Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics.

ABSTRACT: Riboswitches are RNA molecules that regulate gene expression using conformational change, affected by binding of small molecule ligands. A crystal structure of a ligand-bound class II preQ1 riboswitch has been determined in a previous structural study. To gain insight into the dynamics of this riboswitch in solution, eight total molecular dynamic simulations, four with and four without ligand, were performed using the Amber force field. In the presence of ligand, all four of the simulations demonstrated rearranged base pairs at the 3' end, consistent with expected base-pairing from comparative sequence analysis in a prior bioinformatic analysis; this suggests the pairing in this region was altered by crystallization. Additionally, in the absence of ligand, three of the simulations demonstr

SUBMITTER: Aytenfisu AH 

PROVIDER: S-EPMC4604430 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature