Identification of a Different Agonist-Binding Site and Activation Mechanism of the Human P2Y(1) Receptor

The human P2Y(1) receptor (P2Y(1)R) is a purinergic G-protein-coupled receptor (GPCR) that functions as a receptor for adenosine 5′-diphosphate (ADP). An antagonist of P2Y(1)R might potentially have antithrombotic effects, whereas agonists might serve as antidiabetic agents. On the basis of the antagonist-bound MRS2500-P2Y(1)R crystal structure, we constructed computational models of apo-P2Y(1)R and the agonist-receptor complex 2MeSADP-P2Y(1)R. We then performed conventional molecular dynamics (cMD) and accelerated molecular dynamics (aMD) simulations to study the conformational dynamics after binding with agonist/antagonist as well as the P2Y(1)R activation mechanism. We identified a new agonist-binding site of P2Y(1)R that is consistent with previous mutagenesis data. This new site is deeper than those of the agonist ADP in the recently simulated ADP-P2Y(1)R structure and the antagonist MRS2500 in the MRS2500-P2Y(1)R crystal structure. During P2Y(1)R activation, the cytoplasmic end of helix VI shifts outward 9.1 Å, the Ser146(3.47)-Tyr237(5.58) hydrogen bond breaks, a Tyr237(5.58)-Val262(6.37) hydrogen bond forms, and the conformation of the χ1 rotamer of Phe269(6.44) changes from parallel to perpendicular to helix VI. The apo-P2Y(1)R system and the MRS2500-P2Y(1)R system remain inactive. The newly identified agonist binding site and activation mechanism revealed in this study may aid in the design of P2Y(1)R antagonists/agonists as antithrombotic/antidiabetic agents, respectively.