Computer simulation of water in cytochrome c oxidase

Biochimica et Biophysica Acta-Bioenergetics

Volumn 1557, Issue 1-3, 2003, Pages 99-107

  Zheng, Xuehe ^a   Medvedev, Dmitry M ^a   Swanson, Jessica ^a   Stuchebrukhov, Alexei A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Cytochrome c oxidase; Molecular dynamics simulation; Water

Indexed keywords

CYTOCHROME C OXIDASE; WATER;

ARTICLE; CHEMICAL STRUCTURE; COMPUTER SIMULATION; DEHYDRATION; ENZYME ACTIVE SITE; HYDROGEN BOND; MOLECULAR DYNAMICS; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL;

ANIMALS; BINDING SITES; CATALYTIC DOMAIN; CATTLE; COMPUTER SIMULATION; ELECTRON TRANSPORT COMPLEX IV; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTONS; WATER;

BOVINAE;

EID: 0037422418     PISSN: 00052728     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0005-2728(03)00002-1     Document Type: Article

References (43)

1. Wikström M. Curr. Opin. Struct. Biol. 8:1998;480-488.
2. Wikström M. Biophys. Biochim. Acta. 1458:2000;188-198.
3. Michel H. Biochemistry. 38:1999;15129-15140.
4. Gennis R.B. Biophys. Biochim. Acta. 1365:1998;241-248.
5. Zaslavsky D., Gennis R.B. Biochim. Biophys. Acta. 1458:2000;164-179.
6. Stuchebrukhov A.A. Adv. Chem. Phys. 118:2001;1-44.
7. Page C.C., Moser C.C., Chen X., Dutton P.L. Nature. 402:1999;47-52.
8. Moser C.C., Keske J.M., Warncke K., Farid R.S., Dutton P.L. Nature. 355:1992;796-802.
9. Langen R., Chang I., Germanas J.P., Richards J.H., Winkler J.R., Gray H.B. Science. 268:1995;1733-1735.
10. Gray H.B., Winkler J.R. Ann. Rev. Biochem. 65:1996;537-561.
11. Stuchebrukhov A.A. J. Theor. Comp. Chem. 2003 (Jan.-Feb.);. (in press).
12. Agmon N. Isr. J. Chem. 39:1999;493 Agmon N. J. Chim. Phys. (Paris). 93:1996;1714 Agmon N. Chem. Phys. Lett. 244:1995;456-462.
13. Agmon N. Isr. J. Chem. 39:1999;493 Agmon N. J. Chim. Phys. (Paris). 93:1996;1714 Agmon N. Chem. Phys. Lett. 244:1995;456-462.
14. Agmon N. Isr. J. Chem. 39:1999;493 Agmon N. J. Chim. Phys. (Paris). 93:1996;1714 Agmon N. Chem. Phys. Lett. 244:1995;456-462.
15. (a) Nagle J.F., Morovitz H.J. Proc. Nat. Acad. Sci. U. S. A. 75:1978;298
16. (b) Pomes R. Isr. J. Chem. 39:1999;195-387.
17. S. Yoshikawa, private communication.
18. Hofacker I., Schulten K. Proteins. 30:1998;100-107.
19. Riistama S., Hummer G., Puustinen A., Dyer R.B., Woodruff W.H., Wikström M. FEBS Lett. 414:1997;275-280.
20. Pomes R., Hummer G., Wikström M. Biophys. Biochim. Acta. 1365:1998;255-260.
21. Medvedev D.M., Stuchebrukhov A.A. J. Am. Chem. Soc. 122:2000;6571-6582.
22. Yoshikawa S., Shinzawa-Itoh K., Nakashima R., Yaono E.R., Inoue N., Yao M., Fei M.J., Libeu C.P., Mizushima T., Yamaguchi H., Tomizaki T., Tsukihara T. Science. 280:1998;1723-1729.
23. 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. J. Am. Chem. Soc. 117:1995;5179-5197.
24. Kannt A., Lancaster C.R.D., Michel H. Biophys. J. 74:1998;708-721.
25. D. Popovic, A.A. Stuchebrukhov, Electrostatic calculations of cytochrome oxidase, in preparation.
26. Zhang L., Hermans J. Proteins: Struct., Funct. Genet. 24:1996;433-438.
27. NBS tables for chemical thermodynamic properties, 1982.
28. (a) J. Hermans, private communication.
29. (b) Goodford P.J. J. Med. Chem. 28:1985;849-857
30. Wade R.C., Goodford P.J. J. Med. Chem. 36:1993;147-148.
31. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., Klein M.L. J. Chem. Phys. 79:1983;926-935.
32. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. J. Comp. Chem. 4:1983;187-217.
33. Zerner M.C., Ridely J.E., Bacon A., McKelvey J., Edwards W., Head J.D., Culberson C., Cory M.G., Zheng X., Parkinson W., Yu Y., Cameron A., Tamm T., Pearl G., Broo A., Albert e.a.K. ZINDO. 2002;University of Florida, Gainesville, FL. Quantum Theory Project, distributed by Accelrys, 9685 Scranton Road, San Diego, CA 92121-3752, USA.
34. The charges, molecular coordinates, and some other details of the calculation are available in the supplementary material to this paper.
35. The energy evaluations within the protein are done with no dielectric screening of the Coulomb interactions of the partial charges, as no such screening is applied in the bulk state calculations. It is usually assumed that the partial charges are already rescaled to reflect the electronic polarizability of the medium. There is a well-known uncertainly of the Coulomb energy evaluation here, which in some cases may result in an additional factor of 1/1.4 to 1/2.
36. Puustinen A., Wikström M. Proc. Natl. Acad. Sci. U. S. A. 96:1999;35-37.
37. Schmidt B., Florens B.L., Qin L., McCracken J., Ferguson-Miller S. Biophys. J. 82:2002;1391.
38. Riistama S., Puustinen A., Garcia-Horsman A., Iwata S., Michel H., Wikström M. Biophys. Biochim. Acta. 1275:1996;1-8.
39. Finkelstein A. Water Movement Through Lipid Bilayers. 1987;Wiley.
40. Joel Morgan, private communication.
41. H. Michel, EBEC2002 Lecture, Sept. 2002.
42. Results shown in Fig. 4 have been reported at Biophys. Soc. Meeting, San Francisco, Feb. 2002, and at EBEC2002, Sep. 2002, BBA Short Reports 12 (2002) 107.
43. Verkhovsky M.I., Jasaitis A., Wikström M. Biochim. Biophys. Acta. 1506:2001;143-146.