revealed differential patterns of mutational sensitivity and substitution preferences at buried and exposed positions. Prediction of buried-sites solely from the mutational sensitivity data was facilitated by incorporating predicted sequence-based accessibility values. For active-site residues we observed mean sensitivity, specificity and accuracy of 61, 90 and 88% respectively. For buried residues the corresponding figures were 59, 90 and 84% while for exposed non active-site residues these were 98, 44 and 82% respectively. We also identified positions which did not follow these general trends and might require further experimental re-validation. This analysis highlights the ability of deep mutational scans to provide important structural and functional insights, even in the absence of three-dimensional structures determined using conventional structure determination techniques, and also discuss some limitations of the methodology. Frontiers Media S.A. 2021-03-11 /pmc/articles/PMC7991590/ /pubmed/33778004 http://dx.doi.org/10.3389/fmolb.2021.635425 Text en Copyright © 2021 Bhasin and Varadarajan. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Bhasin, Munmun
Varadarajan, Raghavan
Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets
title Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets
title_full Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets
title_fullStr Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets
title_full_unstemmed Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets
title_short Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets
title_sort prediction of function determining and buried residues through analysis of saturation mutagenesis datasets
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7991590/
https://www.ncbi.nlm.nih.gov/pubmed/33778004
http://dx.doi.org/10.3389/fmolb.2021.635425
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