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Abstract

The medaka fish taste receptor T1r2a–T1r3 is a Class C G-protein coupled receptor (GPCR), the X-ray crystal structures of which were reported in 2017. In this study, 1-μs all-atom molecular dynamics (MD) simulations were performed for both ligand-bound and ligand-free T1r2a–T1r3, and the microscopic effects of ligand binding on the dynamic structural ensemble and fluctuations of the receptor were investigated. The results revealed differences in local fluctuations between the ligand-bound and ligand-free states, with these changes varying between T1r2a and T1r3. In particular, T1r2a LB2 showed a tendency toward reduced fluctuations on the longer timescale. Principal component analysis (PCA) revealed larger overall structural changes in the ligand-free state, whereas the ligand-bound state exhibited relatively smaller overall structural changes but showed characteristic changes in the relative arrangement between the LB2 domains. Furthermore, free-energy landscape (FEL) analysis indicated that a broader conformational space was sampled in the ligand-free state, whereas in the ligand-bound state, changes in the relative arrangement between the subunits, particularly involving the LB2 domains, may occur within a relatively restricted conformational region. Taken together, these results suggest that ligand binding does not simply suppress conformational fluctuations of the receptor, but rather alters their magnitude and mode of motion, with the resulting changes potentially manifested as changes in the relative arrangement between the subunits mediated by the LB2 domains.