Isocyanide in biochemistry? A theoretical investigation of the electronic effects and energetics of cyanide ligand protonation in [FeFe]-hydrogenases

Chemistry - A European Journal

Volumn 17, Issue 6, 2011, Pages 1954-1965

  Greco, Claudio ^a   Bruschi, Maurizio ^a   Fantucci, Piercarlo ^a   Ryde, Ulf ^b   Dea Gioia, Luca ^a  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

^b LUND UNIVERSITY   (Sweden)

Author keywords

density functional calculations; hydrogenases; isocyanide ligands; protonation; QM MM methods

Indexed keywords

[FEFE]HYDROGENASES; ACID ENVIRONMENT; ACTIVE SITE; AMINO ACID RESIDUES; CATALYTIC CYCLES; CATALYTIC PROCESS; CYANIDE LIGANDS; DENSITY-FUNCTIONAL CALCULATIONS; ELECTRONIC EFFECTS; ENERGY PROFILE; HYDROGEN BONDING NETWORK; HYDROGENASES; ISOCYANIDE LIGANDS; ISOCYANIDES; METABOLIC PATHS; PROTEIN MATRIX; PROTONATED; QM/MM METHODS; QUANTUM MECHANICAL/MOLECULAR MECHANICAL STUDIES; STATIONARY POINTS; THEORETICAL INVESTIGATIONS;

ALKALINITY; AMINO ACIDS; CYANIDES; DENSITY FUNCTIONAL THEORY; ELECTRONIC PROPERTIES; ENZYMES; HYDROGEN; PROTONATION;

LIGANDS;

HYDROGENASE; IRON HYDROGENASE; IRON SULFUR PROTEIN; LIGAND; NITRILE; PROTON;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; DESULFOVIBRIO DESULFURICANS; ENZYMOLOGY; HYDROGEN BOND; METABOLISM; THERMODYNAMICS;

DESULFOVIBRIO DESULFURICANS; HYDROGEN BONDING; HYDROGENASE; IRON-SULFUR PROTEINS; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NITRILES; PROTONS; THERMODYNAMICS;

EID: 79551468716     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.201001493     Document Type: Article

References (61)

1. T. F. Cummings, Occup. Med. 2004, 54, 82-85
2. R. Gracia, G. Shepherd, Pharmacotherapy 2004, 24, 1358-1365.
3. J. C. Fontecilla-Camps, A. Volbeda, C. Cavazza, Y. Nicolet, Chem. Rev. 2007, 107, 4273-4303.
4. W. Lubitz, E. Reijerse, M. vana Gastel, Chem. Rev. 2007, 107, 4331-4365.
5. Y. Nicolet, C. Piras, P. Legrand, C. E. Hatchikian, J. C. Fontecilla-Camps, Structure 1999, 7, 13-23.
6. B. E. Barton, T. B. Rauchfuss, Inorg. Chem. 2008, 47, 2261-2263
7. C. M. Thomas, T. B. Liu, M. B. Hall, M. Y. Darensbourg, Inorg. Chem. 2008, 47, 7009-7024.
8. C. Greco, M. Bruschi, J. Heimdal, P. Fantucci, L. Dea Gioia, U. Ryde, Inorg. Chem. 2007, 46, 7256-7258.
9. M. Bruschi, C. Greco, M. Kaukonen, P. Fantucci, U. Ryde, L. Dea Gioia, Angew. Chem. 2009, 121, 3555-3558
10. Angew. Chem. Int. Ed. 2009, 48, 3503-3506.
11. S. Ezzaher, J. F. Capon, F. Gloaguen, F. Y. Petillon, P. Schollhammer, J. Talarmin, Inorg. Chem. 2007, 46, 3426-3428.
12. J. I. vana dera Vlugt, T. B. Rauchfuss, C. M. Whaley, S. R. Wilson, J. Am. Chem. Soc. 2005, 127, 16012-16013.
13. M. Bruschi, G. Zampella, P. Fantucci, L. Dea Gioia, Coord. Chem. Rev. 2005, 249, 1620-1640
14. P. E. M. Siegbahn, J. W. Tye, M. B. Hall, Chem. Rev. 2007, 107, 4414-4435.
15. A. J. L. Pombeiro, Inorg. Chem. Commun. 2001, 4, 585-597.
16. S. Almeida, M. daa Silva, J. daa Silva, A. J. L. Pombeiro, J. Chem. Soc. Dalton Trans. 1999, 467-472.
17. L. Noodleman, J. G. Norman, J. Chem. Phys. 1979, 70, 4903-4906
18. L. Noodleman, J. Chem. Phys. 1981, 74, 5737-5743.
19. A. T. Fiedler, T. C. Brunold, Inorg. Chem. 2005, 44, 9322-9334.
20. C. Greco, M. Bruschi, L. Dea Gioia, U. Ryde, Inorg. Chem. 2007, 46, 5911-5921.
21. M. T. Stiebritz, M. Reiher, Inorg. Chem. 2009, 48, 7127-7140.
22. C. Greco, P. Fantucci, U. Ryde, L. Dea Gioia, Int. J. Quantum Chem. 2010, in press, DOI:.
23. Y. Nicolet, A. L. dea Lacey, X. Vernede, V. M. Fernandez, E. C. Hatchikian, J. C. Fontecilla-Camps, J. Am. Chem. Soc. 2001, 123, 1596-1601.
24. N. Reuter, A. Dejaegere, B. Maigret, M. Karplus, J. Phys. Chem. A 2000, 104, 1720-1735.
25. U. Ryde, J. Computer-Aided Mol. Des. 1996, 10, 153-164
26. U. Ryde, M. H. M. Olsson, Int. J. Quantum Chem. 2001, 81, 335-347.
27. R. Ahlrichs, M. Bär, M. Häser, H. Horn, C. Kolmel, Chem. Phys. Lett. 1989, 162, 165-169.
28. Ambera 8, D. A. Case, T. A. Darden, T. E. Cheatham, III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, K. M. Merz, B. Wang, D. A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J. W. Caldwell, W. S. Ross, P. A. Kollman, University of California: San Francisco, CA, 2004
29. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, P. A. Kollman, J. Am. Chem. Soc. 1995, 117, 5179-5197.
30. A. D. Becke, Phys. Rev. A 1988, 38, 3098-3100
31. J. P. Perdew, Phys. Rev. B 1986, 33, 8822-8824.
32. A. Schäfer, C. Huber, R. Ahlrichs, J. Chem. Phys. 1994, 100, 5829-5835.
33. K. Eichkorn, O. Treutler, H. Ãhm, M. Häser, R. Ahlrichs, Chem. Phys. Lett. 1995, 240, 283-289
34. K. Eichkorn, F. Weigend, O. Treutler, R. Ahlrichs, Theor. Chem. Acc. 1997, 97, 119-124.
35. B. H. Besler, K. M. Merz, P. A. Kollman, J. Comput. Chem. 1990, 11, 431-439.
36. F. M. Rusnak, M. W. W. Adams, L. E. Mortenson, E. Munck, J. Biol. Chem. 1987, 262, 38-41
37. M. W. W. Adams, L. E. Mortenson, J. Biol. Chem. 1984, 259, 7045-7055
38. I. C. Zambrano, A. T. Kowal, L. E. Mortenson, M. W. W. Adams, M. K. Johnson, J. Biol. Chem. 1989, 264, 20974-20983
39. C. V. Popescu, E. Munck, J. Am. Chem. Soc. 1999, 121, 7877-7884
40. A. S. Pereira, P. Tavares, I. Moura, J. J. G. Moura, B. H. Huynh, J. Am. Chem. Soc. 2001, 123, 2771-2782.
41. J. W. Peters, W. N. Lanzilotta, B. J. Lemon, L. C. Seefeldt, Science 1998, 282, 1853-1858
42. U. Ryde, C. Greco, L. Dea Gioia, J. Am. Chem. Soc. 2010, 132, 4512-4513.
43. H. J. Fan, M. B. Hall, J. Am. Chem. Soc. 2001, 123, 3828-3829.
44. A. Klamt, J. Phys. Chem. 1995, 99, 2224-2235.
45. M. K. Gilson, B. H. Honig, Biopolymers 1986, 25, 2097-2119.
46. M. Bruschi, C. Greco, P. Fantucci, L. Dea Gioia, Inorg. Chem. 2008, 47, 6056-6071.
47. M. Bruschi, C. Greco, L. Bertini, P. Fantucci, U. Ryde, L. Dea Gioia, J. Am. Chem. Soc. 2010, 132, 4992-4993.
48. G. Zampella, C. Greco, P. Fantucci, L. Dea Gioia, Inorg. Chem. 2006, 45, 4109-4118.
49. (CN) angle, which turned out to be almost linear both in the crystal structure and in the protein-free QM/MM models of the partially oxidized and reduced enzyme (171, 176, and 172°, respectively).
50. S. Zilberman, E. I. Stiefel, M. H. Cohen, R. Car, Inorg. Chem. 2006, 45, 5715-5717.
51. Y. Nicolet, B. J. Lemon, J. C. Fontecilla-Camps, J. W. Peters, Trends Biochem. Sci. 2000, 25, 138-143
52. A. Holzenburg, N. S. Scrutton, Enzyme-Catalyzed Electron and Radical Transfer, Springer, New York, 2000, p.A 506.
53. L. C. Song, C. G. Li, J. H. Ge, Z. Y. Yang, H. T. Wang, J. Zhang, Q. M. Hu, J. Inorg. Biochem. 2008, 102, 1973-1979
54. F. Gloaguen, J. D. Lawrence, T. B. Rauchfuss, J. Am. Chem. Soc. 2001, 123, 9476-9477
55. C. Tard, C. J. Pickett, Chem. Rev. 2009, 109, 2245-2274.
56. X. Zhao, I. P. Georgakaki, M. L. Miller, J. C. Yarbrough, M. Y. Darensbourg, J. Am. Chem. Soc. 2001, 123, 9710-9711
57. F. Gloaguen, J. D. Lawrence, T. B. Rauchfuss, M. Benard, M. M. Rohmer, Inorg. Chem. 2002, 41, 6573-6582
58. W. B. Dong, M. Wang, X. Y. Liu, K. Jin, G. H. Li, F. J. Wang, L. C. Sun, Chem. Commun. 2006, 305-307
59. F. I. Adam, G. Hogarth, I. Richards, J. Organomet. Chem. 2007, 692, 3957-3968
60. C. M. Thomas, O. Rudiger, T. Liu, C. E. Carson, M. B. Hall, M. Y. Darensbourg, Organometallics 2007, 26, 3976-3984
61. C. Greco, M. Bruschi, P. Fantucci, L. Dea Gioia, Eur. J. Inorg. Chem. 2007, 1835-1843.