Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch.

ABSTRACT: Riboswitches are RNA-based genetic control elements that function via a conformational transition mechanism when a specific target molecule binds to its binding pocket. To facilitate an atomic detail interpretation of experimental investigations on the role of the adenine ligand on the conformational properties and kinetics of folding of the add adenine riboswitch, we performed molecular dynamics simulations in both the presence and the absence of the ligand. In the absence of ligand, structural deviations were observed in the J23 junction and the P1 stem. Destabilization of the P1 stem in the absence of ligand involves the loss of direct stabilizing interactions with the ligand, with additional contributions from the J23 junction region. The J23 junction of the riboswitch is found to be m

SUBMITTER: Priyakumar UD 

PROVIDER: S-EPMC2824916 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature