The full activation mechanism of the adenosine A ₁ receptor revealed by GaMD and Su-GaMD simulations

Significance

Clarifying the recognition pathways of agonist and G protein to G protein–coupled receptor (GPCR) is essential to understand the signal transduction mechanism of GPCR. However, it is still challenging to simulate the full activation process of GPCR on a reasonable simulation timescale with conventional molecular dynamics (MD) methods. Here, we developed an MD simulation approach named supervised Gaussian accelerated MD (Su-GaMD) and revealed the full activation mechanism of adenosine (Ado) A ₁ receptor (A ₁R) (including adenosine Ado−A ₁R recognition, preactivation of A ₁R, and A ₁R−G protein recognition) in hundreds of nanoseconds simulations. The whole activation process and the metastable intermediate states revealed in this study could provide complementary structural characterizations to expand our perspectives on A ₁R drug discovery.

Abstract

The full activation process of G protein–coupled receptor (GPCR) plays an important role in cellular signal transduction. However, it remains challenging to simulate the whole process in which the GPCR is recognized and activated by a ligand and then couples to the G protein on a reasonable simulation timescale. Here, we developed a molecular dynamics (MD) approach named supervised (Su) Gaussian accelerated MD (GaMD) by incorporating a tabu-like supervision algorithm into a standard GaMD simulation. By using this Su-GaMD method, from the active and inactive structure of adenosine A ₁ receptor (A ₁R), we successfully revealed the full activation mechanism of A ₁R, including adenosine (Ado)–A ₁R recognition, preactivation of A ₁R, and A ₁R–G protein recognition, in hundreds of nanoseconds of simulations. The binding of Ado to the extracellular side of A ₁R initiates conformational changes and the preactivation of A ₁R. In turn, the binding of G _i2 to the intracellular side of A ₁R causes a decrease in the volume of the extracellular orthosteric site and stabilizes the binding of Ado to A ₁R. Su-GaMD could be a useful tool to reconstruct or even predict ligand–protein and protein–protein recognition pathways on a short timescale. The intermediate states revealed in this study could provide more detailed complementary structural characterizations to facilitate the drug design of A ₁R in the future.