MloK1 Ligand Binding Simulations Indicate an Induced-Fit Mechanism

Abstract

Many ion channels such as the MloK1 channel are steered by ligand binding via conformational changes. Mainly two binding mechanisms have been proposed, induced fit and conformational selection. Using molecular dynamics simulations, we studied ligand binding of cyclic adeonise monophosphate at the cyclic nucleotide binding domain of the MloK1 ion channel of Mesorizobium loti. For this binding domain, both crystal and NMR structures have been determined for both the ligand free as well as for the ligand bound conformation.In the simulations, spontaneous binding was observed, which enabled us to determine reaction coordinates for the ligand binding as well as for the associated conformational change of the protein. We used a combination of force probe simulations, umbrella sampling, and unbiased simulations to determine potentials of mean force along these reaction coordinates, transition rates, as well as free energy differences and barriers between the most relevant substates.Our results are compared with measured affinities and kinetics, and suggest an induced fit-mechanism.