title: Ligand-induced conformational change in the alpha7 nicotinic receptor ligand binding domain.
abstract: Molecular dynamics simulations of a homology model of the ligand binding domain of the alpha7 nicotinic receptor are conducted with a range of bound ligands to induce different conformational states. Four simulations of 15 ns each are run with no ligand, antagonist d-tubocurarine (dTC), agonist acetylcholine (ACh), and agonist ACh with potentiator Ca(2+), to give insight into the conformations of the active and inactive states of the receptor and suggest the mechanism for conformational change. The main structural factor distinguishing the active and inactive states is that a more open, symmetric arrangement of the five subunits arises for the two agonist simulations, whereas a more closed and asymmetric arrangement results for the apo and dTC cases. Most of the difference arises in the lower portion of the ligand binding domain near its connection to the adjacent transmembrane domain. The transfer of the more open state to the transmembrane domain could then promote ion flow through the channel. Variation in how subunits pack together with no ligand bound appears to give rise to asymmetry in the apo case. The presence of dTC expands the receptor but induces rotations in alternate directions in adjacent subunits that lead to an asymmetric arrangement as in the apo case. Ca(2+) appears to promote a slightly greater expansion in the subunits than ACh alone by stabilizing the C-loop and ACh positions. Although the simulations are unlikely to be long enough to view the full conformational changes between open and closed states, a collection of different motions at a range of length scales are observed that are likely to participate in the conformational change.
authors.affiliation: Howard Hughes Medical Institute, NSF Center for Theoretical Biophysics, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA. rhenchman@mccammon.ucsd.edu
authors.forename: Richard H
authors.initials: RH
authors.lastname: Henchman
authors.forename: Hai-Long
authors.initials: HL
authors.lastname: Wang
authors.forename: Steven M
authors.initials: SM
authors.lastname: Sine
authors.forename: Palmer
authors.initials: P
authors.lastname: Taylor
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
mesh_terms: D000109:Acetylcholine / Q000737:chemistry; D000818:Animals; D001665:Binding Sites; D001703:Biophysics / Q000379:methods*; D002118:Calcium / Q000737:chemistry; D003198:Computer Simulation; D007477:Ions; D008024:Ligands; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D009068:Movement; D016011:Normal Distribution; D010100:Oxygen / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011978:Receptors, Nicotinic / Q000737:chemistry*; D012984:Software; D013997:Time Factors; D014403:Tubocurarine / Q000737:chemistry; D064569:alpha7 Nicotinic Acetylcholine Receptor
chemical_list: D007477:Ions; D008024:Ligands; D011978:Receptors, Nicotinic; D064569:alpha7 Nicotinic Acetylcholine Receptor; D000109:Acetylcholine; D010100:Oxygen; D002118:Calcium; D014403:Tubocurarine