A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm.

ABSTRACT: The S-adenosylmethionine-1 (SAM-I) riboswitch mediates expression of proteins involved in sulfur metabolism via formation of alternative conformations in response to binding by SAM. Models for kinetic trapping of the RNA in the bound conformation require annealing of nonadjacent mRNA segments during a transcriptional pause. The entropic cost required to bring nonadjacent segments together should slow the folding process. To address this paradox, we performed molecular dynamics simulations on the SAM-I riboswitch aptamer domain with and without SAM, starting with the X-ray coordinates of the SAM-bound RNA. Individual trajectories are 200 ns, among the longest reported for an RNA of this size. We applied principle component analysis (PCA) to explore the global dynamics differences between th

SUBMITTER: Huang W 

PROVIDER: S-EPMC2770654 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature