Understanding the Recognition Mechanism of Protein-RNA Complexes Using Energy Based Approach

M.      Michael Gromiha; Kiyonobu      Yokota; Kazuhiko      Fukui

Abstract

Protein-RNA interactions perform diverse functions within the cell. Understanding the recognition mechanism of protein-RNA complexes is a challenging task in molecular and computational biology. In this work, we have developed an energy based approach for identifying the binding sites and important residues for binding in protein-RNA complexes. The new approach considers the repulsive interactions as well as the effect of distance between the atoms in protein and RNA in terms of interaction energy, which are not considered in traditional distance based methods to identify the binding sites. We found that the positively charged, polar and aromatic residues are important for binding. These residues influence to form electrostatic, hydrogen bonding and stacking interactions. Our observation has been verified with the experimental binding specificity of protein-RNA complexes and found good agreement with experiments. Further, the propensities of residues/nucleotides in the binding sites of proteins/RNA and their atomic contributions have been derived. Based on these results we have proposed a novel mechanism for the recognition of protein-RNA complexes: the charged and polar residues in proteins initiate recognition with RNA by making electrostatic and hydrogen bonding interactions between them; the aromatic side chains tend to form aromatic-aromatic interactions and the hydrophobic residues aid to stabilize the complex.

Keywords: Protein-RNA complex, interaction energy, cation-π interaction, hydrogen bonds, binding specificity, ribosome, spliceosome, electrostatic interactions, van der Waals interactions, Binding Propensity, Binding Segments, Residue-Pair Preference, U1A Protein-RNA Complex, Ribosomal Protein S7-RNA Complex, stacking interactions, aromatic residues, aromatic-aromatic inter-actions