Understanding the molecular mechanism of umami recognition by T1R1-T1R3 using molecular dynamics simulations

Taste receptor T1R1-T1R3 can be activated by binding to several natural ligands, e.g., l-glutamate and 5′-ribonucleotides etc., thereby stimulating the umami taste. The molecular mechanism of umami recognition at atomic details, however, remains elusive. Here, using homology modeling, molecular docking and molecular dynamics (MD) simulations, we investigate the effects of five natural umami ligands on the structural dynamics of T1R1-T1R3. Our work identifies the key residues that are directly involved in recognizing the binding ligands. In addition, two adjacent binding sites in T1R1 are determined for substrate binding, and depending on the molecular size and chemical properties of the incoming ligand, one or both binding sites can be occupied. More interestingly, the ligand binding can modulate the pocket size, which is likely correlated with the closing and opening motions of T1R1. We then classify these five ligands into two groups according to their different binding effects on T1R1, which likely associate with the distinct umami signals stimulated by various ligands. This work warrants new experimental assays to further validate the theoretical model and provides guidance to design more effective umami ligands. •Revealing the binding effects of five umami ligands on the structural dynamics of T1R1-T1R3 at atomic resolution.•Molecular size and carried charges of the umami ligands determine their specific binding sites.•This work provides further guidance to design more effective and structurally diversified umami substances.