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Nucleic Acids Research Advance Access published online on February 14, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn008
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry

Yao Chi Chen1 and Carmay Lim1,2,*

1Department of Chemistry, National Tsing Hua University, Hsinchu 300 and 2Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan

*To whom correspondence should be addressed. Tel: 011 886 2 2652 3031; Fax: 011 886 2 2788 7641; Email: carmay{at}gate.sinica.edu.tw

Received November 13, 2007. Revised January 7, 2008. Accepted January 8, 2008.

An RNA-binding protein places a surface helix, β-ribbon, or loop in an RNA helix groove and/or uses a cavity to accommodate unstacked bases. Hence, our strategy for predicting RNA-binding residues is based on detecting a surface patch and a disparate cleft. These were generated and scored according to the gas-phase electrostatic energy change upon mutating each residue to Asp–/Glu– and each residue's relative conservation. The method requires as input the protein structure and sufficient homologous sequences to define each residue's relative conservation. It yields as output a priority list of surface patch residues followed by a backup list of surface cleft residues distant from the patch residues for experimental testing of RNA binding. Among the 69 structurally non-homologous proteins tested, 81% possess a RNA-binding site with at least 70% of the maximum number of true positives in randomly generated patches of the same size as the predicted site; only two proteins did not contain any true RNA-binding residues in both predicted regions. Regardless of the protein conformational changes upon RNA-binding, the prediction accuracies based on the RNA-free/bound protein structures were found to be comparable and their binding sites overlapped as long as there are no disordered RNA-binding regions in the free structure that are ordered in the corresponding RNA-bound protein structure.


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