title: Identifying RNA-binding residues based on evolutionary conserved structural and energetic features.
abstract: Increasing numbers of protein structures are solved each year, but many of these structures belong to proteins whose sequences are homologous to sequences in the Protein Data Bank. Nevertheless, the structures of homologous proteins belonging to the same family contain useful information because functionally important residues are expected to preserve physico-chemical, structural and energetic features. This information forms the basis of our method, which detects RNA-binding residues of a given RNA-binding protein as those residues that preserve physico-chemical, structural and energetic features in its homologs. Tests on 81 RNA-bound and 35 RNA-free protein structures showed that our method yields a higher fraction of true RNA-binding residues (higher precision) than two structure-based and two sequence-based machine-learning methods. Because the method requires no training data set and has no parameters, its precision does not degrade when applied to 'novel' protein sequences unlike methods that are parameterized for a given training data set. It was used to predict the 'unknown' RNA-binding residues in the C-terminal RNA-binding domain of human CPEB3. The two predicted residues, F430 and F474, were experimentally verified to bind RNA, in particular F430, whose mutation to alanine or asparagine nearly abolished RNA binding. The method has been implemented in a webserver called DR_bind1, which is freely available with no login requirement at http://drbind.limlab.ibms.sinica.edu.tw.
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan and Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan.
authors.forename: Yao Chi
authors.initials: YC
authors.lastname: Chen
authors.forename: Karen
authors.initials: K
authors.lastname: Sargsyan
authors.forename: Jon D
authors.initials: JD
authors.lastname: Wright
authors.forename: Yi-Shuian
authors.initials: YS
authors.lastname: Huang
authors.forename: Carmay
authors.initials: C
authors.lastname: Lim
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000737:chemistry; D019143:Evolution, Molecular; D006801:Humans; D011485:Protein Binding; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D055672:Static Electricity
chemical_list: D000596:Amino Acids; D004268:DNA-Binding Proteins; D016601:RNA-Binding Proteins; D012313:RNA