Computational study of the absorption spectra of green fluorescent protein mutants

Biopolymers

Volumn 85, Issue 3, 2007, Pages 253-263

  Patnaik, Soumya S ^a   Trohalaki, Steven ^a   Naik, Rajesh R ^a   Stone, Morley O ^a   Pachter, Ruth ^a  

^a AIR FORCE RESEARCH LABORATORY   (United States)

Author keywords

Green fluorescent protein mutants; Molecular dynamics; Time dependent density functional theory

Indexed keywords

COMPUTER SIMULATION; MEDICAL COMPUTING; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; MUTAGENESIS; QUANTUM THEORY;

GREEN FLUORESCENT PROTEIN (GFP); GREEN FLUORESCENT PROTEIN MUTANTS; PROTEIN MUTANTS; TIME-DEPENDENT DENSITY FUNCTIONAL THEORY;

PROTEINS;

GREEN FLUORESCENT PROTEIN; OXYGEN;

ABSORPTION SPECTROSCOPY; ARTICLE; CALCULATION; CHEMICAL STRUCTURE; CHROMATOPHORE; HYDROGEN BOND; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; PROTEIN ANALYSIS; QUANTUM MECHANICS; TEMPERATURE; TIME;

COMPUTER SIMULATION; FLUORESCENCE; GREEN FLUORESCENT PROTEINS; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR STRUCTURE; MUTANT PROTEINS; MUTATION; SERINE; SPECTROPHOTOMETRY;

EID: 33847263415     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.20642     Document Type: Article

References (64)

1. Tsien, R. Y. Annu Rev Biochem 1998, 67, 509-544.
2. Tsien, R. Y. Nat Rev Mol Cell Biol 2003, 4, SS16-SS21.
3. Shaner, N. C.; Steinbach, P. A.; Tsien, R. Y. Nat Methods 2005, 2, 905-909.
4. Zimmer, M. Chem Rev 2002, 102, 759-781.
5. Creemers, T. M. H.; Lock, A. J.; Subramaniam, V.; Jovin, T. M.; Volker, S. Nat Struct Biol 1999, 6, 557-560.
6. Weber, W.; Helms, V.; McCammom, J. A.; Langhoff, P. W. Proc Natl Acad Sci USA 1999, 96, 6177-6182.
7. Chattoraj, M.; King, B. A.; Bublitz, G. U.; Boxer, S. G. Proc Natl Acad Sci USA 1996, 93, 8362-8367.
8. Lossau, H.; Kummer, A.; Heinecke, R.; Pollinger-Dammer, F.; Kompa, C.; Bieser, G.; Jonsson, T.; Silva, C. M.; Yang, M. M.; Youvan, D. C.; Michel-Beyerle, M. E. Chem Phys 1996, 213, 1-16.
9. Winkler, K.; Lindner, J. R.; Subramaniam, V.; Jovin, T. M.; Vohringer, P. Phys Chem Chem Phys 2002, 4, 1072-1081.
10. Martinez, T. J. Acc Chem Res 2006, 39, 119-126.
11. Huppert, D.; Leiderman, P.; Ben-Ziv, M.; Genosar, L.; Cohen, L. J Phys Chem B 2005, 109, 4241-4251.
12. Lill, M. A.; Helms, V. Proc Natl Acad Sci USA 2002, 99, 2778-2781.
13. Yang, F.; Moss, L. G.; Phillips, J. G. N. Nat Biotechnol 1996, 14, 1246-1251.
14. Brejc, K.; Sixma, T. K.; Kitts, P. A.; Kain, S. R.; Tsien, R. Y.; Ormo, M.; Remington, S. J. Proc Natl Acad Sci USA 1997, 94, 2306-2311.
15. Ormo, M.; Cubitt, A. B.; Kallio, K.; Gross, L. A.; Tsien, R. Y.; Remington, S. J. Science 1996, 273, 1392-1395.
16. Helms, V.; Straatsma, T. P.; McCammon, J. A. J Phys Chem B 1999, 103, 3263-3269.
17. Reuter, N.; Lin, H.; Thiel, W. J Phys Chem B 2002, 106, 6310-6321.
18. Nifosi, R.; Tozzini, V. Proteins: Struct Funct Genet 2003, 51, 378-389.
19. Patnaik, S. S.; Trohalaki, S.; Pachter, R. Biopolymers 2004, 75, 441-452.
20. Heim, R.; Cubitt, A. B.; Tsien, R. Y. Nature 1995, 373, 663-664.
21. Cormack, B. P.; Valdivia, R. H.; Falkow, S. Gene 1996, 173, 33-38.
22. Inouye, S.; Ogawa, H.; Yasuda, K.; Umesono, K.; Tsuji, F. I. Gene 1997, 189, 159-162.
23. Delagrave, S.; Hawtin, R. E.; Silva, C. M.; Yang, M. M.; Youvan, D. C. Biotechnology 1995, 13, 151-154.
24. Abbruzzetti, S.; Grandi, E.; Viappiani, C.; Bologna, S.; Campanini, B.; Raboni, S.; Bettati, S.; Mozzarelli, A. J Am Chem Soc 2005, 127, 626-635.
25. Voityuk, A. A.; Michel-Beyerle, M.-E.; Rosch, N. Chem Phys 1998, 231, 13-25.
26. Voityuk, A. A.; Michel-Beyerle, M.-E.; Rosch, N. Chem Phys Lett 1997, 272, 162-167.
27. Voityuk, A. A.; Kumer, A. D.; Michel-Beyerle, M.-E.; Rosch, N. Chem Phys 2001, 269, 83-91.
28. Laino, T.; Nifosi, R.; Tozzini, V. Chem Phys 2004, 298, 17-28.
29. Sinicropi, A.; Andruniow, T.; Ferre, N.; Basosi, R.; Olivucci, M. J Am Chem Soc 2005, 127, 11534-11535.
30. Helms, V.; Winstead, C.; Langhoff, P. W. J Mol Struct (Theochem) 2000, 506, 179-189.
31. Das, A. K.; Hasegawa, J.-Y.; Miyahara, T.; Ehara, M.; Nakatsuji, H. J Comput Chem 2003, 24, 1421-1431.
32. Martin, M. E.; Negri, F.; Olivucci, M. J Am Chem Soc 2004, 126, 5452-5464.
33. Zhang, R.; Nguyen, M. T.; Ceulemans, A. Chem Phys Lett 2005, 404, 250-256.
34. Nemukhin, A. V.; Topol, I. A.; Burt, S. K. J Chem Theory Comput 2006, 2, 292-299.
35. Andersen, L. H.; Lapierre, A.; Nielsen, S. B.; Nielsen, I. B.; Pedersen, S. U.; Pedersen, U. V.; Tomita, S. Eur Phys J D 2002, 20, 597-600.
36. Nielsen, S. B.; Lapierre, A.; Anderson, J. U.; Pedersen, U. V.; Tomita, S.; Andersen, L. H. Phys Rev Lett 2001, 87, 228102-228104.
37. Lopez, X.; Marques, M. A. L.; Castro, A.; Rubio, A. J Am Chem Soc 2005, 127, 12329-12337.
38. Demachy, I.; Ridard, J.; Laguitton-Pasquier, H.; Durnerin, E.; Vallverdu, G.; Archirel, P.; Levy, B. J Phys Chem B 2005, 109, 24121-24133.
39. Marques, M. A. L.; Lopez, X.; Varsano, D.; Castro, A.; Rubio, A. Phys Rev Lett 2003, 90, 258101-258104.
40. Heim, R.; Praser, D. C.; Tsien, R. Y. Proc Natl Acad Sci USA 1994, 91, 12501-12504.
41. Tozzini, V.; Pellegrini, V.; Beltram, F. In Handbook of Organic Photochemistry and Photobiology, Chapter 139; Horsphool, W. M.; Lenci, F., Eds.; CRC Press: Washington, DC, 2003, 4.
42. Jung, G.; Wiehler J.; Zumbusch, A. Biophys J 2005, 88, 1932-1947.
43. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res 2000, 28, 235-242.
44. InsightII. Accelrys: San Diego.
45. CHARMm is a commercial distribution of CHARMM through Accelrys.
46. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187-217.
47. Momany, F. A.; Rone, R. J Comput Chem 1992, 13, 888-900.
48. Maseras, F.; Morokuma, K. J Comput Chem 1995, 16, 1170-1179.
49. Frisch, M. J.; Klene, M.; Robb, M. A.; Blancafort, L. Gaussian 03, Revision B. 05; Gaussian Inc.: Pittsburgh, PA, 2003.
50. Becke, A. D. J Chem Phys 1993, 98, 5648-5652.
51. Becke, A. D. Phys Rev A 1988, 38, 3098-3100.
52. Lee, C.; Yang, W.; Parr, R. G. Phys Rev B 1988, 37, 785-789.
53. Rappé, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A., III; Skiff, W. M. J Am Chem Soc 1992, 114, 10024-10035.
54. Weber, I. T.; Harrison, R. W. Protein Eng 1999, 12, 469-474.
55. Glendening, E. D.; Reed, A. E.; Carpenter, J. E.; Weinhold, F. NBO Version 3.1.
56. Runge, E.; Gross, E. K. U. Phys Rev Lett 1984, 52, 997-1000.
57. Stratmann, R. E.; Scuseria, G. E.; Frisch, M. J. J Chem Phys Lett 1998, 109, 8218-8224.
58. Dreuw, A.; Head-Gordon, M. Chem Rev 2005, 105, 4009-4037.
59. Burke, K.; Werschnik, J.; Gross, E. K. U. J Chem Phys 2005, 123, 062206-062209.
60. Nazeeruddin, M. K.; De Angelis, F.; Fantacci, S.; Selloni, A.; Viscardi, G.; Liska, P.; Ito, S.; Takeru, B.; Gratzel M. J Am Chem Soc 2005, 127, 16835-16847.
61. Kurimoto, M.; Subramony, P.; Gurney, R. W.; Lovell, S.; Chmielewski, J.; Kahn, B. J Am Chem Soc 1999, 121, 6952-6953.
62. Toniolo, A.; Olsen, S.; Manohar, L.; Martinez, T. J. In Femtochemistry and Femtobiology: Ultrafast Events in Molecular Science; Martin, M.; Hynes, J. T., Eds.; Elsevier: Amsterdam, 2004; pp 425-432.
63. Baffour-Awuah, N. Y.; Zimmer, M. Chem Phys 2004, 303, 7-11.
64. Demirel, M. C., Private Communication.