Model of the extracellular domain of the human a7 nAChR based on the crystal structure of the mouse a1 nAChR extracellular domain Maria Konstantakaki a , Socrates J. Tzartos b,c , Konstantinos Poulas b, * , Elias Eliopoulos a, ** a Department of Agricultural Biotechnology, Agricultural University of Athens, 75, Iera Odos, Votanikos, GR11855, Athens, Greece b Department of Pharmacy, University of Patras, Rio-Patras, GR26504, Greece c Department of Biochemistry, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., GR11521, Athens, Greece Received 15 September 2007; received in revised form 17 January 2008; accepted 23 January 2008 Available online 2 February 2008 Abstract Neuronal nicotinic acetylcholine receptors (nAChRs) are important therapeutic targets for various diseases, including Alzheimer’s disease, Parkinson’s disease, and schizophrenia, as well as for cessation of smoking. Based on the recently determined crystal structure of the extracellular domain (ECD) of the mouse nAChR a1 subunit complexed with a-bungarotoxin at 1.94 A ˚ resolution, we have constructed three-dimensional models of the ECD of the monomer, homodimer, and homopentamer of the human a7 nAChR and investigated in detail the interface between the two a7 subunits. The docking of the agonist in the ligand-binding pocket of the human a7 dimer was also performed and found consistent with results from labeling and mutagenesis experiments. Since the nAChR ligand-binding site is a useful target for mutagenesis studies and the rational design of drugs against diseases, these models provide useful information for future work. # 2008 Elsevier Inc. All rights reserved. Keywords: a7 nAChR; a1 nAChR; Homology model; Structure; Extracellular domain; Ligand-binding domain; Rational drug design 1. Introduction Nicotinic acetylcholine receptors (nAChRs), integral mem- brane proteins that respond to the binding of acetylcholine (ACh), are composed of five subunits organized around a central pore perpendicular to the membrane, and consist of two groups: (a) the muscle type, found in fish electric organs and in vertebrate skeletal muscles, where they mediate neuromuscular transmission at the neuromuscular junction, and (b) the neuronal type, found mainly throughout the peripheral and central nervous system, but also in non-neuronal tissues. The muscle-type nAChR consists of five homologous subunits in the stoichiometry (a1) 2 b1gd (embryonic form) or (a1) 2 b1ed (adult form) with two ACh-binding sites per molecule. Neuronal nAChRs consist of a variety of subunits in different combinations. To date, nine a (a2–a10) and three b (b2–b4) neuronal subunit genes have been cloned. The a7 neuronal-type subunit can form homopentamer of five identical a7 subunits with five ACh-binding sites per molecule [1]. nAChRs exist in different states, closed, open or desensitized, while the binding of nicotinic ligands, agonists, or competitive antagonists, affects the equilibrium between the various states. Extensive studies on nAChRs from various species have shown that each subunit consists of: (a) an N-terminal extracellular domain (ECD) of approximately 210–220 amino acids, of which a high proportion forms b strands, and bearing the domain that binds agonists and competitive antagonists [2,3], (b) four small (15–20 residues) hydrophobic transmem- brane domains (M1–M4) and two small hydrophobic loops, linking segments M1–M2 and M2–M3, (c) a larger loop, which varies in size (100–150 residues) and sequence between subunits, and which lies between M3 and M4 and bears phosphorylation sites [4], and (d) the C-terminal region of each subunit, which consists of a small (4–28 residues) hydrophilic extracellular segment [1]. It is well documented that brain nAChRs, including a7, participate in complex functions, such as attention, memory, www.elsevier.com/locate/JMGM Available online at www.sciencedirect.com Journal of Molecular Graphics and Modelling 26 (2008) 1333–1337 Abbreviations: nAChR, nicotinic acetylcholine receptor; ECD, extracellu- lar domain; ACh, acetylcholine. * Corresponding author. Tel.: +30 2610 969953; fax: +30 2610 969954. ** Corresponding author. Tel.: +30 210 5294223; fax: +30 210 5294322. E-mail addresses: kpoulas@upatras.gr (K. Poulas), eliop@aua.gr (E. Eliopoulos). 1093-3263/$ – see front matter # 2008 Elsevier Inc. All rights reserved. doi:10.1016/j.jmgm.2008.01.004