On the origin of fluorescence in bacteriophytochrome infrared fluorescent proteins

Journal of Physical Chemistry B

Volumn 114, Issue 46, 2010, Pages 15362-15369

  Samma, Alex A ^a   Johnson, Chelsea K ^a   Song, Shuang ^a   Alvarez, Samuel ^a   Zimmer, Marc ^a  

^a The Holleran Center for Community Action and Public Policy   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPUTER SIMULATION; FLUORESCENCE; MOLECULAR DYNAMICS; PROTEINS;

CONFORMATIONAL FREEDOM; CONFORMATIONAL SPACE; D-RINGS; DATABASE ANALYSIS; EXCITED-STATE PROTON TRANSFER; FLUORESCENT PROTEIN; HISTIDINE KINASE; MOLECULAR DYNAMICS SIMULATIONS; PROTEIN CAVITY; RHODOPSEUDOMONAS PALUSTRIS; TETRAPYRROLES;

EXCITED STATES;

EID: 78649595332     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp107119q     Document Type: Article

References (70)

1. Roda, A.; Guardigli, M.; Michelini, E.; Mirasoli, M. TrAC, Trends Anal. Chem. 2009, 28, 307
2. Shaner, N. C.; Patterson, G. H.; Davidson, M. W. J. Cell Sci. 2007, 120, 4247
3. Chapman, S.; Faulkner, C.; Kaiserli, E.; Garcia-Mata, C.; Savenkov, E. I.; Roberts, A. G.; Oparka, K. J.; Christie, J. M. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 20038
4. Rice, B. W.; Contag, C. H. Nat. Biotechnol. 2009, 27, 624
5. Jobsis, F. F. Science 1977, 198, 1264
6. Weissleder, R.; Ntziachristos, V. Nat. Med. 2003, 9, 123
7. Branchini, B. R.; Ablamsky, D. M.; Murtiashaw, M. H.; Uzasci, L.; Fraga, H.; Southworth, T. L. Anal. Biochem. 2007, 361, 253
8. Caysa, H.; Jacob, R.; Muther, N.; Branchini, B.; Messerle, M.; Soling, A. Photochem. Photobiol. Sci. 2009, 8, 52
9. Fischer, A. J.; Lagarias, J. C. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 17334
10. Kredel, S.; Oswald, F.; Nienhaus, K.; Deuschle, K.; Roecker, C.; Wolff, M.; Heilker, R.; Nienhaus, G. U.; Wiedenmann, J. PLoS One 2009, 4 e4391
11. Shcherbo, D.; Murphy, C. S.; Ermakova, G. V.; Solovieva, E. A.; Chepurnykh, T. V.; Shcheglov, A. S.; Verkhusha, V. V.; Pletnev, V. Z.; Hazelwood, K. L.; Roche, P. M.; Lukyanov, S.; Zaraisky, A. G.; Davidson, M. W.; Chudakov, D. M. Biochem. J. 2009, 418, 567
12. Suto, K.; Masuda, H.; Takenaka, Y.; Tsuji, F. I.; Mizuno, H. Genes Cells 2009
13. Shu, X. K.; Royant, A.; Lin, M. Z.; Aguilera, T. A.; Lev-Ram, V.; Steinbach, P. A.; Tsien, R. Y. Science 2009, 324, 804
14. Nienhaus, G. U.; Wiedenmann, J. ChemPhysChem 2009, 10, 1369
15. Wagner, J. R.; Zhang, J. R.; von Stetten, D.; Guenther, M.; Murgida, D. H.; Mroginski, M. A.; Walker, J. M.; Forest, K. T.; Hildebrandt, P.; Vierstra, R. D. J. Biol. Chem. 2008, 283, 12212
16. Rockwell, N. C.; Su, Y. S.; Lagarias, J. C. Annu. Rev. Plant Biol. 2006, 57, 837
17. Quail, P. H. Nat. Rev. Mol. Cell Biol. 2002, 3, 85
18. Zimmer, M. Non-retinal chromophoric proteins. In Cis-Trans Isomerizaion in Biochemistry; Duvage, C., Ed.; Wiley-VCH: Weinheim, Germany, 2006; pp 77.
19. Kneip, C.; Hildebrandt, P.; Schlamann, W.; Braslavsky, S. E.; Mark, F.; Schaffner, K. Biochemistry 1999, 38, 15185
20. von Stetten, D.; Seibeck, S.; Michael, N.; Scheerer, P.; Mroginski, M. A.; Murgida, D. H.; Krauss, N.; Heyn, M. P.; Hildebrandt, P.; Borucki, B.; Lamparter, T. J. Biol. Chem. 2007, 282, 2116
21. Andel, F.; Lagarias, J. C.; Mathies, R. A. Biochemistry 1996, 35, 15997
22. Mizutani, Y.; Tokutomi, S.; Kitagawa, T. Biochemistry 1994, 33, 153
23. Rudiger, W.; Thummler, F.; Cmiel, E.; Schneider, S. Proc. Natl. Acad. Sci. U.S.A.: Biol. Sci. 1983, 80, 6244
24. Toh, K. C.; Stojkovic, E. A.; van Stokkum, I. H. M.; Moffat, K.; Kennis, J. T. M. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 9170
25. Silva, G. L.; Ediz, V.; Yaron, D.; Armitage, B. A. J. Am. Chem. Soc. 2007, 129, 5710
26. Olsen, S.; McKenzie, R. H. J. Chem. Phys. 2009, 131
27. Yang, J. S.; Huang, G. J.; Liu, Y. H.; Peng, S. M. Chem. Commun. 2008, 1344
28. Tonge, P. J.; Meech, S. R. J. Photochem. Photobiol., A: Chem. 2009, 205, 1
29. Olsen, S.; Smith, S. C. J. Am. Chem. Soc. 2007, 129, 2054
30. Olsen, S.; McKenzie, R. H. J. Chem. Phys. 2009, 130
31. Maddalo, S. L.; Zimmer, M. Photochem. Photobiol. 2006, 82, 367
32. Fang, C.; Frontiera, R. R.; Tran, R.; Mathies, R. A. Nature 2009, 462, 200
33. 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
34. Shelley, J. C.; Cholleti, A.; Frye, L. L.; Greenwood, J. R.; Timlin, M. R.; Uchimaya, M. Epik: A Software Program for p K (a) Prediction and Protonation State Generation for Drug-like Molecules; University of California San Francisco: San Francisco, CA, 2006.
35. Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440
36. Kaminski, S.; Daminelli, G.; Mroginski, M. A. J. Phys. Chem. B 2009, 113, 945
37. Chang, G.; Guida, W. C.; Still, W. C. J. Am. Chem. Soc. 1989, 111, 4379
38. Saunders, M.; Houk, K.; Wu, Y.-D.; Still, W.; Lipton, M.; Chang, G.; Guida, W. J. Am. Chem. Soc. 1990, 112, 1419
39. Bartol, J.; Comba, P.; Melter, M.; Zimmer, M. J. Comput. Chem. 1999, 20, 1549
40. Kolossvary, I.; Keseru, G. M. J. Comput. Chem. 2001, 22, 21
41. Keseru, G. M.; Kolossvary, I. J. Am. Chem. Soc. 2001, 123, 12708
42. Bowers, K. J. C., E.; Xu, H.; Dror, R. O.; Eastwood, M. P.; Gregersen, B. A.; Klepeis, J. L.; Kolossvary, I.; Moraes, M. A.; Sacerdoti, F. D.; Salmon, J. K.; Shan, Y.; Shaw, D. E. Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters. In Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (SC06), Tampa, FL, Nov 11-17, 2006; ACM Press: New York, 2006.
43. The convex hull or convex envelope for a set of points X in a real vector space V is the minimal convex set containing X. The convex hull of the and τ graphs can be visualized as the area encompassed by an imaginary elastic band that is stretched to surround all the data points.
44. Bruno, I. J.; Cole, J. C.; Edgington, P. R.; Kessler, M.; Macrae, C. F.; McCabe, P.; Pearson, J.; Taylor, R. Acta Crystallogr., Sect. B: Struct. Sci. 2002, 58, 389
45. Shenkin, P.; McDonald, Q. J. Comput. Chem. 1994, 15, 899
46. Kabsch, W. Acta Crystallogr., Sect. A 1976, 32, 922
47. Kabsch, W. Acta Crystallogr., Sect. A 1978, 34, 827
48. Kuhn, D.; Weskamp, N.; Schmitt, S.; Hullermeier, E.; Klebe, G. J. Mol. Biol. 2006, 359, 1023
49. Schmitt, S.; Hendlich, M.; Klebe, G. Angew. Chem., Int. Ed. 2001, 40, 3141
50. Hendlich, M.; Bergner, A.; Gunther, J.; Klebe, G. J. Mol. Biol. 2003, 326, 607
51. Gunther, J.; Bergner, A.; Hendlich, M.; Klebe, G. J. Mol. Biol. 2003, 326, 621
52. Yang, X.; Stojkovic, E. A.; Kuk, J.; Moffatt, K. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 12571
53. Allen, F. H. Acta Crystallogr., Sect. B: Struct. Sci. 2002, 58, 380
54. Kratky, C.; Jorde, C.; Falk, H.; Thirring, K. Tetrahedron 1983, 39, 1859
55. Kratky, C.; Falk, H.; Grubmayr, K. Monatsh. Chem. 1985, 116, 745
56. Kratky, C.; Falk, H.; Grubmayr, K.; Zrunek, U. Monatsh. Chem. 1985, 116, 761
57. Wagner, U.; Kratky, C.; Falk, H.; Woss, H. Monatsh. Chem. 1991, 122, 749
58. Paolesse, R.; Froiio, A.; Nardis, S.; Mastroianni, M.; Russo, M.; Nurco, D. J.; Smith, K. M. J. Porphyrins Phthalocyanines 2003, 7, 585
59. Yamauchi, T.; Mizutani, T.; Wada, K.; Horii, S.; Furukawa, H.; Masaoka, S.; Chang, H. C.; Kitagawa, S. Chem. Commun. 2005, 1309
60. Balch, A. L.; Koerner, R.; Olmstead, M. M.; Mazzanti, M.; Safari, N.; Stclaire, T. J. Chem. Soc., Chem. Commun. 1995, 643
61. Boyd, S. Chem. World 2007, 4, 67
62. Crusats, J.; Benitez, P.; Farrera, J. A.; Rubires, R.; Ribo, J. M. Monatsh. Chem. 1998, 129, 535
63. Schultz, L. W.; Liu, L. Y.; Cegielski, M.; Hastings, J. W. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 1378
64. Megley, C. M.; Dickson, L. A.; Maddalo, S. L.; Chandler, G. J.; Zimmer, M. J. Phys. Chem. B 2009, 113, 302
65. Liu, R. S. H. Acc. Chem. Res. 2001, 34, 555
66. Imamoto, Y.; Kuroda, T.; Kataoka, M.; Shevyakov, S.; Krishnamoorthy, G.; Liu, R. S. H. Angew. Chem., Int. Ed. 2003, 42, 3630
67. Fuss, W.; Kosmidis, C.; Schmid, W. E.; Trushin, S. A. Angew. Chem., Int. Ed. 2004, 43, 4178
68. Yang, L. Y.; Liu, R. S. H.; Boarman, K. J.; Wendt, N. L.; Liu, J. J. Am. Chem. Soc. 2005, 127, 2404
69. Altoe, P.; Climent, T.; De Fusco, G. C.; Stenta, M.; Bottoni, A.; Serrano-Andres, L.; Merchan, M.; Orlandi, G.; Garavelli, M. J. Phys. Chem. B 2009, 113, 15067
70. Filippi, C.; Ziccheddu, M.; Buda, F. J. Chem. Theory Comput. 2009, 5, 2074