Molecular Dynamics Simulation of the Interaction between Taste Receptor Proteins and their Ligands

Abstract

We used molecular dynamics simulations to analyze the structural changes of medaka fish taste receptor proteins T1r2a-T1r3 and three ligands, L-glutamine, L-glutamic acid, and L-alanine, and the movement of water molecules around the ligands. L-glutamic acid, which had a low affinity in the experiment, showed many water molecules after the MD simulation, although the number of crystalline water molecules around the ligand was small in the crystal structure. We were also able to identify similar hydrogen bonds between residues and ligands that are conserved in other class C G protein-coupled receptors. In addition, several water molecules were observed to be alternately hydrogen-bonded to the side chain of the ligand with no characteristic lifetime.