Structure-based bioinformatics analyses of protein-RNA interface toward developing a computational method to predict protein-RNA interface

Kim, T. P. O.; Yura, Kei; Go, Nobuhiro

Protein-RNA interactions play essential roles in a number of regulatory mechanisms of gene expression such as RNA splicing, transport and translation. Computational analyses of protein-DNA interface have been carried out a lot, while those of protein-RNA interface are rare. As the number of available protein-RNA complexes have increased, it is now possible to examine protein-RNA interactions based on 3D structures. We carried out computational analyses of protein-RNA complexes retrieved from PDB. The interface residue propensity was used as a parameter to predict protein-RNA interface. The accuracy of the prediction method was tested by jackknife method, which attained 60% on average. The prediction method was applied to RNA-binding proteins with known 3D structures (mRNA export factors TAP and Mex67).