Solvent effects on the physicochemical properties of the cross-linked histidine-tyrosine ligand of cytochrome C oxidase

Journal of Physical Chemistry B

Volumn 114, Issue 19, 2010, Pages 6409-6425

  McDonald, William J ^a   Einarsdóttir, Ólöf ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION SPECTROSCOPY; AMINO ACIDS; CONTINUUM MECHANICS; CROSSLINKING; DENSITY FUNCTIONAL THEORY; ENZYMES; GAS ABSORPTION; HYDROGEN BONDS; LIGANDS; PHASE INTERFACES; PHENOLS; PHOSPHATASES; PROTONS; PULSE CODE MODULATION; REACTION KINETICS; SOLVATION;

1-METHYLIMIDAZOLE; AQUEOUS SOLVATION; AROMATICITIES; CYTOCHROME C OXIDASE; DEGREE OF ASYMMETRY; ELECTRON-DONATING ABILITY; ELECTRONIC ABSORPTION SPECTRA; GAS-PHASE REACTIONS; GASPHASE; H-ATOM ABSTRACTION; HYDROGEN BONDING INTERACTIONS; IMIDAZOLE MOIETY; ISODESMIC REACTIONS; O-H BOND; ORDER OF MAGNITUDE; PHENOL RINGS; PHENOXYL RADICAL; PHYSICOCHEMICAL PROPERTY; POLARIZABLE CONTINUUM MODEL; PROTON DONORS; QUANTITATIVE PREDICTION; RADICAL REDUCTION; REACTION ENERGY; REDOX POTENTIALS; SOLVATION MODELS; SOLVENT EFFECTS; VIBRATIONAL FREQUENCIES;

REDOX REACTIONS;

EID: 84962343506     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp909574v     Document Type: Article

References (61)

1. Ferguson-Miller, S.; Babcock, G. T. Chem. Rev. 1996, 96, 2889-2907
2. Wikström, M. K. F. Nature 1977, 266, 271-273
3. Muramoto, K.; Hirata, K.; Shinzawa-Itoh, K.; Yoko-o, S.; Yamashita, E.; Aoyama, H.; Tsukihara, T.; Yoshikawa, S. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 7881-7886
4. Yoshikawa, S.; Shinzawa-Itoh, K.; Nakashima, R.; Yanoe, R.; Yamashita, E.; Inoue, N.; Yao, M.; Fei, M. J.; Libeu, C. P.; Mitzushima, T.; Yamaguchi, H.; Tomizaki, T.; Tsukihara, T. Science 1998, 280, 1723-1731
5. DeLano, W. L. The PyMOL Molecular Graphics System; Delano Scientific LLC: San Carlos, CA; http://www.pymol.org, PyMOLX11Hybrid V. 0.97.
6. Brunori, M.; Giuffre, A.; Sarti, P. J. Inorg. Biochem. 2005, 99, 324-336
7. Morgan, J. E.; Verkhovsky, M. I.; Palmer, G.; Wikström, M. K. F. Biochemistry 2001, 40, 6882-6892
8. Blomberg, M. R. A.; Siegbahn, P. E. M.; Babcock, G. T.; Wikström, M. K. F. J. Inorg. Biochem. 2000, 80, 261-269
9. Proshlyakov, D. A.; Pressler, M. A.; Babcock, G. T. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 8020-8025
10. Proshlyakov, D. A.; Pressler, M. A.; DeMaso, C.; Leykam, J. F.; DeWitt, D. L.; Babcock, G. T. Science 2000, 290, 1588-1591
11. Sucheta, A.; Szundi, I.; Einarsdóttir, Ó. Biochemistry 1998, 37, 17905-17914
12. MacMillan, F.; Kannt, A.; Behr, J.; Prisnerk, R.; Michel, H. Biochemistry 1999, 38, 9179-9784
13. Svistunenko, D.; Wilson, M. T.; Cooper, C. E. Biochim. Biophys. Acta 2004, 1655, 372-380
14. Rigby, S. E. J.; Jünemann, S.; Rich, P. R.; Heathcote, P. Biochemistry 2000, 39, 5921-5928
15. Budiman, K.; Kannt, A.; Lyubenova, S.; Richter, O.-M. H.; Ludwig, B.; Michel, H.; MacMillan, F. Biochemistry 2004, 43, 11709-11716
16. Berthomieu, C.; Hienerwadel, R. Biochim. Biophys. Acta 2005, 1707, 51-66
17. Iwaki, M.; Puustinin, A.; Wikström, M.; Rich, P. R. Biochemistry 2003, 42, 8809-8817
18. Iwaki, M.; Puustinin, A.; Wikström, M.; Rich, P. R. Biochemistry 2004, 43, 14370-14378
19. Iwaki, M.; Puustinin, A.; Wikström, M.; Rich, P. R. Biochemistry 2006, 45, 10873-10885
20. Pratt, D. A.; Pesavento, R. P.; van der Donk, W. A. Org. Lett. 2005, 7, 2735-2738
21. McCauley, K. M.; Vrtis, J. M.; Dupont, J.; van der Donk, W. A. Org. Lett. 2000, 122, 2403-2404
22. Aki, M.; Ogura, T.; Naruta, Y.; Le, T. H.; Sato, T.; Kitagawa, T. J. Phys. Chem. A 2002, 106, 3436-3444
23. Kim, S. H.; Aznar, C.; Brynda, M.; Silks, L. A.; Michalczyk, R.; Unkefer, C. J.; Woodruff, W. H.; Britt, R. D. J. Am. Chem. Soc. 2004, 126, 2328-2338
24. Elliott, G. I.; Konopelski, J. P. Org. Lett. 2000, 2, 3055-3057
25. Cappuccio, J. A.; Ayala, I.; Elliott, G. I.; Szundi, I.; Lewis, J.; Konopelski, J. P.; Barry, B. A.; Einarsdóttir, Ó. J. Am. Chem. Soc. 2002, 124, 1750-1760
26. Offenbacher, A.; White, K. N.; Sen, I.; Oliver, A. G.; Konopelski, J. P.; Barry, B. A.; Einarsdóttir, Ó. J. Phys. Chem. B 2009, 113, 7407-7417
27. Barone, V.; Cossi, M. J. Phys. Chem. A 1998, 102, 1995-2001
28. Bu, Y.; Cukier, R. I. J. Phys. Chem. B 2005, 109, 22013-22026
29. Colbran, S. B.; Paddon-Row, M. N. J. Biol. Inorg. Chem. 2003, 8, 855-865
30. Tomson, F.; Bailey, J. A.; Gennis, R. B.; Unkefer, C. J.; Li, Z.; Silks, L. A.; Martinez, R. A.; Donohoe, R. J.; Dyer, R. B.; Woodruff, W. H. Biochemistry 2002, 41, 14383-14390
31. Barone, V.; Cossi, M. J. Phys. Chem. A 1998, 102, 1995-2001
32. Cossi, M.; Rega, N.; Salmani, G.; Barone, V. J. Comput. Chem. 2003, 24, 669-681
33. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, K.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A., Jr. J. Comput. Chem. 1993, 14, 1347-1363
34. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5642
35. Stephens, P. J.; Devlin, F. J.; Chablowski, C. F.; Frisch, M. J. J. Phys. Chem. 1994, 98, 11623-11627
36. Frisch, M. J.; Pople, J. A.; Binkley, J. S. J. Chem. Phys. 1984, 80, 3265-3269
37. Schafer, A.; Horn, H.; Ahlrichs, R. J. Chem. Phys. 1992, 97, 2571-2577 Obtained via anonymous ftp from ftp://ftp.chemie.uni-karlsruhe.de/pub/basen
38. Kendall, R. A.; Dunning, T. H., Jr.; Harrison, R. J. J. Chem. Phys. 1992, 96, 6796-6806
39. Xu, X.; Goddard, W. A., III Proc. Natl. Acad. Sci. 2004, 101, 2673-2677
40. Zhao, Y.; Truhlar, D. G. J. Chem. Theory Comput. 2005, 1, 415-432
41. Santra, B.; Michaelides, A.; Scheffler, M. J. Chem. Phys. 2007, 127, 184104-1-184104-9
42. Adamo, C.; Barone, V. J. Chem. Phys. 1999, 110, 6158-6170
43. Figure generated using MacMolPlt 7.2.1. Bode, B. M.; Gordon, M. S. J. Mol. Graphics Model. 1998, 16, 133-138
44. McDonald, W. J.; Einarsdóttir, Ó. J. Phys. Chem. A 2008, 112, 11400-11413
45. Pulay, P.; Fogarasi, G.; Pang, F.; Boggs, J. E. J. Am. Chem. Soc. 1979, 101, 2550-2560
46. Fogarasi, G.; Zhou, X.; Taylor, P. W.; Pulay, P. J. Am. Chem. Soc. 1992, 114, 8191-8201
47. Pulay, P.; Torok, F. Acta Chim. Acad. Sci. Hung. 1966, 47, 273-297
48. Boatz, J. A.; Gordon, M. S. J. Phys. Chem. 1989, 93, 1819-1826
49. Miertus, S.; Scrocco, E.; Tomasi, J. Chem. Phys. 1981, 55, 117-129
50. Cossi, M.; Barone, V.; Cammi, R.; Tomasi, J. Chem. Phys. Lett. 1996, 255, 327-335
51. Bordwell, F. G.; Hausch, M. J. J. Am. Chem. Soc. 1986, 108, 1979-1985
52. Toyama, A.; Ono, K.; Hashimoto, S.; Takeuchi, H. J. Phys. Chem. A 2002, 106, 3404-3412
53. Range, K.; Ayala, I.; York, D.; Barry, B. A. J. Phys. Chem. B. 2006, 110, 10970-10981
54. Gorbikova, E. A.; Belevich, I.; Wikström, M.; Verkhovsky, M. I. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 10733-10737
55. Gorbikova, E. A.; Wikström, M.; Verkhovsky, M. I. J. Biol. Chem. 2008, 283, 34907-34912
56. Radziszewski, J. G.; Gill, M.; Gorski, A.; Spanget-Larsen, J.; Waluk, J.; Mróz, B. J. J. Chem. Phys. 2001, 115, 9733-9738
57. Tripathy, G. N. R.; Schuler, R. H. J. Chem. Phys. 1984, 84, 113-121
58. Tripathy, G. N. R.; Schuler, R. H. J. Phys. Chem. 1988, 92, 5129-5133
59. Kaila, V. R. I.; Johansson, M. P.; Sundholm, D.; Laakkonen, L.; Wikström, M. Biochim. Biophys. Acta 2009, 1787, 221-233
60. Lonnon, D. G.; Lee, S. T.; Colbran, S. B. J. Am. Chem. Soc. 2007, 129, 5800-5801
61. Cukier, R. I. Biochim. Biophys. Acta 2005, 1706, 134-146