Mapping Allosteric Communication Pipelines in GPCRs from Microsecond Timescale Molecular Dynamics Simulations

Abstract

G protein coupled receptors (GPCRs) are 7 transmembrane (TM) helical proteins that signal through effector proteins bound at the intracellular (IC) interface. Agonist binding at the extracellular (EC) domain triggers conformational change at the IC domain leading to receptor activation. However, the mechanism of allosteric communication and the amino acids involved in the pipelines of allosteric communication (allosteric pathways) are not known yet. In this study, we have mapped the allosteric pipelines of communication in β2-adrenergic receptor (β2AR) using microseconds timescale Molecular Dynamics trajectories. Using mutual information in the internal coordinates, we have compared the allosteric pipelines among three β2AR conformations; inverse agonist bound inactive state, agonist bound intermediate state, and agonist and G protein bound active state. Strong allosteric communication along the TM domains stabilize the receptor in the inactive and active conformations. However the agonist bound intermediate state is dynamic showing weakened communication between the EC and IC domains. We have identified the residues that mediate multiple allosteric pipelines as allosteric hubs. These allosteric hubs have also been identified with the mutations that alter the receptor efficacy without altering the ligand binding. The role of such mutations were not previously understood.We have identified the residue networks involved in a continuous communication pipeline from the EC loops to the G protein coupling site. One of the termination points of the activation signal is the engineered Zn2+ binding site at the IC interface, which is a known positive allosteric modulator binding site in β2AR. We have shown how our method in conjunction with MD simulations can identify allosteric pockets which can then be used for screening allosteric drugs in GPCRs.