Molecular dynamic simulation of the Kv1.2 voltage-gated potassium channel in open and closed state conformations

Journal of Physical Chemistry B

Volumn 112, Issue 51, 2008, Pages 16966-16974

  Han, Ming ^a   Zhang, John Z H ^b,c  

^a NANJING UNIVERSITY   (China)

^b EAST CHINA NORMAL UNIVERSITY   (China)

^c NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMICS; FLOW INTERACTIONS; HYDRATES; LIPIDS; MOLECULAR DYNAMICS; QUANTUM CHEMISTRY; SENSORS;

AZIMUTHAL ROTATIONS; COMPARATIVE ANALYSIS; CONTACT AREAS; FORCE FIELDS; GATING MECHANISMS; LIPID MEMBRANES; MOLECULAR DYNAMIC SIMULATIONS; POTASSIUM CHANNELS; POTASSIUM ION CHANNELS; PROTEIN STABILITIES; S4 SEGMENTS; SALT BRIDGES; STATE MODELS; STRUCTURE AND DYNAMICS; VOLTAGE SENSORS;

CRYSTAL STRUCTURE;

EID: 58149161510     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp807905p     Document Type: Article

References (46)

1. Hille, B. Ion Channels of Excitable Membranes, 3rd ed.; Sinauer: Sunderland, MA, 2001.
2. Bezanilla, F. Physiol. Rev. 2000, 80, 555.
3. Sigworth. F. Q. Rev. Biophys. 1994, 27, 1.
4. Yellen, G. Nature 2002, 419, 35.
5. Tombola, F.; Pathak, M. M.; lsacoff, E. Y. Annu. Rev. Cell Dev. Biol. 2006, 22, 23.
6. Sansom, M. S. P.; Shrivastava, I. H.; Bright. J. N.; Tate, J.; Capener, C. E.; Biggin, P. C. Biochim. Biophvs. Acta 2002, 1565, 294.
7. Roux, B. Curr. Opin. Struct. Biol. 2002, 12, 182.
8. Ash, W. L.; Zlomislie, M. R.; Oloo, E. O.; Tieleman. D. P. Biochim. Biophys. Acta 2004, 1666, 158.
9. Gumbart, J.; Wang, Y.; Aksimentiev, A.; Tajkhorshid, E.; Schulten, K. Curr. Opin. Struct. Biol. 2005, 15, 423.
10. Roux, B.; Schulten, K. Structure 2004, 12, 1343.
11. Tieleman, D. P. Computer simulations of transport through membranes: passive diffusion, pores, channels and transporters. Proc. Aust. Physiol. Soc. 2006, 37, 15.
12. Deol, S. S.; Domene, C.; Bond, P. J.; Sansom, M. S. P. Biophys. J. 2006, 90, 822.
13. Jiang, Y.; Lee, A.; Chen. J.; Ruta, V.; Cadene, M.; Chait, B. T.; MacKinnon. R. Nature 2003, 423, 33.
14. Long, S. B.; Campbell, E. B.; MacKinnon, R. Science 2005, 309. 897.
15. Treptow, W.; Tarek, M. Biophys. J. 2006, 90, L64.
16. Jogmi, V.; Roux, B. Biophys. J. 2007, 93, 3070.
17. Pathak, M. M.; Yarov-Yarovoy, V.; Agarwal, G.; Roux. B.; Barth, P.; Kohout, S.; Tombola, F.; lsacoff, E. Y. Neuron 2007, 56, 124.
18. Kandt, C.; Ash, W. L.; Tieleman, D. P. Methods 2007, 41, 475.
19. Lindahl, E.; Hess, B.; van der Spoel. D. J. Mol. Model. 2001. 7, 306.
20. van der Spoel, D.; Lindahl, E.; Hess, B.; van Buuren, A. R.; Apol, E.; Meulenhoff, P. J.; Tieleman, D. P.; Sijbers, A. L. T. M.; Feenstra, K. A.; van Drunen, R.; Berendsen, H. J. C. Gromacs User Manual, version 3.3; 2005 (www.gromacs.org).
21. Aqvist, J.; Luzhkov, V. Nature 2000, 404, 881.
22. Berger, O.; Edholm, O.; Jahnig, F. Biophys. J. 1997, 72, 2002.
23. 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.; D. Reidel Publishing Company: Dordrecht, The Netherlands, 1981; p 331.
24. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089.
25. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684.
26. Nosé, S. Mol. Phys. 1984, 52, 255.
27. Hoover, W. G. Phys. Rev. A 1985, 31, 1695.
28. Parrinello, M.; Rahman. A. J. Appl. Physiol. 1981, 52, 7182.
29. Hess, B.; Bekker, H.; Berendsen, H. J. C; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463.
30. Mivamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952.
31. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577.
32. Ozdirekcan. S.; Etchebest, C.; Killian, J. A.; Euchs, P. F. J. J. Am. Chem. Soc. 2007, 129, 15174.
33. Sanner, M. F.; Olson. A. J.; Spehner, J. C. Biopolymers 1996. 38. 305.
34. Humphrey, W.: Dalke, A.; Schulten. K. J. Mol. Graphics 1996, 14, 33.
35. Long, S. B.; Tao, X.; Campbell, E. B.; MacKinnon. R. Nature 2007, 450, 376.
36. Seoh. S. A.; Sigg, D.; Papazian, D. M.; Bezanilla. F. Neuron 1996. 16, 1159.
37. Aggarwal, S. K.; MacKinnon. R. Neuron 1996. 16, 1169.
38. Sands, Z. A.; Sansom, M. S. P. Structure 2007, 15, 235.
39. Ahem, C. A.; Horn, R. Trends Neurosci. 2004, 27, 303.
40. Durell, S. R.; Shrivastava. I. H.; Guy, H. R. Biophys. J. 2004, 87, 2116.
41. Lecar, H.; Larsson, H. P.; Grabe, M. Biophys. J. 2003, 85, 2854.
42. Jiang, Y.; Ruta. V.; Chen. J.; Lee. A.; MacKinnon. R. Nature 2003, 423, 42.
43. Ruta, V.: Chen, J.; MacKinnon, R. Cell 2005. 123, 463.
44. Long, S. B.; Campbell. E. B.; MacKinnon, R. Science 2005, 309. 903.
45. Eisenhaber, F.; Lijnzaad, P.; Argos, P.; Sander, C; Scharf, M. J. Comput. Chem. 1995, 16, 273.
46. Greer, J.; Bush, B. L. Proc. Natl. Acad. Sci. U.S.A. 1978, 75, 303.