Optical detection of disordered water within a protein cavity

Journal of the American Chemical Society

Volumn 131, Issue 34, 2009, Pages 12265-12272

  Goldbeck, Robert A ^a   Pillsbury, Marlisa L ^b   Jensen, Russell A ^b   Mendoza, Juan L ^b   Nguyen, Rosa L ^a   Olson, John S ^c   Soman, Jayashree ^c   Kliger, David S ^a   Esquerra, Raymond M ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SAN FRANCISCO STATE UNIVERSITY   (United States)

^c RICE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORBANCE SPECTRUM; ABSORPTION BAND; ACTIVE SITE; DEOXYMYOGLOBIN; DISTAL HISTIDINE; DISTAL POCKET; ELECTRON DENSITY MAPS; HEME POCKETS; HEME PROTEINS; LASER PHOTOLYSIS; LIGAND BINDING; OPTICAL DETECTION; POSITIONAL DISORDER; PROTEIN CAVITY; PROTEIN STRUCTURES; ROBUST SYSTEMS; SOLVENT MOLECULES; TIME-RESOLVED; WATER MOLECULE; WILD TYPES;

CRYSTAL STRUCTURE; HEMOGLOBIN; HYDROGEN; LIGANDS; MOLECULES; PHOTOLYSIS; PORPHYRINS; X RAY CRYSTALLOGRAPHY;

WATER ABSORPTION;

ASPARAGINASE; HEMOPROTEIN; HISTIDINE; HYDROGEN; LEUCINE; LIGAND; MUTANT PROTEIN; MYOGLOBIN; SOLVENT; WATER;

ABSORPTION; ABSORPTION SPECTROSCOPY; ARTICLE; COMPLEX FORMATION; CRYSTAL STRUCTURE; ELECTRON; HYDRATION; HYDROGEN BOND; KINETICS; LASER; LIGAND BINDING; MOLECULAR STABILITY; MUTATION; PHOTOLYSIS; PROTEIN STRUCTURE; WATER CONTENT; WATER TRANSPORT; WILD TYPE;

ANIMALS; CARBON MONOXIDE; LASERS; MODELS, MOLECULAR; MUTANT PROTEINS; MYOGLOBIN; PHOTOLYSIS; SPERM WHALE; WATER;

EID: 69349104053     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja903409j     Document Type: Article

References (48)

1. Teeter, M. M. Annu. Rev. Biophys. Biophys. Chem. 1991, 20, 577-600.
2. Park, S.; Saven, J. G. Proteins 2005, 60, 450-463.
3. Takano, K.; Funahashi, J.; Yamagata, Y.; Fujii, S.; Yutani, K. J. Mol. Biol. 1997, 74, 132-142.
4. Mao, Y.; Ratner, M. A.; Jarrold, M. F. J. Am. Chem. Soc. 2000, 122, 2950-2951.
5. Schutz, C. N.; Warshel, A. Proteins 2002, 44, 400-417.
6. Cheung, M. S.; Garcia, A.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 685-690.
7. Meyer, E. Protein Sci. 1992, 1, 1543-1562.
8. Hofacker, I.; Schulten, K. Proteins 1998, 30, 100-107.
9. Damjanović, A.; Schlessman, J. L.; Fitch, C. A.; García, A. E.; García- Moreno, E. B. Biophys. J. 2007, 93, 2791-2804.
10. Phillips, G. N.; Pettitt, B. M. Protein Sci. 1995, 4, 149-158.
11. Zhang, X. J.; Matthews, B. W. Protein Sci. 1994, 3, 1031-1039.
12. Denisov, V. P.; Halle, B. J. Am. Chem. Soc. 1994, 116, 10324-10325.
13. Imai, T.; Hiraoka, R.; Kovalenko, A.; Hirata, F. Proteins 2007, 66, 804-813.
14. Goldbeck, R. A.; Bhaskaran, S.; Ortega, C.; Mendoza, J. L.; Olson, J. S.; Soman, J.; Kliger, D. S.; Esquerra, R. M. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 1254-1259.
15. Esquerra, R. M.; Goldbeck, R. A.; Kim-Shapiro, D. B.; Kliger, D. S. Biochemistry 1998, 37, 17527-17536.
16. Esquerra, R. M.; Bhaskaran, S.; Pillsbury, M. L.; Mendoza, J. L.; Jensen, R. A.; Lintner, B.; Kliger, D. S.; Goldbeck, R. A. J. Biol. Chem. 2008, 283, 14165-14175.
17. Cao, W.; Christian, J. F.; Champion, P. M.; Rosca, F.; Sage, J. T. Biochemistry 2001, 40, 5728-5737.
18. Rohlfs, R. J.; Mathews, A. J.; Carver, T. E.; Olson, J. S.; Springer, B. A.; Egeberg, K. D.; Sligar, S. G. J. Biol. Chem. 1990, 265, 3168-3176.
19. Smerdon, S. J.; Dodson, G. G.; Wilkinson, A. J.; Gibson, Q. H.; Blackmore, R. S.; Carver, T. E.; Olson, J. S. Biochemistry 1991, 30, 6252-6260.
20. Olson, J. S.; Phillips, G. N. J. Biol. Chem. 1996, 271, 17593-17596.
21. Olson, J. S.; Phillips, G. N. J. Biol. Inorg. Chem. 1997, 2, 544-552.
22. Scott, E. E.; Gibson, Q. H.; Olson, J. S. J. Biol. Chem. 2001, 276, 5177-5188.
23. McNaughton, L.; Hernández, G.; LeMaster, D. M. J. Am. Chem. Soc. 2003, 125, 3813-3820.
24. Dantsker, D.; Roche, C.; Samuni, U.; Blouin, G.; Olson, J. S.; Friedman, J. M. J. Biol. Chem. 2005, 280, 38740-38755.
25. Schotte, F.; Lim, M.; Jackson, T. A.; Smirnov, A. V.; Soman, J.; Olson, J. S.; Phillips, G. N.; Wulff, M.; Anfinrud, P. A. Science 2003, 300, 1944-1947.
26. Schotte, F.; Soman, J.; Olson, J. S.; Wulff, M.; Anfinrud, P. A. J. Struct. Biol. 2004, 147, 235-246.
27. Quillin et al. did not detect significant distal pocket water occupancy in the deoxy V68L Mb crystal structure, but nevertheless did note that unassigned electron density near the distal histidine may have been due to distal water present in a minor protein conformation rotating Leu68 away from the heme iron atom: Quillin, M. L.; Li, T.; Olson, J. S.; Phillips, G. N.; Dou, Y.; Ikeda-Saito, M.; Regan, R.; Carlson, M.; Gibson, Q. H.; Li, H.; Elber, R. J. Mol. Biol. 1995, 245, 416-436.
28. Carver, T. E.; Brantley, R. E.; Singleton, E. W.; Arduini, R. M.; Quillin, M. L.; Phillips, G. N.; Olson, J. S. J. Biol. Chem. 1992, 267, 14443-14450.
29. La Mar, G. N.; Dalichow, F.; Zhao, X.; Dou, Y.; Ikeda-Saito, M.; Chiu, M. L.; Sligar, S. G. J. Biol. Chem. 1994, 269, 29629-29635.
30. Henry, E. R.; Hofrichter, J. Methods Enzymol. 1992, 210, 129-192.
31. Phillips, G. N., Jr.; Arduini, R. M.; Springer, B. A.; Sligar, S. G. Proteins 1990, 7, 358-365
32. Pflugrath, J. W. Acta Crystallogr. 1999, D55, 1718-1725.
33. Brunger, A. T.; Adams, P. D.; Clore, G. M.; Delano, W. L.; Gros, P.; Grosse-Kunstleve, R. W.; Jiang, J.-S.; Kuszewski, J.; Nilges, M.; Pannu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Acta Crystallogr. 1998, D54, 905-921.
34. (a) Nienhaus, K.; Ostermann, A.; Nienhaus, G. U.; Parak, F. G.; Schmidt, M. Biochemistry 2005, 44, 5095-5105.
35. (b) Schmidt, M.; Nienhaus, K.; Pahl, R.; Krasselt, A.; Anderson, S.; Parak, F.; Nienhaus, G. U.; Srajer, V. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 11704-11709.
36. Hirota, S.; Li, T.; Phillips, G. N., Jr.; Olson, J. S.; Mukai, M.; Kitagawa, T. J. Am. Chem. Soc. 1996, 118, 7845-7846.
37. 1), to permit comparison between the variants independently of experimental differences in sample concentration, path length, and photolysis yield.
38. 2, weighted and normalized as shown in Figure 2.
39. Quillin, M. L.; Arduini, R. M.; Olson, J. S.; Phillips, G. N. J. Mol. Biol. 1993, 234, 140-155.
40. -1 s after photolysis appears to be associated with bimolecular CO rebinding rather than water entry.
41. Quillin, M. L. Ph.D. Dissertation, Rice University, 1994.
42. Krzywda, S.; Murshudov, G. N.; Brzozowski, A. M.; Jaskolski, M.; Scott, E. E.; Klizas, S. A.; Gibson, Q. H.; Olson, J. S.; Wilkinson, A. J. Biochemistry 1998, 37, 15896-15907.
43. Christian, J. F.; Unno, M.; Sage, J. T.; Champion, P. M. Biochemistry 1997, 36, 11198-11204.
44. Tian, W. D.; Sage, J. T.; Srajer, V.; Champion, P. M. Phys. Rev. Lett. 1992, 68, 408-411.
45. Dantsker, D.; Samuni, U.; Friedman, J. M.; Agmon, N. Biochim. Biophys. Acta 2005, 1749, 234-251.
46. Merchant, K. A.; Noid, W. G.; Akiyama, R.; Finkelstein, I. J.; Goun, A.; McClain, B. L.; Loring, R. F.; Fayer, M. D. J. Am. Chem. Soc. 2003, 125, 13804-13818.
47. Ishikawa, H.; Kwak, K.; Chung, J. K.; Kim, S.; Fayer, M. D. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 8619-8624.
48. Romberg, R. W.; Kassner, R. J. Biochemistry 1982, 21, 880-886.