Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics

Binding of a small and flexible molecule, ribocil A (non-binder) or B (binder), to the deep pocket of the aptamer domain of the FMN riboswitch was studied by mD-VcMD, which is a generalized-ensemble method based on molecular dynamics (MD) simulation. Ribocil A and B are structurally similar because they are optical isomers mutually. In the initial conformation of simulation, both ligands and the aptamer were completely dissociated in explicit solvent. The resultant free-energy landscape of ribocil B binding to the aptamer was funnel-like, whereas that of ribocil A was rugged, which agrees qualitatively with an experiment. When entering the gate (named "front gate") of the pocket, the ligand interacted with the aptamer by native and non-native {pi}-{pi} stackings, and the stackings restrained the molecular orientation of the ligands to be advantageous to reach the binding site smoothly. The simulation showed another pathway, which also led the ligands to the binding site. Its gate (maned "rear gate") located completely opposite to the front gate on the aptamers surface. However, approach from the rear gate required overcoming a free-energy barrier before reaching the binding site, and the ligands should rotate largely and sharply at the free-energy barrier. This ligands orientation property is discussed referring to a ligand orientation selection mechanism exserted by a membrane protein capturing its ligand.