Structural dynamics of clamshell rotation during the incipient relaxation process of photodissociated carbonmonoxy myoglobin: Statistical analysis by the perturbation ensemble method

Journal of Physical Chemistry B

Volumn 114, Issue 38, 2010, Pages 12340-12348

  Takayanagi, Masayoshi ^a,b   Iwahashi, Chiharu ^a   Nagaoka, Masataka ^a,b  

^a NAGOYA UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL REACTIONS; HEMOGLOBIN; MOLECULAR DYNAMICS; PERTURBATION TECHNIQUES; PHOTODISSOCIATION; PORPHYRINS; STRUCTURAL DYNAMICS; X RAY DIFFRACTION;

ALLOSTERY; DELAY TIME; ENSEMBLE METHODS; ENSEMBLE-AVERAGED; HEME GROUP; MOLECULAR DYNAMICS TRAJECTORIES; PHOTON WAVELENGTH; STATISTICAL ANALYSIS; STRUCTURAL CHANGE; TIME-RESOLVED X-RAY DIFFRACTION; TIME-SCALES; VIBRATIONAL ENERGIES;

ROTATION;

EID: 77957120065     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp9110635     Document Type: Article

References (34)

1. Perutz, M. F.; Wilkinson, A. J.; Paoli, M.; Dobson, G. G. Annu. Rev. Biophys. Biomol. Struct. 1998, 27, 1
2. Leitner, D. M.; Straub, J. E. Proteins: Energy, Heat and Signal Flow (Computation in Chemistry); CRC Press: Boca Raton, FL, 2009.
3. Henry, E. R.; Eaton, W. A.; Hochstrasser, R. M. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 8982
4. Mizutani, Y.; Kitagawa, T. Science 1997, 278, 443
5. Okazaki, I.; Hara, Y.; Nagaoka, M. Chem. Phys. Lett. 2001, 337, 151
6. Sagnella, D. E.; Straub, J. E. J. Phys. Chem. B 2001, 105, 7057
7. Kachalova, G. S.; Popov, A. N.; Bartunik, H. D. Science 1999, 284, 473
8. Schotte, F.; Lim, M.; Jackson, T. A.; Smirnov, A. V.; Soman, J.; Olson, J. S.; Phillips, G. N., Jr.; Wulff, M.; Anfinrud, P. A. Science 2003, 300, 1944
9. Schotte, F.; Soman, J.; Olson, J. S.; Wulff, M.; Anfinrud, P. A. J. Struct. Biol. 2004, 147, 235
10. Hummer, G.; Schotte, F.; Anfinrud, P. A. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15330
11. Sato, A.; Gao, Y.; Kitagawa, T.; Mizutani, Y. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 9627
12. Goodno, G. D.; Astinov, V.; Miller, R. J. D. J. Phys. Chem. A 1999, 103, 10630
13. Takayanagi, M.; Okumura, H.; Nagaoka, M. J. Phys. Chem. B 2007, 111, 864
14. Tomita, A.; Sato, T.; Ichiyanagi, K.; Nozawa, S.; Ichikawa, H.; Chollet, M.; Kawai, F.; Park, S.-Y.; Tsuduki, T.; Yamato, T.; Koshihara, S.; Adachi, S. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 2612
15. Bossa, C.; Anselmi, M.; Roccatano, D.; Amadei, A.; Vallone, B.; Brunori, M.; Di Nola, A. Biophys. J. 2004, 86, 3855
16. Ruscio, J. Z.; Kumar, D.; Schukla, M.; Prisant, M. G.; Murali, T. M.; Onufriev, A. V. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 9204
17. Cohen, J.; Arkhipov, A.; Braun, R.; Schulten, K. Biophys. J. 2006, 91, 1844
18. Nishihara, Y.; Hayashi, S.; Kato, S. Chem. Phys. Lett. 2008, 464, 220
19. Guallar, V.; Jarzecki, A. A.; Friesner, R. A.; Spiro, T. G. J. Am. Chem. Soc. 2006, 128, 5427
20. Balakrishnan, G.; Tsai, C.-H.; Wu, Q.; Case, M. A.; Pevsner, A.; McLendon, G. L.; Ho, C.; Spiro, T. G. J. Mol. Biol. 2004, 340, 857
21. Kneipp, J.; Balakrishnan, G.; Chen, R.; Shen, T.-J.; Sahu, S. C.; Ho, N. T.; Giovannelli, J. L.; Simplaceanu, V.; Ho, C.; Spiro, T. G. J. Mol. Biol. 2006, 356, 335
22. Cramer, H. The Elements of Probability Theory and Some of Its Applications; John Wiley & Sons: New York, 1966.
23. Yamato, T.; Niimura, M.; Go, N. Proteins 1998, 32, 268
24. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Pearlman, D. A.; Crowley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Mathews, D. H.; Schafmeister, C.; Ross, W. S.; Kollman, P. A. AMBER 9; University of California: San Francisco, CA, 2006.
25. Tironi, I. G.; Brunne, R. M.; van Gunsteren, W. F. Chem. Phys. Lett. 1996, 250, 19
26. Cheng, B. X.; Schoenborn, B. P. Acta Crystallogr. 1990, B46, 195
27. Ansari, A.; Berendzen, J.; Bowne, S. F.; Frauenfelder, H.; Iben, I. E. T.; Sauke, T. B.; Shyamsunder, E.; Young, R. D. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 5000
28. Rovira, C.; Schulze, B.; Eichinger, M.; Evanseck, J. D.; Parrinello, M. Biophys. J. 2001, 81, 435
29. Unno, M.; Chiristian, J. F.; Olson, J. S.; Sage, J. T.; Champion, P. M. J. Am. Chem. Soc. 1998, 120, 2670
30. Caughey, W. S.; Shimada, H.; Choc, M. G.; Tucker, M. P. Proc. Natl. Acad. Sci. U.S.A. 1981, 78, 2903
31. Morikis, D.; Champion, P. M.; Springer, B. A.; Sligar, S. G. Biochemistry 1989, 28, 4791
32. Vojtechovsky, J.; Chu, K.; Berendzen, J.; Sweet, R. M.; Schlichting, I. Biophys. J. 1999, 77, 2153
33. Yang, F.; Phillips, G. N., Jr. J. Mol. Biol. 1996, 256, 762
34. Seno, Y.; Go, N. J. Mol. Biol. 1990, 216, 111