Theoretical Investigation of the "CO in"-"CO out" Isomerization in a [2Fe-2S] Ferredoxin: Free Energy Profiles and Redox States

Journal of the American Chemical Society

Volumn 125, Issue 49, 2003, Pages 15224-15232

  Pizzitutti, Francesco ^a,b   Sétif, Pierre ^a   Marchi, Massimo ^a  

^a DIF   (France)

^b SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BACTERIA; COMPUTER SIMULATION; CONFORMATIONS; FREE ENERGY; HYDROGEN BONDS;

ELECTRON TRANSFER;

PROTEINS;

CARBON MONOXIDE; FERREDOXIN;

ANABAENA; ARTICLE; CALCULATION; CYANOBACTERIUM; ELECTRON TRANSPORT; ENERGY; HYDRATION; HYDROGEN BOND; ISOMERISM; MOLECULAR DYNAMICS; OXIDATION REDUCTION REACTION; SIMULATION;

CARBON MONOXIDE; COMPUTER SIMULATION; CYANOBACTERIA; FERREDOXINS; MODELS, MOLECULAR; OXIDATION-REDUCTION; PROTEIN CONFORMATION; SOLUTIONS; THERMODYNAMICS;

EID: 0345529131     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0370286     Document Type: Article

References (41)

1. Holm, R.; Kennepohl, P.; Solomon, E. Chem. Rev. 1996, 96, 2239.
2. Johnson, M. Cur. Opin. Chem. Biol. 1998, 2, 173.
3. Beinert, H.; Holm, R.; Münck Science 1997, 277, 653.
4. Setif, P. Biophys. Acta 2001, 1507, 161.
5. Hurley, J. K.; Morales, R.; Martinez-Julvez, M.; Brodie, T. B.; Medina, M.; Gomez-Moreno, C.; Tollin, G. Biochim. Biophys. Acta 2002, 1554, 5.
6. Setif, P.; Bottin, H. Biochemistry 1994, 33, 8495.
7. Holden, H.; B. L., J.; J. K., H.; Tollin, G.; Oh, B.; Skjeldahl, L.; Chae, Y.; Cheng, H.; Xia, B.; J. L., M. J. Bioenerg. Biomembr 1994, 26, 67.
8. Hurley, J. K.; abd Morales, R.; Martinez-Julvez, M.; Brodie, T.; Medina, M.; Gomez-Moreno, C.; Tollin, G. BBA-Bioenergetics 2002, 1554, 5.
9. Morales, R.; Kachalova, G.; Vellieux, F.; Charon, M.; Frey, M. Acta Crystallogr. D 2000, 56, 1408.
10. Kurisui, G.; Kusunoki, M.; Katoh, E.; Yamazaki, T.; Teshima, K.; Onda, Y.; Kimata-Ariga, Y.; Hase, T. Nat. Struct. Biol. 2001, 8, 117.
11. Setif, P.; Fischer, N.; Lagoutte, B.; Bottin, H.; Rochaix, J.-D. Biochim. Biophys. Acta 2002, 1555, 204.
12. Morales, R.; Chron, M.; Hudry-Clergeon, G.; Pétillot, Y.; Norager, S.; Medina, M.; Frey, M. Biochemistry 1999, 38, 15 764.
13. Li, J.; Nelson, M. R.; Peng, C. Y.; Bashford, D.; Noodleman, L. J. Phys. Chem. A 1998, 102, 6311.
14. Morales, R.; Frey, M.; Mouesca, J. J. Am. Chem. Soc. 2002, 124, 6714.
15. Hurley, J.; Cheng, H.; Xia, B.; Markley, J.; Medina, M.; Gomez-Moreno, C.; Tollin, G. J. Am. Chem. Soc. 1993, 115, 11 698.
16. Procacci, P.; Darden, T.; Pacy, E.; Marchi, M. J. Comput. Chem. 1997, 18, 157.
17. Procacci, P.; Marchi, M. In Advances in the Computer Simulations of Liquid Crystals; Zannoni, C., Pasini, P., Eds.; Proceedings of the NATO-ASI School, Erice 11-21 June 1998, Dodrecht The Netherlands 1999; Kluwer Academic: 1999; 333.
18. Marchi, M.; Procacci, P. J. Chem. Phys. 1998, 109, 5194.
19. Tuckerman, M.; Berne, B. J.; Martyna, G. J. J. Chem. Phys. 1992, 97, 1990.
20. Essmann, U.; Perera. L.; Berkowitz, M. L.; Darden. T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.
21. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. Comput. Phys. 1977, 23, 327.
22. Andersen, H. C. J. Comput. Phys. 1983, 52, 24.
23. Ciccotti, G.; Ryckaert, J.-P. Computer Phys. Rep. 1986, 4, 345.
24. MacKerell, A., Jr.; Bashford, D.; Bellot, M.; Dunbrack, R., Jr.; Evanseck. J.; Field, M.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D.; Prodhom, B.; W. R., II.; Roux, B.; Schlenkrich, M.; Smit, J. Q.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-kuczera, J.; Yin, D.; Karplux, M. J. Phys. Chem B 1998, 102, 3586.
25. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
26. Torrie, G. M.; Valleau, J. P. Chem. Phys. Lett. 1974, 28, 578.
27. Ferrenberg, A. M.; Swendsen, R. H. Phys. Rev. Lett. 1989, 63, 1195.
28. Sterpone, F.; Ceccarelli, M.; Marchi, M. J. Mol. Biol. 2001, 311, 409.
29. Marchi, M.; Sterpone, F.; Ceccarelli, M. J. Am. Chem. Soc. 2002, 124, 6787.
30. Marchi, M. J. Phys. Chem. B 2003, 107, 6598.
31. Ibragimova, G.; Wade, R. Biophys. J. 1998, 74, 2906.
32. Rypniewski, I.; Breiter, D.; Bennins, M.; Wesemberg, G.; Ho, B.; Markley, J.; Rayement, I.; Holde, H. Biochemistry 1991, 30, 4126.
33. Shelley, J. C.; Sprik, M.; Klein, M. L. Langmuir 1993, 9, 916.
34. Marchi, M.; Akasaka, K. J. Phys. Chem. B 2001, 105, 711.
35. Cornell, W. D.; Cieplak, P.; Bavly, C. I.; Gould, I. R.; Merz, K. M., Jr.: Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollmann, P. J. Am. Chem. Soc. 1995, 117, 5179.
36. Ceccarelli, M.; Marchi, M. J. Phys. Chem. B 2003, 107, 5630.
37. Sterpone, F.; Ceccarelli, M.; Marchi, M. J. Phys. Chem. B 2003, 107, 11 208.
38. Hurley, J.; Weber-Main, A.; Stankovich, M.; Benning, M.; Thoden, J.; Vanhooke, J.; Holden, H.; Chae, Y.; Xia, B.; Cheng, H.; Markley, J.; Martinez-Julvez, M.; GomezMoreno, C.; Schmeits, J.; Tollin, G. Biochemistry 1997, 36, 11 100.
39. Bréttel, K. Biochim. Biophys. Acta 1997, 1318, 322.
40. Two Fd7119 conformations are found for each of the two crystallographic molecules: Alternate location A, and alternate location B.
41. -1,39 respectively. Second, from Figure 5, about +9 kcal mol-I are necessary to go from "CO out" to "CO in" in the reduced ferredoxin. The sum of these two energies is our estimate of the electron transfer from PSI to the "CO in" state of ferredoxin.