Nucleic Acids Research Advance Access originally published online on February 14, 2008
Nucleic Acids Research 2008 36(5):e29; doi:10.1093/nar/gkn008
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2008, Vol. 36, No. 5 e29
© 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
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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. Shulman-Peleg, R. Nussinov, and H. J. Wolfson RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases Nucleic Acids Res., January 1, 2009; 37(suppl_1): D369 - D373. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. C. Chen and C. Lim Common physical basis of macromolecule-binding sites in proteins Nucleic Acids Res., December 1, 2008; 36(22): 7078 - 7087. [Abstract] [Full Text] [PDF]
|
|