title: Allosteric effects of sodium ion binding on activation of the m3 muscarinic g-protein-coupled receptor.
abstract: G-protein-coupled receptors (GPCRs) are important membrane proteins that mediate cellular signaling and represent primary targets for about one-third of currently marketed drugs. Recent x-ray crystallographic studies identified distinct conformations of GPCRs in the active and inactive states. An allosteric sodium ion was found bound to a highly conserved D2.50 residue in inactive GPCRs, whereas the D2.50 allosteric pocket became collapsed in active GPCR structures. However, the dynamic mechanisms underlying these observations remain elusive. In this study, we aimed to understand the mechanistic effects of sodium ion binding on dynamic activation of the M3 muscarinic GPCR through long-timescale accelerated molecular dynamics (aMD) simulations. Results showed that with the D2.50 residue deprotonated, the M3 receptor is bound by an allosteric sodium ion and confined mostly in the inactive state with remarkably reduced flexibility. In contrast, the D2.50-protonated receptor does not exhibit sodium ion binding to the D2.50 allosteric site and samples a significantly larger conformational space. The receptor activation is captured and characterized by large-scale structural rearrangements of the transmembrane helices via dynamic hydrogen bond and salt bridge interactions. The residue motions are highly correlated during receptor activation. Further network analysis revealed that the allosteric signaling between residue D2.50 and key residues in the intracellular, extracellular, and orthosteric pockets is significantly weakened upon sodium ion binding.
authors: Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California. Electronic address: yimiao@ucsd.edu.
authors: Yinglong
authors: Y
authors: Miao
authors: Department of Pharmacology, University of California at San Diego, La Jolla, California.
authors: Alisha D
authors: AD
authors: Caliman
authors: Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California; Department of Pharmacology, University of California at San Diego, La Jolla, California; Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California.
authors: J Andrew
authors: JA
authors: McCammon
mesh_terms: D000494:Allosteric Regulation; D000495:Allosteric Site; D000595:Amino Acid Sequence; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding; D043587:Receptor, Muscarinic M3 / Q000737:chemistry* / Q000378:metabolism; D012964:Sodium / Q000494:pharmacology*
chemical_list: D043587:Receptor, Muscarinic M3; D012964:Sodium