P. Corringer, D. Guedin, P. Lestage, and J. Changeux, Nicotinic receptors: allosteric transitions and therapeutic targets in the nervous system, Nat Rev Drug Discov, vol.8, pp.733-750, 2009.

J. Changeux and S. Edelstein, The nicotinic acetylcholine receptor: From molecular biology to cognition, Neuropharmacology, vol.96, 2005.
DOI : 10.1016/j.neuropharm.2015.03.024

J. Changeux and S. Edelstein, Allosteric Mechanisms of Signal Transduction, Science, vol.308, issue.5727, pp.1424-1428, 2005.
DOI : 10.1126/science.1108595

M. Nys, D. Kesters, and C. Ulens, Structural insights into Cys-loop receptor function and ligand recognition, Biochemical Pharmacology, vol.86, issue.8, pp.1042-1053, 2013.
DOI : 10.1016/j.bcp.2013.07.001

V. Whatley and R. Harris, The Cytoskeleton and Neurotransmitter Receptors, Int Rev Neurobiol, vol.39, pp.113-143, 1996.
DOI : 10.1016/S0074-7742(08)60665-0

A. Larsson and J. Engel, Neurochemical and behavioral studies on ethanol and nicotine interactions, Neuroscience & Biobehavioral Reviews, vol.27, issue.8, pp.713-720, 2004.
DOI : 10.1016/j.neubiorev.2003.11.010

V. Bordarenko, D. Mowrey, T. Tillman, E. Seyoum, Y. Xe et al., NMR structures of the human ??7 nAChR transmembrane domain and associated anesthetic binding sites, Biochimica et Biophysica Acta (BBA) - Biomembranes, vol.1838, issue.5, pp.1389-1395, 2014.
DOI : 10.1016/j.bbamem.2013.12.018

A. Auerbach, The Energy and Work of a Ligand-Gated Ion Channel, Journal of Molecular Biology, vol.425, issue.9, pp.1461-1475, 2013.
DOI : 10.1016/j.jmb.2013.01.027

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

H. Nury, C. Renterghem, Y. Weng, A. Tran, M. Baaden et al., X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel, Nature, vol.97, issue.7330, pp.428-431, 2011.
DOI : 10.1038/nature09647

URL : https://hal.archives-ouvertes.fr/hal-00645160

R. Hilf, C. Bertozzi, I. Zimmermann, A. Reiter, D. Trauner et al., Structural basis of open channel block in a prokaryotic pentameric ligand-gated ion channel, Nature Structural & Molecular Biology, vol.277, issue.11, pp.1330-1336, 1933.
DOI : 10.1016/S0010-4655(98)00016-2

H. Nury, F. Poitevin, C. Renterghem, J. Changeux, P. Corringer et al., One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue, Proceedings of the National Academy of Sciences, vol.107, issue.14, pp.6275-6280, 2010.
DOI : 10.1073/pnas.1001832107

R. Hilf and R. Dutzler, Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel, Nature, vol.9, issue.7225, pp.115-118, 2009.
DOI : 10.1073/pnas.93.23.13362

N. Bocquet, H. Nury, M. Baaden, C. Poupon, J. Changeux et al., X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation, Nature, vol.3, issue.7225, pp.111-114, 2009.
DOI : 10.1523/JNEUROSCI.3467-06.2006

I. Zimmermann and R. Dutzler, Ligand Activation of the Prokaryotic Pentameric Ligand-Gated Ion Channel ELIC, PLoS Biology, vol.14, issue.Pt 2, p.21713033, 2011.
DOI : 10.1371/journal.pbio.1001101.s006

R. Hilf and R. Dutzler, X-ray structure of a prokaryotic pentameric ligand-gated ion channel, Nature, vol.111, issue.7185, pp.375-379, 2008.
DOI : 10.1038/nature06717

J. Pan, Q. Chen, D. Willenbring, K. Yoshida, T. Tillman et al., Structure of the pentameric ligand-gated ion channel ELIC cocrystallized with its competitive antagonist acetylcholine, Nature Communications, vol.14, pp.714-724, 2012.
DOI : 10.1038/ncomms1703

G. Gonzalez-gutierrez, L. Cuello, S. Nair, and C. Grosman, Gating of the proton-gated ion channel from Gloeobacter violaceus at pH 4 as revealed by X-ray crystallography, Proceedings of the National Academy of Sciences, vol.110, issue.46, pp.18716-18721, 2013.
DOI : 10.1073/pnas.1313156110

M. Prevost, L. Sauguet, H. Nury, C. Renterghem, C. Huon et al., A locally closed conformation of a bacterial pentameric proton-gated ion channel, Nature Structural & Molecular Biology, vol.369, issue.6, pp.642-649, 2012.
DOI : 10.1016/S0006-3495(93)81293-1

URL : https://hal.archives-ouvertes.fr/hal-00760125

P. Celie, S. Van-rossum-fikkert, W. Van-dijk, K. Brejc, A. Smit et al., Nicotine and Carbamylcholine Binding to Nicotinic Acetylcholine Receptors as Studied in AChBP Crystal Structures, Neuron, vol.41, issue.6, pp.907-914, 2004.
DOI : 10.1016/S0896-6273(04)00115-1

P. Celie, I. Kasheverov, D. Mordvintsev, R. Hogg, P. Van-nierop et al., Crystal structure of nicotinic acetylcholine receptor homolog AChBP in complex with an alpha-conotoxin PnIA variant

P. Celie, R. Klaassen, S. Van-rossum-fikkert, R. Van-elk, P. Van-nierop et al., Crystal Structure of Acetylcholine-binding Protein from Bulinus truncatus Reveals the Conserved Structural Scaffold and Sites of Variation in Nicotinic Acetylcholine Receptors, Journal of Biological Chemistry, vol.280, issue.28, pp.26457-26466, 2005.
DOI : 10.1074/jbc.M414476200

R. Hibbs, Z. Radic, P. Taylor, and D. Johnson, Influence of Agonists and Antagonists on the Segmental Motion of Residues near the Agonist Binding Pocket of the Acetylcholine-binding Protein, Journal of Biological Chemistry, vol.281, issue.51, pp.39708-39718, 2006.
DOI : 10.1074/jbc.M604752200

R. Hibbs, G. Sulzenbacher, J. Shi, T. Talley, S. Conrod et al., Structural determinants for interaction of partial agonists with acetylcholine binding protein and neuronal ??7 nicotinic acetylcholine receptor, The EMBO Journal, vol.11, issue.19, pp.3040-3051, 2009.
DOI : 10.1021/jo00279a042

S. Hansen, G. Sulzenbacher, T. Huxford, P. Marchot, P. Taylor et al., Structures of Aplysia AChBP complexes with nicotinic agonists and antagonists reveal distinctive binding interfaces and conformations, The EMBO Journal, vol.92, issue.20, pp.3635-3646, 2005.
DOI : 10.1016/0014-5793(90)81231-C

C. Ulens, R. Hogg, P. Celie, D. Bertrand, V. Tsetlin et al., Structural determinants of selective ??-conotoxin binding to a nicotinic acetylcholine receptor homolog AChBP, Proceedings of the National Academy of Sciences, vol.103, issue.10, pp.3615-3620, 2006.
DOI : 10.1073/pnas.0507889103

Y. Bourne, S. Hansen, G. Sulzenbacher, T. Talley, T. Huxford et al., Structural Comparison of Three Crystalline Complexes of a Peptidic Toxin With a Synaptic Acetylcholine Recognition Protein, Journal of Molecular Neuroscience, vol.30, issue.1-2, pp.103-104, 2006.
DOI : 10.1385/JMN:30:1:103

URL : https://hal.archives-ouvertes.fr/hal-00134316

Y. Bourne, Z. Radic, R. Aráoz, T. Talley, E. Benoit et al., Structural determinants in phycotoxins and AChBP conferring high affinity binding and nicotinic AChR antagonism, Proceedings of the National Academy of Sciences, vol.107, issue.13, pp.6076-6081, 2010.
DOI : 10.1073/pnas.0912372107

URL : https://hal.archives-ouvertes.fr/hal-00464306

Y. Bourne, T. Talley, S. Hansen, P. Taylor, and P. Marchot, Crystal structure of a CBTX-AChBP complex reveals essential interactions between snake alpha-neurotoxins and nicotinic receptors, EMBO J, vol.24, pp.112-115, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00021395

S. Hansen and P. Taylor, Galanthamine and Non-competitive Inhibitor Binding to ACh-binding Protein: Evidence for a Binding Site on Non-??-subunit Interfaces of Heteromeric Neuronal Nicotinic Receptors, Journal of Molecular Biology, vol.369, issue.4, pp.895-890, 2007.
DOI : 10.1016/j.jmb.2007.03.067

S. Dutertre, C. Ulens, R. Buttner, A. Fish, R. Van-elk et al., AChBP-targeted ??-conotoxin correlates distinct binding orientations with nAChR subtype selectivity, The EMBO Journal, vol.57, issue.16, pp.3858-3860, 2007.
DOI : 10.1038/sj.emboj.7601785

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952216

E. Edink, P. Rucktooa, K. Retra, A. Akdemir, T. Nahar et al., Fragment Growing Induces Conformational Changes in Acetylcholine-Binding Protein: A Structural and Thermodynamic Analysis, Journal of the American Chemical Society, vol.133, issue.14, pp.5363-5371, 2011.
DOI : 10.1021/ja110571r

P. Rucktooa, A. Smit, and T. Sixma, Insight in nAChR subtype selectivity from AChBP crystal structures, Biochemical Pharmacology, vol.78, issue.7, pp.777-787, 2009.
DOI : 10.1016/j.bcp.2009.06.098

URL : https://hal.archives-ouvertes.fr/hal-00509510

V. Tsetlin and F. Hucho, Nicotinic acetylcholine receptors at atomic resolution, Current Opinion in Pharmacology, vol.9, issue.3, pp.306-310, 2009.
DOI : 10.1016/j.coph.2009.03.005

V. Costa, A. Nistri, A. Cavalli, and P. Carloni, 4 neuronal nicotinic receptor, British Journal of Pharmacology, vol.95, issue.Suppl. 1, pp.921-931, 2003.
DOI : 10.1038/sj.bjp.0705498

F. Gao, N. Bren, T. Burghardt, S. Hansen, R. 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.8443-8451, 2005.
DOI : 10.1074/jbc.M412389200

S. Amiri, M. Sansom, and P. Biggin, Molecular dynamics studies of AChBP with nicotine and carbamylcholine: the role of water in the binding pocket, Protein Engineering Design and Selection, vol.20, issue.7, pp.353-359, 2007.
DOI : 10.1093/protein/gzm029

M. Hosseini-naveh, Z. Malliavin, T. Maragliano, L. Cottone, G. Ciccotti et al., Conformational Changes in Acetylcholine Binding Protein Investigated by Temperature Accelerated Molecular Dynamics, PLoS ONE, vol.32, issue.2, p.24551117, 2014.
DOI : 10.1371/journal.pone.0088555.s014

R. Hibbs and E. Gouaux, Principles of activation and permeation in an anion-selective Cys-loop receptor, Nature, vol.33, issue.7349, pp.54-60, 2011.
DOI : 10.1038/nature10139

T. Althoff, R. Hibbs, S. Banerjee, and E. Gouaux, X-ray structures of GluCl in apo states reveal a gating mechanism of Cys-loop receptors, Nature, vol.16, issue.7514, pp.333-337, 2014.
DOI : 10.1038/nature13669

P. Miller and A. Aricescu, Crystal structure of a human GABAA receptor, Nature, vol.106, issue.7514, pp.270-275, 2014.
DOI : 10.1038/nature13293

G. Hassaine, C. Deluz, L. Grasso, R. Wyss, M. Tol et al., X-ray structure of the mouse serotonin 5-HT3 receptor, Nature, vol.57, issue.7514, pp.276-281, 2014.
DOI : 10.1038/nature13552

URL : https://hal.archives-ouvertes.fr/hal-01102530

R. Law, R. Henchman, and J. Mccammon, A gating mechanism proposed from a simulation of a human ??7 nicotinic acetylcholine receptor, Proceedings of the National Academy of Sciences, vol.102, issue.19, pp.6813-6818, 2005.
DOI : 10.1073/pnas.0407739102

X. Cheng, H. Wang, B. Grant, S. Sine, and J. Mccammon, Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors, PLoS Comput Biol, vol.2, pp.1173-1184, 2006.

X. Cheng, B. Lu, B. Grant, R. Law, and J. Mccammon, Channel Opening Motion of ??7 Nicotinic Acetylcholine Receptor as Suggested by Normal Mode Analysis, Journal of Molecular Biology, vol.355, issue.2, pp.310-324, 2006.
DOI : 10.1016/j.jmb.2005.10.039

X. Cheng, I. Ivanov, H. Wang, S. Sine, and J. Mccammon, Nanosecond-Timescale Conformational Dynamics of the Human ??7 Nicotinic Acetylcholine Receptor, Biophysical Journal, vol.93, issue.8, pp.2622-2634, 2007.
DOI : 10.1529/biophysj.107.109843

A. Taly, M. Delarue, T. Grutter, M. Nilges, N. Novere et al., Normal Mode Analysis Suggests a Quaternary Twist Model for the Nicotinic Receptor Gating Mechanism, Biophysical Journal, vol.88, issue.6, pp.3954-3965, 2005.
DOI : 10.1529/biophysj.104.050229

URL : https://hal.archives-ouvertes.fr/pasteur-00162514

R. Bergmann, K. Kongsbak, P. Sã¸rensen, T. Sander, and T. Balle, NMR structures of the human ?7 nAChR transmembrane domain and associated anesthetic binding sites, PLoS One, vol.8, p.23308109, 2013.

Y. R. Hurdiss, E. Greiner, T. Lape, R. Sivilotti, L. Biggin et al., Agonist and Antagonist Binding in Human Glycine Receptors, Biochemistry, vol.53, pp.6041-6051, 2014.

N. Calimet, M. Simoes, J. Changeux, M. Karplus, A. Taly et al., PNAS Plus: From the Cover: A gating mechanism of pentameric ligand-gated ion channels, Proceedings of the National Academy of Sciences, vol.110, issue.42, pp.3987-3996, 2013.
DOI : 10.1073/pnas.1313785110

O. Yoluk, T. Bromstrup, E. Bertaccini, J. Trudell, and E. Lindahl, Stabilization of the GluCl Ligand-Gated Ion Channel in the Presence and??Absence of Ivermectin, Biophysical Journal, vol.105, issue.3, pp.640-647, 2013.
DOI : 10.1016/j.bpj.2013.06.037

M. Cheng and R. Coalson, Energetics and Ion permeation Characteristics in a Glutamate-Gated Chloride (GluCl) Receptor Channel, The Journal of Physical Chemistry B, vol.116, issue.46, pp.13637-13643, 2012.
DOI : 10.1021/jp3074915

C. Bouzat, F. Gumilar, G. Spitzmaul, H. Wang, D. Rayes et al., Coupling of agonist binding to channel gating in an ACh-binding protein linked to an ion channel, Nature, vol.60, issue.7002, pp.896-900, 2004.
DOI : 10.1074/jbc.M203396200

W. Lee and S. Sine, Principal pathway coupling agonist binding to channel gating in nicotinic receptors, Nature, vol.70, issue.7065, pp.243-247, 2005.
DOI : 10.1016/0263-7855(96)00018-5

N. Mukhtasimova, C. Free, and S. Sine, Initial Coupling of Binding to Gating Mediated by Conserved Residues in the Muscle Nicotinic Receptor, The Journal of General Physiology, vol.254, issue.1, pp.23-39, 2005.
DOI : 10.1085/jgp.116.3.449

D. Reeves, M. Jansen, M. Bali, T. Lemster, and M. Akabas, A Role for the ??1-??2 Loop in the Gating of 5-HT3 Receptors, Journal of Neuroscience, vol.25, issue.41, pp.9358-9366, 2005.
DOI : 10.1523/JNEUROSCI.1045-05.2005

N. Novã¨re, T. Grutter, and J. Changeux, Models of the extracellular domain of the nicotinic receptors and of agonist-and Ca 2+ binding sites, Proc Natl Acad Sci, vol.98, pp.3210-3215, 2002.

G. Grazioso, A. Cavalli, M. Amici, M. Recanatini, and C. Micheli, Alpha7 nicotinic acetylcholine receptor agonists: Prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach, Journal of Computational Chemistry, vol.23, issue.15, pp.2593-2602, 2008.
DOI : 10.1002/jcc.21019

M. Martã-renom, A. Stuart, A. Fiser, R. Sã¡nchez, F. Melo et al., Comparative Protein Structure Modeling of Genes and Genomes, Annual Review of Biophysics and Biomolecular Structure, vol.29, issue.1, pp.291-325, 2000.
DOI : 10.1146/annurev.biophys.29.1.291

L. Forrest, C. Tang, and B. Honig, On the Accuracy of Homology Modeling and Sequence Alignment Methods Applied to Membrane Proteins, Biophysical Journal, vol.91, issue.2, pp.508-517, 2006.
DOI : 10.1529/biophysj.106.082313

C. Notredame, D. Higgins, J. Heringa, and . T-coffee, T-coffee: a novel method for fast and accurate multiple sequence alignment, Journal of Molecular Biology, vol.302, issue.1, pp.205-217, 2000.
DOI : 10.1006/jmbi.2000.4042

N. Eswar, B. Webb, M. Marti-renom, M. Madhusudhan, D. Eramian et al., Comparative Protein Structure Modeling using Modeller, Current Protoc Bioinformatics, vol.5, pp.1-30, 2006.

R. Laskowski, M. Macarthur, D. Moss, and J. Thornton, PROCHECK: a program to check the stereochemical quality of protein structures, Journal of Applied Crystallography, vol.26, issue.2, pp.283-291, 1993.
DOI : 10.1107/S0021889892009944

V. Chen, W. Arendall, J. Headd, D. Keedy, R. Immormino et al., : all-atom structure validation for macromolecular crystallography, Acta Crystallographica Section D Biological Crystallography, vol.285, issue.1, pp.12-21, 2010.
DOI : 10.1107/S0907444909042073

S. Lovell, I. Davis, W. Arendall, P. De-bakker, J. Word et al., Structure validation by C?? geometry: ??,?? and C?? deviation, Proteins: Structure, Function, and Bioinformatics, vol.320, issue.3, pp.437-450, 2003.
DOI : 10.1002/prot.10286

P. Benkert, M. Künzli, and T. Schwede, QMEAN server for protein model quality estimation, Nucleic Acids Research, vol.37, issue.Web Server, pp.510-514, 2009.
DOI : 10.1093/nar/gkp322

W. Delano, The PyMOL Molecular Graphics Systemml: http://www.pymol.org. DeLano Scientific, Available, vol.fromml, 2002.

D. Bahsford and M. Karplus, pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model, Biochemistry, vol.29, issue.44, pp.10219-10225, 1990.
DOI : 10.1021/bi00496a010

R. Anandakrishnan, B. Aguilar, and A. Onufriev, H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations, Nucleic Acids Research, vol.40, issue.W1, pp.537-541, 2012.
DOI : 10.1093/nar/gks375

J. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid et al., Scalable molecular dynamics with NAMD, Journal of Computational Chemistry, vol.84, issue.16, pp.1781-1802, 2005.
DOI : 10.1002/jcc.20289

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2486339

D. Quigley and M. Probert, Langevin dynamics in constant pressure extended systems, The Journal of Chemical Physics, vol.120, issue.24, pp.11432-11441, 2004.
DOI : 10.1063/1.1755657

J. Wang, W. Wang, P. Kollmann, and D. Case, Development and testing of a general amber force field, Journal of Computational Chemistry, vol.17, issue.9, pp.1157-1174, 2005.
DOI : 10.1002/jcc.20035

M. Frisch, G. Trucks, H. Schlegel, G. Scuseria, M. Robb et al., Gaussian 03, Revision B.02, 2003.

U. Essmann, L. Perera, M. Berkowitz, T. Darden, H. Lee et al., A smooth particle mesh Ewald method, The Journal of Chemical Physics, vol.103, issue.19, pp.8577-8593, 1995.
DOI : 10.1063/1.470117

J. Ryckaert, G. Ciccotti, and H. Berendsen, Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, Journal of Computational Physics, vol.23, issue.3, pp.327-341, 1977.
DOI : 10.1016/0021-9991(77)90098-5

D. Lebard, J. Henin, R. Eckenhoff, M. Klein, and G. Brannigan, General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity, PLoS Computational Biology, vol.22, issue.5, p.22693438, 2012.
DOI : 10.1371/journal.pcbi.1002532.s008

URL : https://hal.archives-ouvertes.fr/hal-01498104

E. Yaffe, D. Fishelovitch, H. Wolfson, D. Halperin, and R. Nussinov, MolAxis: a server for identification of channels in macromolecules, Nucleic Acids Research, vol.36, issue.Web Server, pp.210-215, 2008.
DOI : 10.1093/nar/gkn223

D. Baptista-hon, T. Deeb, J. Lambert, J. Peters, and T. Hales, The Minimum M3-M4 Loop Length of Neurotransmitter-activated Pentameric Receptors Is Critical for the Structural Integrity of Cytoplasmic Portals, Journal of Biological Chemistry, vol.288, issue.30, pp.21558-21568, 2013.
DOI : 10.1074/jbc.M113.481689

R. Henchman, H. Wang, S. Sine, P. Taylor, and J. Mccammon, Asymmetric Structural Motions of the Homomeric ??7 Nicotinic Receptor Ligand Binding Domain Revealed by Molecular Dynamics Simulation, Biophysical Journal, vol.85, issue.5, pp.3007-3018, 2003.
DOI : 10.1016/S0006-3495(03)74720-1

O. Beckstein and M. Sansom, The influence of geometry, surface character, and flexibility on the permeation of ions and water through biological pores, Physical Biology, vol.1, issue.1, pp.42-52, 2004.
DOI : 10.1088/1478-3967/1/1/005

S. Murail, B. Wallner, J. Trudell, E. Bertaccini, and E. Lindahl, Microsecond Simulations Indicate that Ethanol Binds between Subunits and Could Stabilize an Open-State Model of a Glycine Receptor, Biophysical Journal, vol.100, issue.7, p.21463577, 2011.
DOI : 10.1016/j.bpj.2011.02.032

A. Taly, P. Corringer, T. Grutter, L. Prado, M. Karplus et al., Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors, Proceedings of the National Academy of Sciences, vol.103, issue.45, pp.16965-16970, 2006.
DOI : 10.1073/pnas.0607477103

URL : https://hal.archives-ouvertes.fr/pasteur-00161366

A. Hung, K. Tai, and M. Sansom, Molecular Dynamics Simulation of the M2 Helices within the Nicotinic Acetylcholine Receptor Transmembrane Domain: Structure and Collective Motions, Biophysical Journal, vol.88, issue.5, pp.3321-3333, 2005.
DOI : 10.1529/biophysj.104.052878

D. Mowrey, M. Cheng, L. Liu, D. Willenbring, X. Lu et al., Asymmetric Ligand Binding Facilitates Conformational Transitions in Pentameric Ligand-Gated Ion Channels, Journal of the American Chemical Society, vol.135, issue.6, pp.2172-2180, 2013.
DOI : 10.1021/ja307275v

C. Song and C. B. , Ion Conduction in Ligand-Gated Ion Channels: Brownian Dynamics Studies of Four Recent Crystal Structures, Biophysical Journal, vol.98, issue.3, pp.404-411, 2010.
DOI : 10.1016/j.bpj.2009.10.032

H. Wang, X. Cheng, P. Taylor, J. Mccammon, and S. Sine, Control of Cation Permeation through the Nicotinic Receptor Channel, PLoS Computational Biology, vol.124, issue.2, p.18282090, 2008.
DOI : 0022-1295(2004)124[0679:OTIOAF]2.0.CO;2

L. Sauguet, F. Poitevin, S. Murail, C. Renterghem, G. Moraga-cid et al., Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels, The EMBO Journal, vol.8, issue.5, pp.728-741, 2013.
DOI : 10.1073/pnas.1009313107

URL : https://hal.archives-ouvertes.fr/hal-01084646

X. Xiu, A. Hanek, and J. Wang, A Unified View of the Role of Electrostatic Interactions in Modulating the Gating of Cys Loop Receptors, M508635200 PMID, pp.41655-41666, 2005.
DOI : 10.1074/jbc.M508635200

S. Li, S. Huang, N. Bren, K. Noridomi, C. Dellisanti et al., Ligand-binding domain of an ??7-nicotinic receptor chimera and its complex with agonist, Nature Neuroscience, vol.269, issue.10, pp.1253-1259, 2011.
DOI : 10.1523/JNEUROSCI.0448-08.2008

M. Zouridakis, P. Giastas, E. Zarkadas, D. Chroni-tzartou, P. Bregestovski et al., Crystal structures of free and antagonist-bound states of human ??9 nicotinic receptor extracellular domain, Nature Structural & Molecular Biology, vol.8, issue.11, pp.976-980, 2014.
DOI : 10.1038/nsmb.2900

F. Gao, N. Bern, A. Little, H. Wang, S. Hansen et al., Curariform Antagonists Bind in Different Orientations to Acetylcholine-binding Protein, Journal of Biological Chemistry, vol.278, issue.25, pp.23020-23026, 2003.
DOI : 10.1074/jbc.M301151200

D. Yan and M. White, Spatial orientation of the antagonist granisetron in the ligand-binding site of the 5-HT3 receptor, Molecular Pharmacology, vol.68, issue.2, pp.365-71, 2005.
DOI : 10.1124/mol.105.011957

F. Zhu and G. Hummer, Pore opening and closing of a pentameric ligand-gated ion channel, Proceedings of the National Academy of Sciences, vol.107, issue.46, p.21041674, 2010.
DOI : 10.1073/pnas.1009313107

R. Howard, S. Murail, K. Ondricek, P. Corringer, and E. Lindahl, Structural basis for alcohol modulation of a pentameric ligand-gated ion channel, Proceedings of the National Academy of Sciences, vol.108, issue.29, pp.12149-12154, 2011.
DOI : 10.1073/pnas.1104480108

O. Schueler-furman, C. Wang, P. Bradley, K. Misura, and D. Baker, Progress in Modeling of Protein Structures and Interactions, Science, vol.310, issue.5748, pp.638-642, 2005.
DOI : 10.1126/science.1112160

F. Khalili-araghi, V. Jogini, V. Yarov-yarovoy, E. Tajkhorshid, B. Roux et al., Calculation of the Gating Charge for the Kv1.2 Voltage-Activated Potassium Channel, Biophysical Journal, vol.98, issue.10, pp.2189-2198, 2010.
DOI : 10.1016/j.bpj.2010.02.056

S. Lindert, J. Meiler, and J. Mccammon, Iterative Molecular Dynamics???Rosetta Protein Structure Refinement Protocol to Improve Model Quality, Journal of Chemical Theory and Computation, vol.9, issue.8, pp.3843-3847, 2013.
DOI : 10.1021/ct400260c

A. Raval, S. Piana, M. Eastwood, R. Dror, and D. Shaw, Refinement of protein structure homology models via long, all-atom molecular dynamics simulations, Proteins: Structure, Function, and Bioinformatics, vol.5, issue.Suppl 1, pp.2071-2079, 2012.
DOI : 10.1002/prot.24098

A. Shahsavar, J. Kastrup, E. Nielsen, J. Kristensen, M. Gajhede et al., Crystal Structure of Lymnaea stagnalis AChBP Complexed with the Potent nAChR Antagonist DH??E Suggests a Unique Mode of Antagonism, PLoS ONE, vol.7, issue.8, p.22927902, 2012.
DOI : 10.1371/journal.pone.0040757.s003

L. Sauguet, A. Shahsavar, F. Poitevin, C. Huon, A. Menny et al., Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation, Proceedings of the National Academy of Sciences, vol.111, issue.3, pp.966-971, 2014.
DOI : 10.1073/pnas.1314997111

M. Kinde, Q. Chen, M. Lawless, D. Mowrey, J. Xu et al., Conformational Changes Underlying Desensitization of the Pentameric Ligand-Gated Ion Channel ELIC, Structure, vol.23, issue.6, pp.995-1004, 2015.
DOI : 10.1016/j.str.2015.03.017

L. Maragliano, A. Fischer, E. Vanden-eijnden, and G. Ciccotti, String method in collective variables: Minimum free energy paths and isocommittor surfaces, The Journal of Chemical Physics, vol.125, issue.2, pp.24106-24120, 2006.
DOI : 10.1063/1.2212942

P. Bolhuis, D. Chandler, C. Dellago, P. Geissler, . Transition et al., : Throwing Ropes Over Rough Mountain Passes, in the Dark, Annual Review of Physical Chemistry, vol.53, issue.1, pp.291-318, 2002.
DOI : 10.1146/annurev.physchem.53.082301.113146

R. Czerminski and R. Elber, Self-avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems, International Journal of Quantum Chemistry, vol.4, issue.S24, pp.167-186, 1990.
DOI : 10.1002/qua.560382419

W. Kabsch, A solution for the best rotation to relate two sets of vectors, Acta Crystallographica Section A, vol.32, issue.5, pp.922-923, 1976.
DOI : 10.1107/S0567739476001873