Light-induced structural changes in the active site of the BLUF domain in AppA by Raman spectroscopy

Journal of Physical Chemistry B

Volumn 109, Issue 25, 2005, Pages 12620-12626

  Unno, Masashi ^a   Sano, Ryota ^a   Masuda, Shinji ^b,c   Ono, Taka Aki ^b   Yamauchi, Seigo ^a  

^a TOHOKU UNIVERSITY   (Japan)

^b INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

^c TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITES; SIGNALING STATES; STRUCTURAL CHANGES; VIBRATIONAL SPECTRUM;

ACTIVATION ENERGY; CONFORMATIONS; HYDROGEN BONDS; INFRARED RADIATION; PROTEINS; RAMAN SPECTROSCOPY; ULTRAVIOLET RADIATION;

AROMATIC COMPOUNDS;

APPA PROTEIN, RHODOBACTER SPHAEROIDES; BACTERIAL PROTEIN; FLAVOPROTEIN; ISOALLOXAZINE; RIBOFLAVIN DERIVATIVE;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; HYDROGEN BOND; LIGHT; METABOLISM; PROTEIN MOTIF; RAMAN SPECTROMETRY; VIBRATION;

AMINO ACID MOTIFS; BACTERIAL PROTEINS; BINDING SITES; FLAVINS; FLAVOPROTEINS; HYDROGEN BONDING; LIGHT; MODELS, MOLECULAR; MOLECULAR CONFORMATION; SPECTRUM ANALYSIS, RAMAN; VIBRATION;

EID: 22744445702     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0522664     Document Type: Article

References (30)

1. van der Horst, M. A.; Hellingwerf, K. J. Acc. Chem. Res. 2004, 37, 13-20.
2. Salomon, M.; Christie, J. M.; Knieb, E.; Lempert, U.; Briggs, W. R. Biochemistry 2000, 39, 9401-9410.
3. Gomelsky, M.; Klug, G. Trends Biochem. Sci. 2002, 27, 497-500.
4. Masuda, S.; Bauer, C. E. Cell 2002, 110, 613-23.
5. Iseki, M.; Matsunaga, S.; Murakami, A.; Ohno, K.; Shiga, K.; Yoshida, K. ; Sugai, M.; Takahashi, T.; Hori, T.; Watanabe, M. Nature 2002, 415, 1047-51.
6. Masuda, S.; Hasegawa, K.; Ishii, A.; Ono, T. Biochemistry 2004, 43, 5304-5313.
7. Hasegawa, K.; Masuda, S.; Ono, T. Biochemistry 2004, 43, 14979-14986.
8. Hasegawa, K.; Masuda, S.; Ono, T. Plant Cell Physiol. 2005, 46, 136-146.
9. Rajagopal, S.; Key, J. M.; Purcell, E. B.; Boerema, D. J.; Moffat, K. Photochem. Photobiol. 2005, 80, 542-547.
10. Fukushima, Y.; Okajima, K.; Shibata, Y.; Ikeuchi, M.; Itoh, S. Biochemistry 2005, 44, 5149-5158.
11. Gauden, M.; Yeremenko, S.; Laan, W.; van Stokkum, I. H. M.; Ihalainen, J. A.; van Grondelle, R.; Hellingwerf, K. J.; Kennis, J. T. M. Biochemistry 2005, 44, 3653-3662.
12. Kraft, B. J.; Masuda, S.; Kikuchi, J.; Dragnea, V.; Tollin, G.; Zaleski, J. M.; Bauer, C. E. Biochemistry 2003, 42, 6726-6734.
13. Laan W.; van der Horst M. A.; van Stokkum I. H.; Hellingwerf, K. J. Photochem. Photobiol. 2003, 78, 290-297.
14. Masuda, S.; Hasegawa, K.; Ono, T. Biochemistry 2005, 44, 1215-1224.
15. Unno, M.; Kumauchi, M.; Sasaki, I.; Tokunaga, F.; Yamauchi, S. J. Phys. Chem. B 2003, 107, 2837-2845.
16. Unno, M.; Kumauchi, M.; Hamada, N.; Tokunaga, F.; Yamauchi, S. J. Biol. Chem. 2004, 279, 23855-23858.
17. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision B.04; Gaussian, Inc.: Wallingford, CT, 2004.
18. Foresman, J. B.; Head-Gordon, M.; Pople, J. A.; Frisch, M. J. J. Phys. Chem. 1992, 96, 135-149.
19. Stratmann, R. E.; Scuseria, G. E.; Frisch, M. J. J. Chem. Phys. 1998, 109, 8218-8224.
20. Bowman, W. D.; Spiro, T. G. Biochemistry 1981, 20, 3313-3318.
21. Kim, M.; Carey, P. R. J. Am. Chem. Soc. 1993, 115, 7015-7016.
22. Harada, I.; Takeuchi, H. In Spectroscopy of Biological Systems; Clark, R. J. H.; Hester, R. E., Eds.; John Wiley & Sons: Chichester, U. K., 1981; Vol. 13, 113-175.
23. -1.
24. Laan W.; Bednarz T.; Heberle J.; Hellingwerf K. J. Photochem. Photobiol. Sci. 2004, 3, 1011-1016.
25. Zheng, Y.; Dong, J.; Palfey, B. A.; Carey, P. R. Biochemistry 1999, 38, 16727-16732.
26. Hazekawa, I.; Nishina, Y.; Sato, K.; Shichiri, M.; Miura, R.; Shiga, K. J. Biochem. 1997, 121, 1147-1154.
27. -1. Further DFT studies are in progress to achieve a qualitative agreement with experiments.
28. For model 3c, water molecules W2 and W4 are replaced with penta-1,5-diol. Note that, in the absence of W3 molecule, water W2 formed a hydrogen bond with the N3-H moiety in the optimized structure.
29. Unno, M.; Kumauchi, M.; Sasaki, J.; Tokunaga, F.; Yamauchi, S. Biochemistry 2002, 41, 5668-5674.
30. Wang, J.; Ortiz-Maldonado, M.; Entsch, B.; Massey, V.; Ballou, D.; Gatti, D. L. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 608-613.