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An efficient visualization tool for the analysis of protein mutation matrices

BACKGROUND: It is useful to develop a tool that would effectively describe protein mutation matrices specifically geared towards the identification of mutations that produce either wanted or unwanted effects, such as an increase or decrease in affinity, or a predisposition towards misfolding. Here,...

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Detalles Bibliográficos
Autores principales: David, Maria Pamela C, Lapid, Carlo M, Daria, Vincent Ricardo M
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390542/
https://www.ncbi.nlm.nih.gov/pubmed/18442400
http://dx.doi.org/10.1186/1471-2105-9-218
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author David, Maria Pamela C
Lapid, Carlo M
Daria, Vincent Ricardo M
author_facet David, Maria Pamela C
Lapid, Carlo M
Daria, Vincent Ricardo M
author_sort David, Maria Pamela C
collection PubMed
description BACKGROUND: It is useful to develop a tool that would effectively describe protein mutation matrices specifically geared towards the identification of mutations that produce either wanted or unwanted effects, such as an increase or decrease in affinity, or a predisposition towards misfolding. Here, we describe a tool where such mutations are efficiently identified, categorized and visualized. To categorize the mutations, amino acids in a mutation matrix are arrang according to one of three sets of physicochemical characteristics, namely hydrophilicity, size and polarizability, and charge and polarity. The magnitude and frequences of mutations for an alignment are subsequently described using color information and scaling factors. RESULTS: To illustrate the capabilities of our approach, the technique is used to visualize and to compare mutation patterns in evolving sequences with diametrically opposite characteristics. Results show the emergence of distinct patterns not immediately discernible from the raw matrices. CONCLUSION: Our technique enables effective categorization and visualization of mutations by using specifically-arranged mutation matrices. This tool has a number of possible applications in protein engineering, notably in simplifying the identification of mutations and/or mutation trends that are associated with specific engineered protein characteristics and behavior.
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spelling pubmed-23905422008-05-21 An efficient visualization tool for the analysis of protein mutation matrices David, Maria Pamela C Lapid, Carlo M Daria, Vincent Ricardo M BMC Bioinformatics Software BACKGROUND: It is useful to develop a tool that would effectively describe protein mutation matrices specifically geared towards the identification of mutations that produce either wanted or unwanted effects, such as an increase or decrease in affinity, or a predisposition towards misfolding. Here, we describe a tool where such mutations are efficiently identified, categorized and visualized. To categorize the mutations, amino acids in a mutation matrix are arrang according to one of three sets of physicochemical characteristics, namely hydrophilicity, size and polarizability, and charge and polarity. The magnitude and frequences of mutations for an alignment are subsequently described using color information and scaling factors. RESULTS: To illustrate the capabilities of our approach, the technique is used to visualize and to compare mutation patterns in evolving sequences with diametrically opposite characteristics. Results show the emergence of distinct patterns not immediately discernible from the raw matrices. CONCLUSION: Our technique enables effective categorization and visualization of mutations by using specifically-arranged mutation matrices. This tool has a number of possible applications in protein engineering, notably in simplifying the identification of mutations and/or mutation trends that are associated with specific engineered protein characteristics and behavior. BioMed Central 2008-04-28 /pmc/articles/PMC2390542/ /pubmed/18442400 http://dx.doi.org/10.1186/1471-2105-9-218 Text en Copyright © 2008 David et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
David, Maria Pamela C
Lapid, Carlo M
Daria, Vincent Ricardo M
An efficient visualization tool for the analysis of protein mutation matrices
title An efficient visualization tool for the analysis of protein mutation matrices
title_full An efficient visualization tool for the analysis of protein mutation matrices
title_fullStr An efficient visualization tool for the analysis of protein mutation matrices
title_full_unstemmed An efficient visualization tool for the analysis of protein mutation matrices
title_short An efficient visualization tool for the analysis of protein mutation matrices
title_sort efficient visualization tool for the analysis of protein mutation matrices
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390542/
https://www.ncbi.nlm.nih.gov/pubmed/18442400
http://dx.doi.org/10.1186/1471-2105-9-218
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