Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis

The differential modulation of agonist and antagonist binding to opioid receptors (ORs) by sodium (Na+) has been known for decades. To shed light on the molecular determinants, thermodynamics, and kinetics of Na+ translocation through the μ-OR (MOR), we used a multi-ensemble Markov model framework combining equilibrium and non-equilibrium atomistic molecular dynamics simulations of Na+ binding to MOR active or inactive crystal structures embedded in an explicit lipid bilayer. We identify an energetically favorable, continuous ion pathway through the MOR active conformation only, and provide, for the first time: i) estimates of the energy differences and required timescales of Na+ translocation in inactive and active MORs, ii) estimates of Na+-induced changes to agonist binding validated by radioligand measurements, and iii) testable hypotheses of molecular determinants and correlated motions involved in this translocation, which are likely to play a key role in MOR signaling.Author summary: Notwithstanding years of research supporting the notion that μ-opioid receptor (MOR) function can be modulated by sodium ions (Na+), a complete understanding of Na+ translocation through the receptor and its effect on ligand binding at MOR requires additional information. Here, we use computer simulations to elucidate the energetics involved in sodium binding at inactive and active MOR, the timescales of sodium translocation through these receptor conformations, and the molecular determinants involved in this process.