Universality of the Sodium Ion Binding Mechanism in Class A G-Protein-Coupled Receptors

The allosteric modulation of G-protein-coupled receptors (GPCRs) by sodium ions has received significant attention as crystal structures of several receptors show Na⁺ ions bound to the inactive conformations at the conserved Asp^2.50. To date, structures from 24 families of GPCRs have been determined, though mechanistic insights into Na⁺ binding to the allosteric site are limited. We performed hundreds-of-microsecond long simulations of 18 GPCRs and elucidated their Na⁺ binding mechanism. In class A GPCRs, the Na⁺ ion binds to the conserved residue 2.50 whereas in class B receptors, it binds at 3.43b, 6.53b, and 7.49b. Using Markov state models, we obtained the free energy profiles and kinetics of Na⁺ binding to the allosteric site, which reveal a conserved mechanism of Na⁺ binding for GPCRs and show the residues that act as major barriers for ion diffusion. Furthermore, we also show that the Na⁺ ion can bind to GPCRs from the intracellular side when the allosteric site is inaccessible from the extracellular side.