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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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Formato: | Online Artículo Texto |
Lenguaje: | English |
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MDPI
2021
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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. |
format | Online Article Text |
id | pubmed-8698372 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT pazosflorencio predictionofproteinsitesandphysicochemicalpropertiesrelatedtofunctionalspecificity |