Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch.

ABSTRACT: Riboswitches are a novel class of genetic control elements that function through the direct interaction of small metabolite molecules with structured RNA elements. The ligand is bound with high specificity and affinity to its RNA target and induces conformational changes of the RNA's secondary and tertiary structure upon binding. To elucidate the molecular basis of the remarkable ligand selectivity and affinity of one of these riboswitches, extensive all-atom molecular dynamics simulations in explicit solvent (approximately 1 micros total simulation length) of the aptamer domain of the guanine sensing riboswitch are performed. The conformational dynamics is studied when the system is bound to its cognate ligand guanine as well as bound to the non-cognate ligand adenine and in its free form

SUBMITTER: Villa A 

PROVIDER: S-EPMC2724292 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature