Ligand Binding Mechanism and Its Relationship with Conformational Changes in Adenine Riboswitch.

ABSTRACT: Riboswitches are naturally occurring RNA aptamers that control the expression of essential bacterial genes by binding to specific small molecules. The binding with both high affinity and specificity induces conformational changes. Thus, riboswitches were proposed as a possible molecular target for developing antibiotics and chemical tools. The adenine riboswitch can bind not only to purine analogues but also to pyrimidine analogues. Here, long molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) computational methodologies were carried out to show the differences in the binding model and the conformational changes upon five ligands binding. The binding free energies of the guanine riboswitch aptamer with C74U mutation complexes were compared

SUBMITTER: Hu G 

PROVIDER: S-EPMC7139962 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature