Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics.

ABSTRACT: Conformational equilibrium within the ubiquitous GNRA tetraloop motif was simulated at the ensemble level, including 10 000 independent all-atom molecular dynamics trajectories totaling over 110 micros of simulation time. This robust sampling reveals a highly dynamic structure comprised of 15 conformational microstates. We assemble a Markov model that includes transitions ranging from the nanosecond to microsecond timescales and is dominated by six key loop conformations that contribute to fluctuations around the native state. Mining of the Protein Data Bank provides an abundance of structures in which GNRA tetraloops participate in tertiary contact formation. Most predominantly observed in the experimental data are interactions of the native loop structure within the minor groove of adjac

SUBMITTER: DePaul AJ 

PROVIDER: S-EPMC2919701 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature