Effect of protein environment on the shape resonances of RNA pyrimidine nucleobases: Insights from a model system

Abstract

In this work, we investigate the effect of an amino acid environment on nucleobase-centered anion radical shape resonances, using uracil as a model system for pyrimidine bases in RNA. Anionic uracil–glycine complexes were used to model the RNA–protein interactions. The resonance positions and widths of these complexes were simulated using the equation of motion coupled cluster method coupled with resonance via the Padé approach. Our results show that in the transient negative ion (TNI, i.e., the anion radical of glycine:uracil complex), glycine stabilizes nucleobase-centered resonances through hydrogen bonding, thereby increasing the lifetime of TNI. Simultaneously, a glycine-centered resonance demonstrates the ability of amino acids to capture the electron density and divert it away from the uracil nucleobase. At the micro-solvation level, this modeling indicates that amino acids would have more influence on nucleobase-centered resonances in the TNI than that displayed by the corresponding aqueous environment.