Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot.

ABSTRACT: Massive all-atom molecular dynamics simulations were conducted across a distributed computing network to study the folding, unfolding, misfolding and conformational plasticity of the high-efficiency frameshifting double mutant of the 26 nt potato leaf roll virus RNA pseudoknot. Our robust sampling, which included over 40 starting structures spanning the spectrum from the extended unfolded state to the native fold, yielded nearly 120 μs of cumulative sampling time. Conformational microstate transitions on the 1.0 ns to 10.0 μs timescales were observed, with post-equilibration sampling providing detailed representations of the conformational free energy landscape and the complex folding mechanism inherent to the pseudoknot motif. Herein, we identify and characterize two alternative native st

SUBMITTER: Q Nguyen KK 

PROVIDER: S-EPMC5416846 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature