N. Unwin, Refined Structure of the Nicotinic Acetylcholine Receptor at 4?? Resolution, Journal of Molecular Biology, vol.346, issue.4, pp.967-989, 2005.
DOI : 10.1016/j.jmb.2004.12.031

N. Unwin and Y. Fujiyoshi, Gating Movement of Acetylcholine Receptor Caught by Plunge-Freezing, Journal of Molecular Biology, vol.422, issue.5, pp.617-634, 2012.
DOI : 10.1016/j.jmb.2012.07.010

S. M. Sine, End-Plate Acetylcholine Receptor: Structure, Mechanism, Pharmacology, and Disease, Physiological Reviews, vol.92, issue.3, pp.1189-1234, 2012.
DOI : 10.1152/physrev.00015.2011

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489064

S. V. Jadey, P. Purohit, I. Bruhova, T. M. Gregg, and A. Auerbach, Design and control of acetylcholine receptor conformational change, Proc. Natl. Acad. Sci. USA, pp.4328-4333, 2011.
DOI : 10.1073/pnas.1016617108

X. Liu, Y. Xu, H. Li, X. Wang, H. Jiang et al., Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor, PLoS Computational Biology, vol.32, issue.1, p.19, 2008.
DOI : 10.1371/journal.pcbi.0040019.sg004

F. Gao, N. Bren, T. P. Burghardt, S. Hansen, R. H. Henchman et al., Agonist-mediated Conformational Changes in Acetylcholine-binding Protein Revealed by Simulation and Intrinsic Tryptophan Fluorescence, Journal of Biological Chemistry, vol.280, issue.9, pp.280-8443, 2005.
DOI : 10.1074/jbc.M412389200

R. J. Law, R. H. Henchman, and J. Mccammon, A gating mechanism proposed from a simulation of a human ??7 nicotinic acetylcholine receptor, Proc. Natl. Acad. Sci. USA, pp.6813-6818, 2005.
DOI : 10.1073/pnas.0407739102

X. Cheng, H. Wang, B. Grant, S. M. Sine, and J. A. Mccammon, Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors, PLoS Computational Biology, vol.14, issue.9, p.134, 2006.
DOI : 1093-3263(1996)014[0033:VVMD]2.0.CO;2

X. Cheng, I. Ivanov, H. Wang, S. M. Sine, and J. A. Mccammon, Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family, J. Am. Chem. Soc, pp.129-8217, 2007.

J. Leech, J. Prins, and J. Hermans, SMD: visual steering of molecular dynamics for protein design, IEEE Computational Science and Engineering, vol.3, issue.4, pp.38-45, 1996.
DOI : 10.1109/99.556511

P. Chau, Process and thermodynamics of ligand???receptor interaction studied using a novel simulation method, Chemical Physics Letters, vol.334, issue.4-6, pp.343-351, 2001.
DOI : 10.1016/S0009-2614(00)01427-5

S. Wells, S. Menor, B. M. Hespenheide, and M. F. Thorpe, Constrained geometric simulation of diffusive motion in proteins, Physical Biology, vol.2, issue.4, pp.127-136, 2005.
DOI : 10.1088/1478-3975/2/4/S07

J. L. Kozuska, I. M. Paulsen, W. J. Belfield, I. L. Martin, D. J. Cole et al., Impact of intracellular domain flexibility upon properties of activated human 5-HT3 receptors, Br. J. Pharmacol, pp.171-1617, 2014.

C. C. Jolley, S. A. Wells, B. M. Hespenheide, M. F. Thorpe, and P. Fromme, Docking of Photosystem I Subunit C Using a Constrained Geometric Simulation, Journal of the American Chemical Society, vol.128, issue.27, pp.128-8803, 2006.
DOI : 10.1021/ja0587749

H. Li, S. A. Wells, J. E. Jimenez-roldan, R. A. Romer, Y. Zhao et al., Protein flexibility is key to cisplatin crosslinking in calmodulin, Protein Science, vol.286, issue.9, pp.1269-1279, 2012.
DOI : 10.1002/pro.2111

M. Sun, M. B. Rose, S. K. Ananthanarayanan, D. J. Jacobs, and C. M. Yengo, Characterization of the pre-force-generation state in the actomyosin cross-bridge cycle, Proc. Natl. Acad. Sci. USA 105, pp.8631-8863, 2008.
DOI : 10.1073/pnas.0710793105

S. Fulle, N. A. Christ, E. Kestner, and H. Gohlke, HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations, Journal of Chemical Information and Modeling, vol.50, issue.8, pp.50-1489, 2010.
DOI : 10.1021/ci100101w

A. Metz, C. Pfleger, H. Kopitz, S. Pfeiffer-marek, K. H. Barringhaus et al., Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein???Protein Interface, Journal of Chemical Information and Modeling, vol.52, issue.1, pp.52-120, 2011.
DOI : 10.1021/ci200322s

S. A. Wells, Geometric Simulation of Flexible Motion in Proteins, Protein Dynamics, pp.173-192, 2013.
DOI : 10.1007/978-1-62703-658-0_10

C. C. David and D. J. Jacobs, Characterizing protein motions from structure, Journal of Molecular Graphics and Modelling, vol.31, pp.31-41, 2011.
DOI : 10.1016/j.jmgm.2011.08.004

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667955

R. A. Laskowski, M. W. Macarthur, D. S. Moss, and J. M. Thornton, PROCHECK: a program to check the stereochemical quality of protein structures, Journal of Applied Crystallography, vol.26, issue.2, pp.26-283, 1993.
DOI : 10.1107/S0021889892009944

O. F. Lange and H. Grubmüller, Generalized correlation for biomolecular dynamics, Proteins: Structure, Function, and Bioinformatics, vol.29, issue.4, pp.1053-1061, 2006.
DOI : 10.1002/prot.20784

URL : http://hdl.handle.net/11858/00-001M-0000-0012-E632-5

V. Kukhtina, D. Kottwitz, H. Strauss, B. Heise, N. Chebotareva et al., Intracellular domain of nicotinic acetylcholine receptor: the importance of being unfolded, Journal of Neurochemistry, vol.346, issue.1, pp.63-67, 2006.
DOI : 10.1111/j.1471-4159.2005.03468.x

X. Cheng, B. Lu, B. Grant, R. J. Law, and J. A. Mccammon, Channel Opening Motion of ??7 Nicotinic Acetylcholine Receptor as Suggested by Normal Mode Analysis, Journal of Molecular Biology, vol.355, issue.2, pp.355-310, 2006.
DOI : 10.1016/j.jmb.2005.10.039

R. H. Henchman, H. L. Wang, S. M. Sine, P. Taylor, and J. A. Mccammon, Asymmetric structural motions of the homomeric ?7 nicotinic acetylcholine receptor as suggested by normal mode analysis, J. Mol. Biol, pp.355-310, 2003.

O. K. Steinlein and D. Bertrand, Neuronal nicotinic acetylcholine receptors: From the genetic analysis to neurological diseases, Biochemical Pharmacology, vol.76, issue.10, pp.1175-1183, 2008.
DOI : 10.1016/j.bcp.2008.07.012

X. Shen, J. M. Brengman, S. Edvardson, S. M. Sine, and A. G. Engel, Highly fatal fast-channel syndrome caused by AChR ?? subunit mutation at the agonist binding site, Neurology, vol.79, issue.5, pp.449-454, 2012.
DOI : 10.1212/WNL.0b013e31825b5bda

A. R. Fersht, R. J. Leatherbarrow, and T. N. Wells, Quantitative analysis of structure???activity relationships in engineered proteins by linear free-energy relationships, Nature, vol.2, issue.6076, pp.284-286, 1986.
DOI : 10.1038/322284a0

A. Mitra, G. D. Cymes, and A. Auerbach, Dynamics of the acetylcholine receptor pore at the gating transition state, Proceedings of the National Academy of Sciences USA, pp.15069-21507, 2005.
DOI : 10.1073/pnas.0505090102

P. Purohit, A. Mitra, and A. Auerbach, A stepwise mechanism for acetylcholine receptor channel gating, Nature, vol.102, issue.7138, pp.930-933, 2007.
DOI : 10.1038/nature05721

N. Calimet, M. Simoes, J. Changeux, M. Karplus, A. Taly et al., A gating mechanism of pentameric ligand-gated ion channels, Proc. Natl. Acad. Sci. USA, pp.3987-3996, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01498070

G. Gonzalez-gutierrez and C. Grosman, Bridging the Gap between Structural Models of Nicotinic Receptor Superfamily Ion Channels and Their Corresponding Functional States, Journal of Molecular Biology, vol.403, issue.5, pp.403-693, 2010.
DOI : 10.1016/j.jmb.2010.09.026