Structural Characterization of RNA-Binding Sites of Proteins: Preliminary Results

Date
2007-01-01
Authors
Towfic, Fadi
Gemperline, David
Caragea, Cornelia
Wu, Feihong
Dobbs, Drena
Dobbs, Drena
Honavar, Vasant
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Computer ScienceGenetics, Development and Cell BiologyBioinformatics and Computational Biology
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.

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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.

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