Molecular dynamics simulation on the allosteric analysis of the c-di-GMP class I riboswitch induced by ligand binding.

摘要: Riboswitches are RNA molecules that regulate gene expression using conformation change, affected by binding of small molecule ligands. Although a number ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations the aptamers in order understand mechanism specific In this paper, we use dynamics simulations on series models characterize and domain c-di-GMP class I (GEMM-I) riboswitch. The results revealed has stable state with folded P2 P3 helix, an unfolded P1 helix open pocket. first Mg ions structurally favorable for successive binding. forms when bound. Three key junctions J1/2, J2/3 J1/3 GEMM-I riboswitch contributing formation found. ligand induces riboswitch's regulation through direct allosteric communication network from sites J1/2 indirect ones those communicating via media.