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Structural Characterization of RNA-Binding Sites of Proteins: Preliminary Results
Genetics, Development and Cell Biology Presentations, Posters and Proceedings
  • Fadi Towfic, Iowa State University
  • David C. Gemperline, Carthage College
  • Cornelia Caragea, Iowa State University
  • Feihong Wu, Iowa State University
  • Drena Dobbs, Iowa State University
  • Vasant Honavar, Iowa State University
Document Type
Conference Proceeding
Conference
2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops
Publication Version
Accepted Manuscript
Publication Date
1-1-2007
DOI
10.1109/BIBMW.2007.4425401
Conference Title
2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops
Conference Date
November 2-4, 2007
Geolocation
(37.5482697, -121.98857190000001)
Abstract

We explore whether protein-RNA interfaces differ from non-interfaces in terms of their structural features and whether structural features vary according to the type of the bound RNA (e.g., mRNA, siRNA...etc.), using a nonredundant dataset of 147 protein chains extracted from protein-RNA complexes in the protein data bank. Our analysis of surface roughness, solid angle and CX value of amino acid residues for each of the protein chains in the dataset shows that: The protein-RNA interface residues tend to be protruding compared to non-interface residues and tend to have higher surface roughness and exhibit moderately convex or concave solid angles. Furthermore, the protein chains in protein-RNA interfaces that contain Viral RNA and rRNA significantly differ from those that contain dsRNA, mRNA siRNA, snRNA, SRP RNA and tRNA with respect to their CX values. The results of this analysis suggests the possibility of using such structural features to reliably identify protein-RNA interface residues when the structure of the protein is available but the structures of complexes formed by the protein with RNA are not.

Comments

This is a proceeding from IEEE International Conference on Bioinformatics and Biomedicine Workshops (2007): 60-66, doi: 10.1109/BIBMW.2007.4425401. Posted with permission.

Rights
© 2007 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Copyright Owner
IEEE
Language
en
File Format
application/pdf
Citation Information
Fadi Towfic, David C. Gemperline, Cornelia Caragea, Feihong Wu, et al.. "Structural Characterization of RNA-Binding Sites of Proteins: Preliminary Results" Freemont, California(2007) p. 60 - 66
Available at: http://works.bepress.com/drena-dobbs/48/