Influence of Mg²⁺ Distribution on the Stability of Folded States of the Twister Ribozyme Revealed Using Grand Canonical Monte Carlo and Generative Deep Learning Enhanced Sampling.

ABSTRACT: Metal ions, particularly magnesium ions (Mg²⁺), play a role in stabilizing the tertiary structures of RNA molecules. Theoretical models and experimental techniques show that metal ions can change RNA dynamics and how it transitions through different stages of folding. However, the specific ways in which metal ions contribute to the formation and stabilization of RNA's tertiary structure are not fully understood at the atomic level. Here, we combined oscillating excess chemical potential Grand Canonical Monte Carlo (GCMC) and metadynamics to bias toward the sampling of unfolded states using reaction coordinates generated by machine learning allowing for examination of Mg²⁺-RNA interactions that contribute to stabilizing folded states of the pseudoknot found in the Twis

SUBMITTER: Sengul MY 

PROVIDER: S-EPMC10249389 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature