Structure and dynamics of the full-length M 1 muscarinic acetylcholine receptor studied by molecular dynamics simulations L. Michel Espinoza-Fonseca a, * , Alessandro Pedretti b , Giulio Vistoli b a Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA b Istituto di Chimica Farmaceutica ‘‘Pietro Pratesi’’, Facolta ` di Farmacia, Universita ` di Milano, Viale Abruzzi 42, I-20131, Milano, Italy Received 30 July 2007, and in revised form 1 September 2007 Available online 15 September 2007 Abstract The three-dimensional structure of full-length structure of the M 1 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 p-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 exper- imental 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. Ó 2007 Elsevier Inc. All rights reserved. Keywords: Muscarinic M 1 receptor; G-protein coupled proteins; Molecular dynamics simulations; Acetylcholine receptor; Alzheimer’s disease Muscarinic acetylcholine receptors (mAChR) 1 belong to the superfamily of the G-protein coupled receptors (GPCRs), which are characterized by a rhodopsin-like folding pattern (seven helical transmembrane domains). In mammals, five different types of mAChRs, M 1 –M 5 , have been identified and biochemically characterized. These receptors are widely distributed throughout the human body and mediate distinct physiological functions, accord- ing to their location and subtype [1,2]. For example, mAChR M 3 has been shown to play a role in detrusor contraction within the bladder, while some experimental evidence has suggested that M 2 receptor may have a role in mediating indirect contractions as well as inhibition of detrusor relaxation [3,4]. Although the localization of mAChRs has been exten- sively studied, particular interest has been paid to their localization in the brain. Such receptors have been found to modulate neuronal excitability, synaptic plasticity and feedback regulation of the neurotransmitter acetylcholine (ACh) by activating several signal pathways. The five receptors are expressed in different regions of the brain [5]. For example, M 1 mAChR is abundant in neocortex, hippocampus and neostratium pyramidal cells, while M 3 is primarily expressed in hippocampus, thalamus and stra- tial GABAergic neurons [6]. Studies performed on the function of M 1 mAChR in the brain have shown that this receptor is highly involved in higher cognitive processes such as memory and learning. 0003-9861/$ - see front matter Ó 2007 Elsevier Inc. All rights reserved. doi:10.1016/j.abb.2007.09.002 * Corresponding author. E-mail address: mef@ddt.biochem.umn.edu (L.M. Espinoza-Fonseca). 1 Abbreviations used: mAChR, muscarinic acetylcholine receptors; GPCRs, G-protein coupled receptors; ACh, acetylcholine; AD, Alzhei- mer’s disease; POPC, palmitoyl-2-oleoyl-sn-glycerol-phosphatidylcholine. www.elsevier.com/locate/yabbi Available online at www.sciencedirect.com Archives of Biochemistry and Biophysics 469 (2008) 142–150 ABB