Contributions and competition of Mg²⁺ and K⁺ in folding and stabilization of the Twister ribozyme.

ABSTRACT: Native folded and compact intermediate states of RNA typically involve tertiary structures in the presence of divalent ions such as Mg²⁺ in a background of monovalent ions. In a recent study, we have shown how the presence of Mg²⁺ impacts the transition from partially unfolded to folded states through a "push-pull" mechanism where the ion both favors and disfavors the sampling of specific phosphate-phosphate interactions. To further understand the ion atmosphere of RNA in folded and partially folded states results from atomistic umbrella sampling and oscillating chemical potential grand canonical Monte Carlo/molecular dynamics (GCMC/MD) simulations are used to obtain atomic-level details of the distributions of Mg²⁺ and K⁺ ions around Twister RNA

SUBMITTER: Kognole AA 

PROVIDER: S-EPMC7566569 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature