Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations

Proceedings of the National Academy of Sciences of the United States of America

Volumn 101, Issue 43, 2004, Pages 15330-15334

  Hummer, Gerhard ^a,b   Schotte, Friedrich ^a   Anfinrud, Philip A ^a,b  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; MYOGLOBIN;

AMPLITUDE MODULATION; ANALYTIC METHOD; ARTICLE; CHEMICAL STRUCTURE; CRYSTALLOGRAPHY; DISSOCIATION; LIGAND BINDING; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FUNCTION; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

CARBON MONOXIDE; CRYSTALLOGRAPHY, X-RAY; OXYGEN; PROTEIN CONFORMATION; PROTEINS;

EID: 7444230904     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0405295101     Document Type: Article

References (44)

1. Austin, R. H., Beeson, K. W., Eisenstein, L., Frauenfelder, H. & Gunsalus, I. C. (1975) Biochemistry 14, 5355-5373.
2. Brooks, C. L., III, Karplus, M. & Pettitt, B. M. (1988) Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics (Wiley, New York).
3. McCammon, J. A. & Harvey, S. C. (1987) Dynamics of Proteins and Nucleic Acids (Cambridge Univ. Press, New York).
4. Carver, T. E., Brantley, R. E., Jr., Singleton, E. W., Arduini, R. M., Quillin, M. L., Phillips, G. N., Jr., & Olson, J. S. (1992) J. Biol. Chem. 267, 14443-14450.
5. Lim, M., Jackson, T. A. & Anfinrud, P. A. (1995) Science 269, 962-966.
6. Lim, M., Jackson, T. A. & Anfinrud, P. A. (1997) Nat. Struct. Biol. 4, 209-214.
7. Merchant, K. A., Noid, W. G., Akiyama, R., Finkelstein, I. J., Goun, A., McClain, B. L., Loring, R. F. & Fayer, M. D. (2003) J. Am. Chem. Soc. 125, 13804-13818.
8. Frauenfelder, H., Sligar, S. G. & Wolynes, P. G. (1991) Science 254, 1598-1603.
9. Schlichting, I., Berendzen, J., Phillips, G. N., Jr., & Sweet, R. M. (1994) Nature 371, 808-812.
10. Srajer, V., Teng, T., Ursby, T., Pradervand, C., Ren, Z., Adachi, S., Schildkamp, W., Bourgeois, D., Wulff, M. & Moffat, K. (1996) Science 274, 1726-1729.
11. Chu, K., Vojtchovsky, J., McMahon, B. H., Sweet, R. M., Berendzen, J. & Schlichting, I. (2000) Nature 403, 921-923.
12. Ostermann, A., Waschipky, R., Parak, F. G. & Nienhaus, G. U. (2000) Nature 404, 205-208.
13. Brunori, M., Vallone, B., Cutruzzola, F., Travaglini-Allocatelli, C., Berendzen, J., Chu, K., Sweet, R. M. & Schlichting, I. (2000) Proc. Natl. Acad. Sci. USA 97, 2058-2063.
14. Srajer, V., Ren, Z., Teng, T. Y., Schmidt, M., Ursby, T., Bourgeois, D., Pradervand, C., Schildkamp, W., Wulff, M. & Moffat, K. (2001) Biochemistry 40, 13802-13815.
15. Schotte, F., Lim, M., Jackson, T. A., Smirnov, A. V., Soman, J., Olson, J. S., Phillips, G. N., Jr., Wulff, M. & Anfinrud, P. A. (2003) Science 300, 1944-1947.
16. Bourgeois, D., Vallone, B., Schotte, F., Arcovito, A., Miele, A. E., Sciara, G., Wulff, M., Anfinrud, P. & Brunori, M. (2003) Proc. Natl. Acad. Sci. USA 100, 8704-8709.
17. Case, D. A. & Karplus, M. (1979) J. Mol. Biol. 132, 343-368.
18. Henry, E. R., Levitt, M. & Eaton, W. A. (1985) Proc. Natl. Acad. Sci. USA 82, 2034-2038.
19. Elber, R. & Karplus, M. (1990) J. Am. Chem. Soc. 112, 9161-9175.
20. Straub, J. E. & Karplus, M. (1991) Chem. Phys. 158, 221-248.
21. Schaad, O., Zhou, H. X., Szabo, A., Eaton, W. A. & Henry, E. R. (1993) Proc. Natl. Acad. Sci. USA 90, 9547-9551.
22. Ma, J., Huo, S. & Straub, J. E. (1997) J. Am. Chem. Soc. 119, 2541-2551.
23. Vitkup, D., Petsko, G. A. & Karplus, M. (1997) Nat. Struct. Biol. 4, 202-208.
24. Meller, J. & Elber, R. (1998) Biophys. J. 74, 789-802.
25. Nutt, D. R. & Meuwly, M. (2003) Biophys. J. 85, 3612-3623.
26. Nutt, D. R. & Meuwly, M. (2004) Proc. Natl. Acad. Sci. USA 101, 5998-6002.
27. Bossa, C., Anselmi, M., Roccatano, D., Amadei, A., Vallone, B., Brunori, M. & Di Nola, A. (2004) Biophys. J. 86, 3855-3862.
28. Steinbach, P. J. & Brooks, B. R. (1993) Proc. Natl. Acad. Sci. USA 90, 9135-9139.
29. Kachalova, G. S., Popov, A. N. & Bartunik, H. D. (1999) Science 284, 473-476.
30. Spiro, T. G. & Kozlowski, P. M. (2001) Acc. Chem. Res. 34, 137-144.
31. Perutz, M. F. & Mathews, F. S. (1966) J. Mol. Biol. 21, 199-202.
32. Bourgeois, D., Ursby, T., Wulff, M., Pradervand, C., Legrand, A., Schildkamp, W., Laboure, S., Srajer, S., Teng, T. Y., Roth, M. & Moffat, K. (1996) J. Synchrotron Radiat. 3, 65-74.
33. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W. & Kollman, P. A. (1995) J. Am. Chem. Soc. 117, 5179-5197.
34. Darden, T., York, D. & Pedersen, L. (1993) J. Chem. Phys. 98, 10089-10092.
35. Giammona, D. A. (1984) Ph.D. thesis (Univ. of California, Davis).
36. Quillin, M. L., Arduini, R. M., Olson, J. S. & Phillips, G. N., Jr. (1993) J. Mol. Biol. 234, 140-155.
37. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. (1983) J. Chem. Phys. 79, 926-935.
38. Straatsma, T. P. & Berendsen, H. J. C. (1988) J. Chem. Phys. 89, 5876-5886.
39. Schotte, F., Soman, J., Olson, J. S. & Anfinrud, P. A. (2004) J. Struct. Biol. 127, 235-246.
40. Tilton, R. F., Jr., Kuntz, I. D., Jr., & Petsko, G. A. (1984) Biochemistry 23, 2849-2857.
41. Li, H., Elber, R. & Straub, J. E. (1993) J. Biol. Chem. 268, 17908-17916.
42. Yang, F. & Phillips, G. N., Jr. (1996) J. Mol. Biol. 256, 762-774.
43. Pauling, L. (1964) Nature 203, 182-183.
44. Springer, B. A., Sligar, S. G., Olson, J. S. & Phillips, G. N., Jr. (1994) Chem. Rev. 94, 699-714.