A mutation data matrix for transmembrane proteins
The widely used Mutation Data Matrix (MDM), is an amino acid comparison matrix calculated from a study of the exchange probabilities (or odds) derived from an analysis of the evolutionary changes seen in groups of very similar proteins. In this work, a mutation data matrix is calculated for membrane...
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| Veröffentlicht in: | FEBS letters 1994-02, Vol.339 (3), p.269-275 |
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| container_title | FEBS letters |
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| creator | Jones, D.T. Taylor, W.R. Thornton, J.M. |
| description | The widely used Mutation Data Matrix (MDM), is an amino acid comparison matrix calculated from a study of the exchange probabilities (or odds) derived from an analysis of the evolutionary changes seen in groups of very similar proteins. In this work, a mutation data matrix is calculated for membrane spanning segments. This new mutation data matrix is found to be very different from matrices calculated from general sequence sets which are biased towards water-soluble globular proteins, and the differences are discussed in the context of specific structural requirements of membrane spanning segments. This new matrix will help improve the accuracy of integral membrane protein sequence alignments, and could also be of use in the rational design of site directed mutagenesis experiments for this class of proteins. |
| doi_str_mv | 10.1016/0014-5793(94)80429-X |
| format | Article |
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In this work, a mutation data matrix is calculated for membrane spanning segments. This new mutation data matrix is found to be very different from matrices calculated from general sequence sets which are biased towards water-soluble globular proteins, and the differences are discussed in the context of specific structural requirements of membrane spanning segments. This new matrix will help improve the accuracy of integral membrane protein sequence alignments, and could also be of use in the rational design of site directed mutagenesis experiments for this class of proteins.</description><identifier>ISSN: 0014-5793</identifier><identifier>EISSN: 1873-3468</identifier><identifier>DOI: 10.1016/0014-5793(94)80429-X</identifier><identifier>PMID: 8112466</identifier><identifier>CODEN: FEBLAL</identifier><language>eng</language><publisher>Amsterdam: Elsevier B.V</publisher><subject>Amino acid ; Amino Acid Sequence ; Amino Acids - analysis ; Amino Acids - genetics ; Analytical, structural and metabolic biochemistry ; Biological and medical sciences ; Biological Evolution ; Comparison matrix ; Evolution ; Fundamental and applied biological sciences. 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In this work, a mutation data matrix is calculated for membrane spanning segments. This new mutation data matrix is found to be very different from matrices calculated from general sequence sets which are biased towards water-soluble globular proteins, and the differences are discussed in the context of specific structural requirements of membrane spanning segments. This new matrix will help improve the accuracy of integral membrane protein sequence alignments, and could also be of use in the rational design of site directed mutagenesis experiments for this class of proteins.</description><subject>Amino acid</subject><subject>Amino Acid Sequence</subject><subject>Amino Acids - analysis</subject><subject>Amino Acids - genetics</subject><subject>Analytical, structural and metabolic biochemistry</subject><subject>Biological and medical sciences</subject><subject>Biological Evolution</subject><subject>Comparison matrix</subject><subject>Evolution</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>General aspects, investigation methods</subject><subject>Membrane protein</subject><subject>Membrane Proteins - chemistry</subject><subject>Membrane Proteins - genetics</subject><subject>Molecular Sequence Data</subject><subject>Mutation</subject><subject>Probability</subject><subject>Protein Structure, Secondary</subject><subject>Proteins</subject><subject>Transmembrane segment</subject><issn>0014-5793</issn><issn>1873-3468</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1994</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkMtKAzEUQIMotT7-QGEWIroYzWsyyUaopVWh4Eahu5BmMhCZR00yav_eTKd0Ka4uuffcRw4AFwjeIYjYPYSIplkuyI2gtxxSLNLlARgjnpOUUMYPwXiPHIMT7z9gfHMkRmDEEcKUsTFAk6Tuggq2bZJCBZXUKjj7k5StS4JTja9NvYrRJGvXBmMbfwaOSlV5c76Lp-B9PnubPqeL16eX6WSR6oyhZUpKA3E8o0QYZoxQnOeYcI4U5hoKnnFBMcwhixDLSUY5KhTnJMcMrhSilJyC62FuXPzZGR9kbb02VRWPaTsvEWMEE8EjSAdQu9Z7Z0q5drZWbiMRlL0p2WuQvQYpqNyaksvYdrmb361qU-ybdmpi_WpXV16rqowStPV7jAiBKRcRmw_Yt63M5l-r5Xz2iPtCnxd0m-3veRgGmSj1yxonvbam0aawzuggi9b-_aFfAbaUeQ</recordid><startdate>19940221</startdate><enddate>19940221</enddate><creator>Jones, D.T.</creator><creator>Taylor, W.R.</creator><creator>Thornton, J.M.</creator><general>Elsevier B.V</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>19940221</creationdate><title>A mutation data matrix for transmembrane proteins</title><author>Jones, D.T. ; Taylor, W.R. ; Thornton, J.M.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c561X-3fe02346f120563427723881a28c0985894207060236735481da8837260ba1443</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1994</creationdate><topic>Amino acid</topic><topic>Amino Acid Sequence</topic><topic>Amino Acids - analysis</topic><topic>Amino Acids - genetics</topic><topic>Analytical, structural and metabolic biochemistry</topic><topic>Biological and medical sciences</topic><topic>Biological Evolution</topic><topic>Comparison matrix</topic><topic>Evolution</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>General aspects, investigation methods</topic><topic>Membrane protein</topic><topic>Membrane Proteins - chemistry</topic><topic>Membrane Proteins - genetics</topic><topic>Molecular Sequence Data</topic><topic>Mutation</topic><topic>Probability</topic><topic>Protein Structure, Secondary</topic><topic>Proteins</topic><topic>Transmembrane segment</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Jones, D.T.</creatorcontrib><creatorcontrib>Taylor, W.R.</creatorcontrib><creatorcontrib>Thornton, J.M.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>FEBS letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Jones, D.T.</au><au>Taylor, W.R.</au><au>Thornton, J.M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A mutation data matrix for transmembrane proteins</atitle><jtitle>FEBS letters</jtitle><addtitle>FEBS Lett</addtitle><date>1994-02-21</date><risdate>1994</risdate><volume>339</volume><issue>3</issue><spage>269</spage><epage>275</epage><pages>269-275</pages><issn>0014-5793</issn><eissn>1873-3468</eissn><coden>FEBLAL</coden><abstract>The widely used Mutation Data Matrix (MDM), is an amino acid comparison matrix calculated from a study of the exchange probabilities (or odds) derived from an analysis of the evolutionary changes seen in groups of very similar proteins. In this work, a mutation data matrix is calculated for membrane spanning segments. This new mutation data matrix is found to be very different from matrices calculated from general sequence sets which are biased towards water-soluble globular proteins, and the differences are discussed in the context of specific structural requirements of membrane spanning segments. This new matrix will help improve the accuracy of integral membrane protein sequence alignments, and could also be of use in the rational design of site directed mutagenesis experiments for this class of proteins.</abstract><cop>Amsterdam</cop><pub>Elsevier B.V</pub><pmid>8112466</pmid><doi>10.1016/0014-5793(94)80429-X</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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| language | eng |
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| source | MEDLINE; Elsevier ScienceDirect Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Alma/SFX Local Collection |
| subjects | Amino acid Amino Acid Sequence Amino Acids - analysis Amino Acids - genetics Analytical, structural and metabolic biochemistry Biological and medical sciences Biological Evolution Comparison matrix Evolution Fundamental and applied biological sciences. Psychology General aspects, investigation methods Membrane protein Membrane Proteins - chemistry Membrane Proteins - genetics Molecular Sequence Data Mutation Probability Protein Structure, Secondary Proteins Transmembrane segment |
| title | A mutation data matrix for transmembrane proteins |
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