{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T19:30:05Z","timestamp":1680377405411},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1937,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Membrane proteins are both abundant and important in cells, but the small number of solved structures restricts our understanding of them. Here we consider whether membrane proteins undergo different substitutions from their soluble counterparts and whether these can be used to improve membrane protein alignments, and therefore improve prediction of their structure.<\/jats:p>\n               <jats:p>Results: We construct substitution tables for different environments within membrane proteins. As data is scarce, we develop a general metric to assess the quality of these asymmetric tables. Membrane proteins show markedly different substitution preferences from soluble proteins. For example, substitution preferences in lipid tail-contacting parts of membrane proteins are found to be distinct from all environments in soluble proteins, including buried residues. A principal component analysis of the tables identifies the greatest variation in substitution preferences to be due to changes in hydrophobicity; the second largest variation relates to secondary structure. We demonstrate the use of our tables in pairwise sequence-to-structure alignments (also known as \u2018threading\u2019) of membrane proteins using the FUGUE alignment program. On average, in the 10\u201325% sequence identity range, alignments are improved by 28 correctly aligned residues compared with alignments made using FUGUE's default substitution tables. Our alignments also lead to improved structural models.<\/jats:p>\n               <jats:p>Availability: Substitution tables are available at: http:\/\/www.stats.ox.ac.uk\/proteins\/resources.<\/jats:p>\n               <jats:p>Contact: \u00a0deane@stats.ox.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr230","type":"journal-article","created":{"date-parts":[[2011,6,17]],"date-time":"2011-06-17T23:32:32Z","timestamp":1308353552000},"page":"i15-i23","source":"Crossref","is-referenced-by-count":19,"title":["Environment specific substitution tables improve membrane protein alignment"],"prefix":"10.1093","volume":"27","author":[{"given":"Jamie R.","family":"Hill","sequence":"first","affiliation":[{"name":"1 Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, 2UCB Celltech, Branch of UCB Pharma S.A., 208 Bath Road, Slough SL1 3WE, UK and 3Department of Biochemistry, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sebastian","family":"Kelm","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, 2UCB Celltech, Branch of UCB Pharma S.A., 208 Bath Road, Slough SL1 3WE, UK and 3Department of Biochemistry, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiye","family":"Shi","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, 2UCB Celltech, Branch of UCB Pharma S.A., 208 Bath Road, Slough SL1 3WE, UK and 3Department of Biochemistry, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China"},{"name":"1 Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, 2UCB Celltech, Branch of UCB Pharma S.A., 208 Bath Road, Slough SL1 3WE, UK and 3Department of Biochemistry, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charlotte M.","family":"Deane","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, 2UCB Celltech, Branch of UCB Pharma S.A., 208 Bath Road, Slough SL1 3WE, UK and 3Department of Biochemistry, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,6,14]]},"reference":[{"key":"2023012512025426200_B1","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1186\/1741-7007-7-50","article-title":"Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin","volume":"7","author":"Alm\u00e9n","year":"2009","journal-title":"BMC Biol."},{"key":"2023012512025426200_B2","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012512025426200_B3","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023012512025426200_B4","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012512025426200_B5","doi-asserted-by":"crossref","first-page":"5894","DOI":"10.1073\/pnas.77.10.5894","article-title":"Bacteriorhodopsin is an inside-out protein","volume":"77","author":"Engelman","year":"1980","journal-title":"Proc. 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