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Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity

Specificity Determining Positions (SDPs) are protein sites responsible for functional specificity within a family of homologous proteins. These positions are extracted from a family’s multiple sequence alignment and complement the fully conserved positions as predictors of functional sites. SDP anal...

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Autor principal: Pazos, Florencio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8698372/
https://www.ncbi.nlm.nih.gov/pubmed/34940354
http://dx.doi.org/10.3390/bioengineering8120201
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author Pazos, Florencio
author_facet Pazos, Florencio
author_sort Pazos, Florencio
collection PubMed
description Specificity Determining Positions (SDPs) are protein sites responsible for functional specificity within a family of homologous proteins. These positions are extracted from a family’s multiple sequence alignment and complement the fully conserved positions as predictors of functional sites. SDP analysis is now routinely used for locating these specificity-related sites in families of proteins of biomedical or biotechnological interest with the aim of mutating them to switch specificities or design new ones. There are many different approaches for detecting these positions in multiple sequence alignments. Nevertheless, existing methods report the potential SDP positions but they do not provide any clue on the physicochemical basis behind the functional specificity, which has to be inferred a-posteriori by manually inspecting these positions in the alignment. In this work, a new methodology is presented that, concomitantly with the detection of the SDPs, automatically provides information on the amino-acid physicochemical properties more related to the change in specificity. This new method is applied to two different multiple sequence alignments of homologous of the well-studied RasH protein representing different cases of functional specificity and the results discussed in detail.
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spelling pubmed-86983722021-12-24 Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity Pazos, Florencio Bioengineering (Basel) Article Specificity Determining Positions (SDPs) are protein sites responsible for functional specificity within a family of homologous proteins. These positions are extracted from a family’s multiple sequence alignment and complement the fully conserved positions as predictors of functional sites. SDP analysis is now routinely used for locating these specificity-related sites in families of proteins of biomedical or biotechnological interest with the aim of mutating them to switch specificities or design new ones. There are many different approaches for detecting these positions in multiple sequence alignments. Nevertheless, existing methods report the potential SDP positions but they do not provide any clue on the physicochemical basis behind the functional specificity, which has to be inferred a-posteriori by manually inspecting these positions in the alignment. In this work, a new methodology is presented that, concomitantly with the detection of the SDPs, automatically provides information on the amino-acid physicochemical properties more related to the change in specificity. This new method is applied to two different multiple sequence alignments of homologous of the well-studied RasH protein representing different cases of functional specificity and the results discussed in detail. MDPI 2021-12-03 /pmc/articles/PMC8698372/ /pubmed/34940354 http://dx.doi.org/10.3390/bioengineering8120201 Text en © 2021 by the author. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Pazos, Florencio
Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity
title Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity
title_full Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity
title_fullStr Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity
title_full_unstemmed Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity
title_short Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity
title_sort prediction of protein sites and physicochemical properties related to functional specificity
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8698372/
https://www.ncbi.nlm.nih.gov/pubmed/34940354
http://dx.doi.org/10.3390/bioengineering8120201
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