Maximum Allowed Solvent Accessibilites of Residues in Proteins

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dc.creatorTien, Matthew Z.- The University of Chicago, Chicago, Illinoisen
dc.creatorMeyer, Austin G. - Texas Tech University Health Sciences Center, Lubbock, Texas,en
dc.creatorSydykova, Dariyaen
dc.creatorSpielman, Stephanie J.en
dc.creatorWilke, Claus O.en
dc.date.accessioned2014-12-15T17:10:21Zen
dc.date.available2014-12-15T17:10:21Zen
dc.date.issued2013-11-21en
dc.descriptionMatthew Z. Tien, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, United States of Americaen
dc.descriptionAustin G. Meyer, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of Americaen
dc.descriptionAustin G. Meyer, Dariya K. Sydykova, Stephanie J. Spielman, Claus O. Wilke, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of Americaen
dc.descriptionDariya K. Sydykova, Stephanie J. Spielman, Claus O. Wilke, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of Americaen
dc.descriptionDariya K. Sydykova, Stephanie J. Spielman, Claus O. Wilke, Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of Americaen
dc.description.abstractThe relative solvent accessibility (RSA) of a residue in a protein measures the extent of burial or exposure of that residue in the 3D structure. RSA is frequently used to describe a protein's biophysical or evolutionary properties. To calculate RSA, a residue's solvent accessibility (ASA) needs to be normalized by a suitable reference value for the given amino acid; several normalization scales have previously been proposed. However, these scales do not provide tight upper bounds on ASA values frequently observed in empirical crystal structures. Instead, they underestimate the largest allowed ASA values, by up to 20%. As a result, many empirical crystal structures contain residues that seem to have RSA values in excess of one. Here, we derive a new normalization scale that does provide a tight upper bound on observed ASA values. We pursue two complementary strategies, one based on extensive analysis of empirical structures and one based on systematic enumeration of biophysically allowed tripeptides. Both approaches yield congruent results that consistently exceed published values. We conclude that previously published ASA normalization values were too small, primarily because the conformations that maximize ASA had not been correctly identified. As an application of our results, we show that empirically derived hydrophobicity scales are sensitive to accurate RSA calculation, and we derive new hydrophobicity scales that show increased correlation with experimentally measured scales.en
dc.description.catalogingnoteEmail: wilke@austin.utexas.eduen
dc.description.departmentCenter for Computational Biology and Bioinformaticsen
dc.description.departmentIntegrative Biologyen
dc.description.sponsorshipThis work was supported by National Institutes of Health (http://nih.gov/) grant R01 GM088344 to COW. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.identifier.Filenamejournal.pone.0080635.pdfen
dc.identifier.citationTien MZ, Meyer AG, Sydykova DK, Spielman SJ, Wilke CO (2013) Maximum Allowed Solvent Accessibilites of Residues in Proteins. PLoS ONE 8(11): e80635. doi:10.1371/journal.pone.0080635en
dc.identifier.doiDOI: 10.1371/journal.pone.0080635en
dc.identifier.urihttp://hdl.handle.net/2152/27868en
dc.language.isoEnglishen
dc.publisherPLOS Oneen
dc.rightsAdministrative deposit of works to UT Digital Repository: This works author(s) is or was a University faculty member, student or staff member; this article is already available through open access at http://www.plosone.org. The public license is specified as CC-BY: http://creativecommons.org/licenses/by/4.0/. The library makes the deposit as a matter of fair use (for scholarly, educational, and research purposes), and to preserve the work and further secure public access to the works of the University.en
dc.subjectalanineen
dc.subjectbiophysicsen
dc.subjectcrystal structureen
dc.subjectdihedral anglesen
dc.subjectprotein structure determinationen
dc.subjectstructural proteinsen
dc.subjectvaporsen
dc.titleMaximum Allowed Solvent Accessibilites of Residues in Proteinsen
dc.typeArticleen

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