Contribution of Electrostatics in RNA-Protein binding

Abstract

Proteins interact with nucleic acids to control gene regulation and expression. In order to understand these control processes in atomic detail, the structural and energetic basis for the specificity and stability of binding must be elucidated. Various protein-DNA complexes were studied in detail previously. Protein- tRNA interactions are also very specific but have not been studied computationally. This chapter reports detailed study of electrostatic interactions between tRNAgln and GlnRS. At physiological pH, tRNA has regular (-) ve charges along their chains, which would produce electric field around them. Salt effect on tRNA binding to Aminoacyl tRNA synthetase has been computationally studied extensively with Poission Boltzmann equation. Values of various components of free energy term contributing to the total salt dependent electrostatic free energy are calculated e.g., coulombic energy, reaction field energy, ionic contribution, osmotic pressure term and rho-phi term. Finally total electrostatic energy is calculated at different salt concentrations. The log-log plot of association constants versus KCl concentration shows monotonic decrease in affinity with increasing KCl concentration. The slope of the straight line corresponds to a cation release stoichiometry of 1.7 for this complex. It is found here that tRNA has weaker electric field around it and the decrease in the association constant with increasing monovalent ion concentration is relatively small for cognate tRNA binding when compared to known DNA-protein interactions. Amount of ion-release is low. The electroneutral nature of tRNA binding domain may be responsible for this low ion release stoichiometry.