Figure 6
From: Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A1 Receptor
PAM binding closed a salt bridge E172ECL2-K265ECL3 in the A1AR extracellular vestibule: (A) A 2D PMF profile of the E172ECL2-K265ECL3 distance and NECA RMSD relative to the starting bound conformation obtained from AMBER dual-boost GaMD simulation of the “A1AR + NECA” system. The Cδ atom in E172 and Nζ atom in K265 were used to calculate the distance. (B) Three low-energy states, “Open”, “Intermediate” and “Closed”, identified in (A) are shown using the X-ray structure of antagonist DU172-bound A1AR (PDB: 5UEN), cryo-EM structure of adenosine-Gi-bound A1AR (PDB: 6D9H) and GaMD predicted structure of the NECA and PAM PD81723 co-bound A1AR. (C,D) 2D PMF profiles of the E172ECL2-K265ECL3 distance and PAM occupancy at the ECL2 allosteric site obtained from AMBER dual-boost GaMD simulations of the (C) “A1AR + NECA + PD81723” and (D) “A1AR + NECA + VCP171” systems. PAM binding biased conformation ensemble of the E172ECL2-K265ECL3 salt bridge towards the closed state, leading to stabilized agonist binding at the orthosteric site.
