Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study.

ABSTRACT: Riboswitches are mRNA-based molecules capable of controlling the expression of genes. They undergo conformational changes upon ligand binding, and as a result, they inhibit or promote the expression of the associated gene. The close connection between structural rearrangement and function makes a detailed knowledge of the molecular interactions an important step to understand the riboswitch mechanism and efficiency. We have performed all-atom molecular dynamics simulations of the adenine-sensing add A-riboswitch to study the breaking of the kissing loop, one key tertiary element in the aptamer structure. We investigated the aptamer domain of the add A-riboswitch in complex with its cognate ligand and in the absence of the ligand. The opening of the hairpins was simulated using umbrella sam

SUBMITTER: Allner O 

PROVIDER: S-EPMC3683926 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature