Academic Journal
Maximum Allowed Solvent Accessibilites of Residues in Proteins
| العنوان: | Maximum Allowed Solvent Accessibilites of Residues in Proteins |
|---|---|
| المؤلفون: | Tien, Matthew Z.- The University of Chicago, Chicago, Illinois, Meyer, Austin G. - Texas Tech University Health Sciences Center, Lubbock, Texas, Sydykova, Dariya, Spielman, Stephanie J., Wilke, Claus O. |
| بيانات النشر: | PLOS One |
| سنة النشر: | 2013 |
| المجموعة: | The University of Texas at Austin: Texas ScholarWorks |
| مصطلحات موضوعية: | alanine, biophysics, crystal structure, dihedral angles, protein structure determination, structural proteins, vapors |
| الوصف: | Matthew Z. Tien, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, United States of America ; Austin G. Meyer, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America ; Austin 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 America ; Dariya 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 America ; Dariya K. Sydykova, Stephanie J. Spielman, Claus O. Wilke, Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America ; The 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 ... |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | application/pdf |
| اللغة: | English |
| Relation: | Tien 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.0080635; http://hdl.handle.net/2152/27868; journal.pone.0080635.pdf |
| DOI: | 10.1371/journal.pone.0080635 |
| الاتاحة: | http://hdl.handle.net/2152/27868 https://doi.org/10.1371/journal.pone.0080635 |
| Rights: | Administrative 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. |
| رقم الانضمام: | edsbas.8F7A3563 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1371/journal.pone.0080635 |
|---|