Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure.

ABSTRACT: Restrained molecular dynamics simulations are a robust, though perhaps underused, tool for the end-stage refinement of biomolecular structures. We demonstrate their utility-using modern simulation protocols, optimized force fields, and inclusion of explicit solvent and mobile counterions-by re-investigating the solution structures of two RNA hairpins that had previously been refined using conventional techniques. The structures, both domain 5 group II intron ribozymes from yeast ai5γ and Pylaiella littoralis, share a nearly identical primary sequence yet the published 3D structures appear quite different. Relatively long restrained MD simulations using the original NMR restraint data identified the presence of a small set of violated distance restraints in one structure and a possibly inco

SUBMITTER: Henriksen NM 

PROVIDER: S-EPMC3405240 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature