Structural characterization of RNA-binding sites of proteins: Preliminary results

Fadi Towfic, Cornelia Caragea, Drena Dobbs, David C. Gemperline, Feihong Wu, Vasant Honavar

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

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 non-redundant 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.

Original languageEnglish (US)
Title of host publicationProceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW
Pages60-66
Number of pages7
DOIs
StatePublished - Dec 1 2007
Event2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW - San Jose, CA, United States
Duration: Nov 2 2007Nov 4 2007

Publication series

NameProceedings - 2007 IEEE International Conference on Bioinformaticsand Biomedicine Workshops, BIBMW

Other

Other2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW
CountryUnited States
CitySan Jose, CA
Period11/2/0711/4/07

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All Science Journal Classification (ASJC) codes

  • Biomedical Engineering

Cite this

Towfic, F., Caragea, C., Dobbs, D., Gemperline, D. C., Wu, F., & Honavar, V. (2007). Structural characterization of RNA-binding sites of proteins: Preliminary results. In Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW (pp. 60-66). [4425401] (Proceedings - 2007 IEEE International Conference on Bioinformaticsand Biomedicine Workshops, BIBMW). https://doi.org/10.1109/BIBMW.2007.4425401