Correlation analysis for protein evolutionary family based on amino acid position mutations and application in PDZ domain.
BACKGROUND: It has been widely recognized that the mutations at specific directions are caused by the functional constraints in protein family and the directional mutations at certain positions control the evolutionary direction of the protein family. The mutations at different positions, even dista...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2010-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2950854?pdf=render |
| _version_ | 1818096766208180224 |
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| author | Qi-Shi Du Cheng-Hua Wang Si-Ming Liao Ri-Bo Huang |
| author_facet | Qi-Shi Du Cheng-Hua Wang Si-Ming Liao Ri-Bo Huang |
| author_sort | Qi-Shi Du |
| collection | DOAJ |
| description | BACKGROUND: It has been widely recognized that the mutations at specific directions are caused by the functional constraints in protein family and the directional mutations at certain positions control the evolutionary direction of the protein family. The mutations at different positions, even distantly separated, are mutually coupled and form an evolutionary network. Finding the controlling mutative positions and the mutative network among residues are firstly important for protein rational design and enzyme engineering. METHODOLOGY: A computational approach, namely amino acid position conservation-mutation correlation analysis (CMCA), is developed to predict mutually mutative positions and find the evolutionary network in protein family. The amino acid position mutative function, which is the foundational equation of CMCA measuring the mutation of a residue at a position, is derived from the MSA (multiple structure alignment) database of protein evolutionary family. Then the position conservation correlation matrix and position mutation correlation matrix is constructed from the amino acid position mutative equation. Unlike traditional SCA (statistical coupling analysis) approach, which is based on the statistical analysis of position conservations, the CMCA focuses on the correlation analysis of position mutations. CONCLUSIONS: As an example the CMCA approach is used to study the PDZ domain of protein family, and the results well illustrate the distantly allosteric mechanism in PDZ protein family, and find the functional mutative network among residues. We expect that the CMCA approach may find applications in protein engineering study, and suggest new strategy to improve bioactivities and physicochemical properties of enzymes. |
| first_indexed | 2024-12-10T23:09:50Z |
| format | Article |
| id | doaj.art-1cc5a161001e47e7b86858f3b9d85b68 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T23:09:50Z |
| publishDate | 2010-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-1cc5a161001e47e7b86858f3b9d85b682022-12-22T01:29:59ZengPublic Library of Science (PLoS)PLoS ONE1932-62032010-01-01510e1320710.1371/journal.pone.0013207Correlation analysis for protein evolutionary family based on amino acid position mutations and application in PDZ domain.Qi-Shi DuCheng-Hua WangSi-Ming LiaoRi-Bo HuangBACKGROUND: It has been widely recognized that the mutations at specific directions are caused by the functional constraints in protein family and the directional mutations at certain positions control the evolutionary direction of the protein family. The mutations at different positions, even distantly separated, are mutually coupled and form an evolutionary network. Finding the controlling mutative positions and the mutative network among residues are firstly important for protein rational design and enzyme engineering. METHODOLOGY: A computational approach, namely amino acid position conservation-mutation correlation analysis (CMCA), is developed to predict mutually mutative positions and find the evolutionary network in protein family. The amino acid position mutative function, which is the foundational equation of CMCA measuring the mutation of a residue at a position, is derived from the MSA (multiple structure alignment) database of protein evolutionary family. Then the position conservation correlation matrix and position mutation correlation matrix is constructed from the amino acid position mutative equation. Unlike traditional SCA (statistical coupling analysis) approach, which is based on the statistical analysis of position conservations, the CMCA focuses on the correlation analysis of position mutations. CONCLUSIONS: As an example the CMCA approach is used to study the PDZ domain of protein family, and the results well illustrate the distantly allosteric mechanism in PDZ protein family, and find the functional mutative network among residues. We expect that the CMCA approach may find applications in protein engineering study, and suggest new strategy to improve bioactivities and physicochemical properties of enzymes.http://europepmc.org/articles/PMC2950854?pdf=render |
| spellingShingle | Qi-Shi Du Cheng-Hua Wang Si-Ming Liao Ri-Bo Huang Correlation analysis for protein evolutionary family based on amino acid position mutations and application in PDZ domain. PLoS ONE |
| title | Correlation analysis for protein evolutionary family based on amino acid position mutations and application in PDZ domain. |
| title_full | Correlation analysis for protein evolutionary family based on amino acid position mutations and application in PDZ domain. |
| title_fullStr | Correlation analysis for protein evolutionary family based on amino acid position mutations and application in PDZ domain. |
| title_full_unstemmed | Correlation analysis for protein evolutionary family based on amino acid position mutations and application in PDZ domain. |
| title_short | Correlation analysis for protein evolutionary family based on amino acid position mutations and application in PDZ domain. |
| title_sort | correlation analysis for protein evolutionary family based on amino acid position mutations and application in pdz domain |
| url | http://europepmc.org/articles/PMC2950854?pdf=render |
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