Exploring the Ion-Mediated RNA Interactions of a Helix-Junction-Helix RNA Model through Well-Tempered Metadynamics Simulations

Abstract

RNA's capability to fold into specific conformations allows it to fulfill numerous biological functions. Since RNA structure often consists of rigid double-stranded helices connected by flexible single-stranded junctions, helix-junction-helix (HJH) system serves as a viable model to study RNA dynamics. Available experimental data on this model has shown that metrics such as radius of gyration and helix-to-helix distance do not follow a monotonic trend when ionic concentrations increase. For this reason, all-atom molecular dynamics simulations at various [KCl] were carried out to investigate the conformations of the RNA HJH model. The conformational ensemble of the RNA was explored by molecular dynamics, umbrella sampling, and metadynamics simulations. Results allowed computing the free energy surface and populations of stable states, providing a direct comparison between experiments. Ensemble averages computed from conformational ensembles closely match experimental results, providing a verified source of atomically detailed conformations for the HJH system. Analysis of ion distribution and base stacking was performed to understand their contributions to modulate the conformational states and the non-monotonic changes reported upon change in ionic strength.