{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:33:21Z","timestamp":1767962001562,"version":"3.49.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The \u03b2-barrel is a ubiquitous fold that is deployed to accomplish a wide variety of biological functions including membrane-embedded pores. Key influences of \u03b2-barrel lumen diameter include the number of \u03b2-strands (n) and the degree of shear (S), the latter value measuring the extent to which the \u03b2-sheet is tilted within the \u03b2-barrel. Notably, it has previously been reported that the shear value for small antiparallel \u03b2-barrels (n\u226424) typically ranges between n and 2n. Conversely, it has been suggested that the \u03b2-strands in giant antiparallel \u03b2-barrels, such as those formed by pore forming cholesterol-dependent cytolysins (CDC), are parallel relative to the axis of the \u03b2-barrel, i.e. S=0. The S=0 arrangement, however, has never been observed in crystal structures of small \u03b2-barrels. Therefore, the structural basis for how CDCs form a \u03b2-barrel and span a membrane remains to be understood.<\/jats:p>\n               <jats:p>Results: Through comparison of molecular models with experimental data, we are able to identify how giant CDC \u03b2-barrels utilize a \u2018near parallel\u2019 arrangement of \u03b2-strands where S=n\/2. Furthermore, we show how side-chain packing within the \u03b2-barrel lumen is an important limiting factor with respect to the possible shear values for small \u03b2-barrels (n\u226424 \u00a0\u03b2-strands). In contrast, our models reveal no such limitation restricts the shear value of giant \u03b2-barrels (n&amp;gt;24\u00a0\u03b2-strands). Giant \u03b2-barrels can thus access a different architecture compared with smaller \u03b2-barrels.<\/jats:p>\n               <jats:p>Contact: \u00a0michelle.dunstone@monash.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts152","type":"journal-article","created":{"date-parts":[[2012,3,31]],"date-time":"2012-03-31T00:24:47Z","timestamp":1333153487000},"page":"1299-1302","source":"Crossref","is-referenced-by-count":25,"title":["Predicting giant transmembrane \u03b2-barrel architecture"],"prefix":"10.1093","volume":"28","author":[{"given":"Cyril F.","family":"Reboul","sequence":"first","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics and 3Department of Microbiology, Monash University, Clayton, VIC 3800, Australia"},{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics and 3Department of Microbiology, Monash University, Clayton, VIC 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Khalid","family":"Mahmood","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics and 3Department of Microbiology, Monash University, Clayton, VIC 3800, Australia"},{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics and 3Department of Microbiology, Monash University, Clayton, VIC 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James C.","family":"Whisstock","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics and 3Department of Microbiology, Monash University, Clayton, VIC 3800, Australia"},{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics and 3Department of Microbiology, Monash University, Clayton, VIC 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michelle A.","family":"Dunstone","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics and 3Department of Microbiology, Monash University, Clayton, VIC 3800, Australia"},{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics and 3Department of Microbiology, Monash University, Clayton, VIC 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,3,30]]},"reference":[{"key":"2023012512302992800_B1","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1074\/jbc.M410466200","article-title":"The 1.8\u2013A crystal structure of human tear lipocalin reveals an extended branched cavity with capacity for multiple ligands","volume":"280","author":"Breustedt","year":"2005","journal-title":"J. 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