Structure and dynamics of the full-length M1 muscarinic acetylcholine receptor studied by molecular dynamics simulations

Abstract

The three-dimensional structure of full-length structure of the M1 muscarinic receptor was obtained through the fragmental homology modeling procedure. A 10-ns molecular dynamics (MD) simulation of the protein imbedded in a lipid slab and surrounded by water molecules was further used to relax the model. It was found that the homology model corresponded to the conformation in the ground state, since no significant motions of the backbone of transmembrane domains were observed. Furthermore, the reliability of the model was validated by analyzing key inter-helical contacts, sidechain–sidechain interactions, the formation of stable aromatic microdomains (clusters) and the docking of acetylcholine to its binding site. Moreover, a few conserved interactions observed in the X-ray structure of rhodopsin, such as inter-helical sidechain–sidechain hydrogen bonds were accurately reproduced in the MD simulation. The coupling of ACh to its binding site was found to be dominated by π-cation and salt bridge interactions, while its conformational space was restrained through van der Waals and hydrogen bond interactions. In general, such features were in very good agreement with the available experimental as well as with theoretical data. Considering the above, the structural information obtained in this study can be used a starting point to investigate the activation mechanism of the receptor and the ability to develop selective agonists and allosteric modulators which could be used for the treatment of Alzheimer’s disease.