Structural Studies of the 3',3'-cGAMP Riboswitch Induced by Cognate and Noncognate Ligands Using Molecular Dynamics Simulation.

ABSTRACT: Riboswtich RNAs can control gene expression through the structural change induced by the corresponding small-molecule ligands. Molecular dynamics simulations and free energy calculations on the aptamer domain of the 3',3'-cGAMP riboswitch in the ligand-free, cognate-bound and noncognate-bound states were performed to investigate the structural features of the 3',3'-cGAMP riboswitch induced by the 3',3'-cGAMP ligand and the specificity of ligand recognition. The results revealed that the aptamer of the 3',3'-cGAMP riboswitch in the ligand-free state has a smaller binding pocket and a relatively compact structure versus that in the 3',3'-cGAMP-bound state. The binding of the 3',3'-cGAMP molecule to the 3',3'-cGAMP riboswitch induces the rotation of P1 helix through the allosteric communicati

SUBMITTER: Li C 

PROVIDER: S-EPMC6274999 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature