Structural and spectral characterizations of C1C2 channelrhodopsin and its mutants by molecular simulations

Chemical Physics Letters

Volumn 556, Issue , 2013, Pages 266-271

  Kamiya, Motoshi ^a   Kato, Hideaki E ^b   Ishitani, Ryuichiro ^b   Nureki, Osamu ^b   Hayashi, Shigehiko ^a  

^a KYOTO UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION ENERGIES; ABSORPTION MAXIMA; BIOTECHNOLOGICAL TOOLS; CHANNEL GATING; ELECTROSTATIC CONTRIBUTIONS; ENERGY CALCULATION; ENGINEERING DESIGN; ION CHANNEL; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SIMULATIONS; PROTEIN STRUCTURES; SITE-SPECIFIC; SPECTRAL CHARACTERIZATION; SPECTRAL PROPERTIES; STRUCTURAL MODELS;

HYDROGEN; HYDROGEN BONDS; MODEL STRUCTURES; MOLECULAR DYNAMICS; SPECTRUM ANALYZERS; X RAY CRYSTALLOGRAPHY;

PROTEINS;

EID: 84872281071     PISSN: 00092614     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cplett.2012.11.066     Document Type: Article

References (48)

1. G. Nagel, D. Ollig, M. Fuhrmann, S. Kateriya, A.M. Musti, E. Bamberg, and P. Hegemann Science 296 2002 2395
2. G. Nagel Proc. Natl. Acad. Sci. USA 100 2003 13940
3. K. Deisseroth, G. Feng, A.K. Majewska, G. Miesenböck, A. Ting, and M.J. Schnitzer J. Neurosci. 26 2006 10380
4. S. Kleinlogel Nat. Methods 8 2011 1083
5. J.Y. Lin, M.Z. Lin, P. Steinbach, and R.Y. Tsien Biophys. J. 96 2009 1803
6. F. Zhang Nat. Neurosci. 11 2008 631
7. E.G. Govorunova, E.N. Spudich, C.E. Lane, O.A. Sineshchekov, and J.L. Spudich mBio 2 2011 e00115
8. K. Welke, J.S. Frähmcke, H.C. Watanabe, P. Hegemann, and M. Elstner J. Phys. Chem. B 115 2011 15119
9. H.C. Watanabe J. Biol. Chem. 287 2012 7456
10. H. Wang J. Biol. Chem. 284 2009 5685
11. H.E. Kato Nature 482 2012 369
12. O. Yizhar Nature 477 2011 171
13. M. Prigge, F. Schneider, S.P. Tsunoda, C. Shilyansky, J. Wietek, K. Deisseroth, and P. Hegemann J. Biol. Chem. 287 2012 31804
14. M. Hoffmann J. Am. Chem. Soc. 128 2006 10808
15. K. Shimono, M. Kitami, M. Iwamoto, and N. Kamo Biophys. Chem. 87 2000 225
16. E. Ritter, K. Stehfest, A. Berndt, P. Hegemann, and F.J. Bartl J. Biol. Chem. 283 2008 35033
17. J. Gumbart, L.G. Trabuco, E. Schreiner, E. Villa, and K. Schulten Structure 17 2009 1453
18. J.C. Phillips J. Comput. Chem. 26 2005 1781
19. A.D. MacKerell Jr., M. Feig, and C.L. Brooks III J. Comput. Chem. 25 2004 1400
20. A.D. MacKerell Jr. J. Phys. Chem. B 102 1998 3586
21. S.E. Feller, G. Gawrisch, and A.D. MacKerell Jr. J. Am. Chem. Soc. 124 2002 318
22. M. Schlenkrich, J. Brickmann, A.D. MacKerell Jr., and M. Karplus Biological Membranes: A Molecular Perspective from Computation and Experiment 1996 Birkhäuser Switzerland
23. D. Beglov, and B. Roux J. Chem. Phys. 100 1994 9050
24. E. Tajkhorshid, B. Paizs, and S. Suhai J. Phys. Chem. B 101 1997 8021
25. E. Tajkhorshid, and S. Suhai J. Phys. Chem. B 103 1999 5581
26. E. Tajkhorshid, J. Baudry, K. Schulten, and S. Suhai Biophys. J. 78 2000 683
27. M. Nina, B. Roux, and J.C. Smith Biophys. J. 68 1995 25
28. J. Baudry, S. Crouzy, B. Roux, and J.C. Smith J. Chem. Inf. Comput. Sci. 37 1997 1018
29. S. Hayashi, and I. Ohmine J. Phys. Chem. B 104 2000 10678
30. S. Hayashi, E. Tajkhorshid, E. Pebay-Peyroula, A. Royant, E.M. Landau, J. Navarro, and K. Schulten J. Phys. Chem. B 105 2001 10124
31. U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen J. Chem. Phys. 103 1995 8577
32. M.W. Schmidt J. Comput. Chem. 14 1993 1347
33. K. Hirao Chem. Phys. Lett. 190 1992 374
34. H. Nakano J. Chem. Phys. 99 1993 7983
35. L. Ren Biochemistry 40 2001 13906
36. C.I. Bayly, P. Cieplak, W. Cornell, and P.A. Kollman J. Phys. Chem. 97 1993 10269
37. W. Humphrey, A. Dalke, and K. Schulten J. Mol. Graphics 14 1996 33
38. K. Feldbauer, D. Zimmermann, V. Pintschovius, J. Spitz, C. Bamann, and E. Bamberg Proc. Natl. Acad. Sci. USA 106 2009 12317
39. M. Nack, I. Radu, M. Gossing, C. Bamann, E. Bamberg, G.F. von Mollard, and J. Heberle Photochem. Photobiol. Sci. 9 2010 194
40. S. Hayashi, E. Tajkhorhsid, and K. Schulten Biophys. J. 83 2002 1281
41. L.A. Gunaydin, O. Yizhar, A. Berndt, V.S. Sohal, K. Deisseroth, and P. Hegemann Nat. Neurosci. 13 2010 387
42. M. Wanko J. Phys. Chem. B 109 2005 3606
43. K. Fujimoto, S. Hayashi, J. Hasegawa, and H. Nakatsuji J. Chem. Theory Comput. 3 2007 605
44. H. Houjou, Y. Inoue, and M. Sakurai J. Phys. Chem. B 105 2001 867
45. A. Kianianmomeni, K. Stehfest, G. Nematollahi, P. Hegemann, and A. Hallmann Plant Physiol. 151 2009 347
46. K. Shimono, T. Hayashi, Y. Ikeura, Y. Sudo, M. Iwamoto, and N. Kamo J. Biol. Chem. 278 2003 23882
47. T. Marti, H. Otto, T. Mogi, S.J. Rösselet, M.P. Heyn, and H.G. Khorana J. Biol. Chem. 266 1991 6919
48. T. Kosugi, and S. Hayashi J. Chem. Theory Comput. 8 2012 322