Conformational dynamics of the nicotinic acetylcholine receptor channel: A 35-ns molecular dynamics simulation study

Journal of the American Chemical Society

Volumn 127, Issue 4, 2005, Pages 1291-1299

  Xu, Yechun ^a   Barrantes, Francisco J ^b   Luo, Xiaomin ^a   Chen, Kaixian ^a   Shen, Jianhua ^a   Jiang, Hualiang ^a,c  

^a SHANGHAI INSTITUTE OF MATERIA MEDICA   (China)

^b Instituto de Investigaciones Bioquimicas Bahia Blanca   (Argentina)

^c EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; ION SELECTIVE MEMBRANES; LIPIDS; MOLECULAR STRUCTURE; PROTEINS;

CONFORMATIONAL DYNAMICS; LIPID MOLECULES; RECEPTORS; TRANSMEMBRANE (TM);

MOLECULAR DYNAMICS;

DIPALMITOYLPHOSPHATIDYLCHOLINE; ION CHANNEL; MEMBRANE PROTEIN; NEUROTRANSMITTER; NICOTINIC RECEPTOR;

ARTICLE; CELL COMMUNICATION; CHANNEL GATING; CONFORMATION; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MEMBRANE POTENTIAL; MOLECULAR DYNAMICS; NEUROTRANSMISSION; PROTON NUCLEAR MAGNETIC RESONANCE; SIMULATION;

1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE; COMPUTER SIMULATION; ION CHANNEL GATING; ION CHANNELS; LIPID BILAYERS; MEMBRANES, ARTIFICIAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RECEPTORS, NICOTINIC; THERMODYNAMICS;

EID: 13644270375     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja044577i     Document Type: Article

References (47)

1. Barrantes, F. J. The nicotinic acetylcholine receptor: Current views and future trends; Springer-Verlag: Berlin/Heidelberg, Germany, and Landers Georgetown, TX, 1998.
2. Barrantes, F. J. Curr. Opin. Drug Discovery Dev. 2003, 6, 620-632.
3. Hucho, F.; Weise, C. Angew. Chem., Int. Ed. 2001, 40, 3100-3116.
4. Corringer, P.-J.; Le Novere, N.; Changeux, J.-P. Annu. Rev. Pharmacol. Toxicol. 2000, 40, 431-458.
5. Karlin, A. Nat. Rev. Neuronsci. 2002, 3, 102-114.
6. Unwin, N. J. Mol. Biol. 1993, 229, 1101-1124.
7. Ortells, M. O.; Lunt, G. G. Protein Eng. 1996, 9, 51-59.
8. Le Novere, N.; Corringer, P. J.; Changeux, J. P. Biophys. J. 1999, 76, 2329-2345.
9. Miyazawa, A.; Fujiyoshi, Y.; Unwin, N. Nature 2003, 423, 949-955.
10. Unwin, N. Nature 1995, 373, 37-43.
11. Kessel, A.; Shental-Bechor, D.; Haliloglu, T.; Ben-Tal, N. Biophys. J. 2003, 85, 3431-3444.
12. Kessel, A.; Haliloglu, T.; Ben-Tal, N. Biophys. J. 2003, 85, 3687-3695.
13. Sankararamakrishnan, R.; Adcock, C.; Sansom, M. S. P. Biophys. J. 1996, 71, 1659-1671.
14. Law, R. J.; Forrest, L. R.; Ranatunga, K. M.; Rocca, P. L.; Tieleman, D. P.; Sansom, M. S. P. Proteins: Struct. Funct. Genet. 2000, 39, 47-55.
15. Law, R. J.; Tieleman, D. P.; Sansom, M. S. P. Biophys. J. 2003, 84, 14-27.
16. Adcock, C.; Smith, G. R.; Sansom, M. S. P. Eur. Biophys. J. 2000, 29, 29-37.
17. Beckstein, O.; Biggin, P. C.; Bond, P.; Bright, J. N.; Domene, C.; Grottesi, A.; Holyoake, J.; Sansom, M. S. P. FEBS Lett. 2003, 555, 85-90.
18. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Interaction models for water in relation to protein hydration. In Intermolecular Forces; Pullman, B., Ed.; Reidel: Dordrecht, The Netherlands, 1981; pp 331-342.
19. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43-56.
20. Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306-317.
21. (a) van Gunsteren, W. F.; Berendsen, H. J. C. Gromos-87 manual; Biomos BV: Groningen, The Netherlands, 1987.
22. (b) van Buuren A. R.; Marrink, S. J.; Berendsen, H. J. C. J. Phys. Chem. 1993, 97, 9206-9212.
23. (c) van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hunenberger, P. H.; Kruger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulations: The GROMOS96 Manual and User Guide; Vdf Hochschulverlag AG an der ETH Zurich: Zurich, Switzerland, 1996.
24. Tieleman, D. P.; Sansom, M. S. P.; Berendsen, H. J. C. Biophys. J. 1999, 76, 40-49.
25. Berger, O.; Edholm, O.; Jahnig, F. Biophys. J. 1997, 72, 2002-2013.
26. Marrink, S. J.; Berger, O.; Tieleman, P.; Jahnig, F. Biophys. J. 1998, 74, 931-943.
27. Tieleman, D. P.; Berendsen, H. J. C.; Sansom, M. S. P. Biophys. J. 1999, 76, 1757-1769.
28. Hess, B.; Bekker, B.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463-1472.
29. Darden, T. A.; York, D. M.; Pedersen, L. G. J. Chem. Phys. 1993, 98, 10089-10092.
30. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8592.
31. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
32. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577-2637.
33. Smart, O. S.; Goodfellow, J. M.; Wallace, B. A. Biophys. J. 1993, 65, 2455-2460.
34. Smart, O. S.; Neduvelil, J. G.; Wang, X.; Wallace, B. A.; Sansom, M. S. P. J. Mol. Graphics 1996, 14, 354-360.
35. Smart, O. S.; Breed, J.; Smith, G. R.; Sansom, M. S. P. Biophys. J. 1997, 72, 1109-1126.
36. Methot, N.; Ritchie, B. D.; Blanton, M. P.; Baenziger, J. E. J. Biol. Chem. 2001, 276, 23726-23732.
37. Blanton, M. P.; Cohen, J. B. Biochemistry 1994, 33, 2859-2872.
38. Tamamizu, S.; Guzman, G. R.; Santiago, J.; Rojas, L. V.; McNamee, M. G.; Lasalde-Dominicci, J. A. Biochemistry 2000, 39, 4666-4673.
39. Methot, N.; Baenziger, J. E. Biochemistry 1998, 37, 14815-14822.
40. Corbin, J.; Methot, N.; Wang, H. H.; Baenziger, J. E.; Blanton, M. P. J. Biol. Chem. 1998, 273, 771-777.
41. Opella, S. J.; Marassi, F. M.; Gesell, J. J.; Valente, A. P.; Kim, Y.; Oblatt-Montal, M.; Montal, M. Nat. Struct. Biol. 1999, 6, 374-379.
42. Lugovskoy, A. A.; Maslennikov, I. V.; Utkin, Y. N.; Tsetlin, V. I.; Cohen, J. B.; Arseniev, A. S. Eur. J. Biochem. 1998, 255, 455-461.
43. Pashkov, V. S.; Maslennikov, I. V.; Tchikin, L. D.; Efremov, R. G.; Ivanov, V. T.; Arseniev, A. S. FEBS Lett. 1999, 457, 117-121.
44. Lee, Y. H.; Li, L.; Lasalde, J.; Rojas, L.; McNamee, M.; Ortiz-Miranda, S. I.; Pappone, P. Biophys. J. 1994, 66, 646-653.
45. Bouzat, C.; Bren, N.; Sine, S. M. Neuron 1994, 13, 1395-1402.
46. daCosta, C. J. B.; Ogrel, A. A.; McCardy, E. A.; Blanton, M. P.; Baenziger, J. E. J. Biol. Chem. 2002, 277, 201-208.
47. Labarca, C.; Nowak, M. W.; Zhang, H.; Tang, L.; Deshpande, P.; Lester, H. A. Nature 1995, 376, 514-516.