Effect of Protein Environment on the Shape Resonances of RNA Nucleobases: Insights From a Model System

TL;DR

This study investigates how amino acid environments, modeled by glycine, influence the shape resonances of uracil in RNA, revealing stabilization effects and electron density shifts that are more pronounced than in aqueous environments.

Contribution

It introduces a computational approach to analyze amino acid effects on RNA nucleobase resonances using uracil-glycine complexes and advanced quantum chemistry methods.

Findings

Glycine stabilizes nucleobase resonances via hydrogen bonding.

Amino acids can shift electron density away from uracil.

Amino acid effects are stronger than in aqueous environments.

Abstract

In this work, the effect of amino acid environment on the nucleobase-centered anion radical shape resonances is investigated by employing uracil as a model system for pyrimidine base in RNA. Anionic uracil-glycine complexes have been used to model the RNA-protein interactions. The resonance positions and widths of these complexes have been simulated using the equation of motion coupled cluster method coupled with resonance via Pad\'e approach. Our work shows that in the transient negative ion (TNI, or, the anion radical of glycine:uracil complex), glycine stabilizes the nucleobase-centered resonances through hydrogen bonding, increasing the lifetime of TNI. At the same time, a glycine-centered resonance shows the ability of amino acids to capture the electron density and move 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.