JBIC Journal of Biological Inorganic Chemistry

, Volume 14, Issue 6, pp 853–862 | Cite as

Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from Desulfovibrio gigas

  • Bruno L. Victor
  • António M. Baptista
  • Cláudio M. SoaresEmail author
Original Paper


Rubredoxin:oxygen oxidoreductase (ROO) is the terminal oxidase of a soluble electron transfer chain found in Desulfovibrio gigas. This protein belongs to the flavodiiron family and was initially described as an oxygen reductase, converting this substrate to water and acting as an oxygen-detoxifying system. However, more recent studies evidenced also the ability for this protein to act as a nitric oxide reductase, suggesting an alternative physiological role. To clarify the apparent bifunctional nature of this protein, we performed molecular dynamics simulations of the protein, in different redox states, together with O2 and NO molecules in aqueous solution. The two small molecules were parameterized using free-energy calculations of the hydration process. With these simulations we were able to identify specific protein paths that allow the diffusion of both these molecules through the protein towards the catalytic centers. Also, we have tried to characterize the preference of ROO towards the presence of O2 and/or NO at the active site. By using free-energy simulations, we did not find any significant preference for ROO to accommodate both O2 and NO. Also, from our molecular dynamics simulations we were able to identify similar diffusion profiles for both O2 and NO molecules. These two conclusions are in good agreement with previous experimental works stating that ROO is able to catalyze both O2 and NO.


Rubredoxin:oxygen oxidoreductase Diffusion Oxygen Nitric oxide Molecular dynamics 



We thank João Vicente and Miguel Teixeira for fruitful discussions about FDPs. This work was supported by grants 36560/1999/FCT-Sapiens and by fellowship SFRH/BD/10622/2002 from Fundação para a Ciência ea Tecnologia, Portugal.

Supplementary material

775_2009_497_MOESM1_ESM.pdf (353 kb)
Supplementary material 1 (PDF 352 kb)


  1. 1.
    Andersson JO, Sjogren AM, Davis LA, Embley TM, Roger AJ (2003) Curr Biol 13:94–104PubMedCrossRefGoogle Scholar
  2. 2.
    Vicente JB, Carrondo MA, Teixeira M, Frazão C (2007) In: Messerschmidt A (ed) Handbook of metalloproteins. Wiley, New York, pp 1–19Google Scholar
  3. 3.
    Vicente JB, Carrondo MA, Teixeira M, Frazao C (2008) Methods Enzymol 437:3–19PubMedCrossRefGoogle Scholar
  4. 4.
    Chen L, Liu MY, LeGall J, Fareleira P, Santos H, Xavier AV (1993) Biochem Biophys Res Commun 193:100–105PubMedCrossRefGoogle Scholar
  5. 5.
    Frazão C, Silva G, Gomes CM, Matias P, Coelho R, Sieker L, Macedo S, Liu MY, Oliveira S, Teixeira M, Xavier AV, Rodrigues-Pousada C, Carrondo MA, LeGall J (2000) Nat Struct Biol 7:1041–1045PubMedCrossRefGoogle Scholar
  6. 6.
    Dilling W, Cypionka H (1990) FEMS Microbiol Lett 71:123–128Google Scholar
  7. 7.
    Santos H, Fareleira P, Xavier A, Chen L, Liu MY, LeGall J (1993) Biochem Biophy Res Commun 195:551–557CrossRefGoogle Scholar
  8. 8.
    Gardner A, Helmick R, Gardner P (2002) J Biol Chem 277:8172–8177Google Scholar
  9. 9.
    Gomes CM, Giuffrè A, Forte H, Vicente JB, Saraiva L, Brunori M, Teixeira M (2002) J Biol Chem 277:25273–25276Google Scholar
  10. 10.
    Gomes CM, Vicente JB, Wasserfallen A, Teixeira M (2000) Biochemistry 39:16230–16237PubMedCrossRefGoogle Scholar
  11. 11.
    Rodrigues R, Vicente JB, Felix R, Oliveira S, Teixeira M, Rodrigues-Pousada C (2006) J Bacteriol 188:2745–2751PubMedCrossRefGoogle Scholar
  12. 12.
    Silaghi-Dumitrescu R, Ng KY, Viswanathan R, Kurtz DM Jr (2005) Biochemistry 44:3572–3579PubMedCrossRefGoogle Scholar
  13. 13.
    Chen L, Liu MY, LeGall J, Fareleira P, Santos H, Xavier AV (1993) Eur J Biochem 216:443–448PubMedCrossRefGoogle Scholar
  14. 14.
    Gomes CM, Silva G, Oliveira S, LeGall J, Liu MY, Xavier AV, Rodrigues-Pousada C, Teixeira M (1997) J Biol Chem 272:22502–22508PubMedCrossRefGoogle Scholar
  15. 15.
    Victor BL, Vicente JB, Rodrigues R, Oliveira S, Rodrigues-Pousada C, Frazão C, Gomes CM, Teixeira M, Soares CM (2003) J Biol Inorg Chem 8:475–488PubMedGoogle Scholar
  16. 16.
    Saraiva LM, Vicente JB, Teixeira M (2004) Adv Microb Physiol 49:77–129Google Scholar
  17. 17.
    DeLano WL (2003) PyMOL. DeLano Scientific, San CarlosGoogle Scholar
  18. 18.
    Cohen J, Kim K, King P, Seibert M, Schulten K (2005) Structure 13:1321–1329PubMedCrossRefGoogle Scholar
  19. 19.
    Cohen J, Kim K, Posewitz M, Ghirardi ML, Schulten K, Seibert M, King P (2005) Biochem Soc Trans 33:80–82PubMedCrossRefGoogle Scholar
  20. 20.
    Montet Y, Amara P, Volbeda A, Vernede X, Hatchikian EC, Field MJ, Frey M, Fontecilla-Camps JC (1997) Nat Struct Biol 4:523–526PubMedCrossRefGoogle Scholar
  21. 21.
    Teixeira VH, Baptista AM, Soares CM (2006) Biophys J 91:2035–2045PubMedCrossRefGoogle Scholar
  22. 22.
    Lancaster JR (1994) Proc Natl Acad Sci USA 91:8137–8141Google Scholar
  23. 23.
    Elber R, Karplus M (1990) J Am Chem Soc 112:9161–9175CrossRefGoogle Scholar
  24. 24.
    Hofacker I, Schulten K (1998) Proteins Struct Funct Genet 30:100–107PubMedCrossRefGoogle Scholar
  25. 25.
    Wilhelm E, Battino R, Wilcock RJ (1977) Chem Rev 77:219–262CrossRefGoogle Scholar
  26. 26.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA Jr, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cuik Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Baboul AG, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Gonzalez C, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Andres JL, Head-Gordon M, Replogle ES, Pople JA (1998) Gaussian 98. Gaussian, PittsburghGoogle Scholar
  27. 27.
    Bayly CI, Cieplak P, Cornell WD, Kollman PA (1993) J Phys Chem 97:10269–10280CrossRefGoogle Scholar
  28. 28.
    Cohen J, Arkhipov A, Braun R, Schulten K (2006) Biophys J 91:1844–1857PubMedCrossRefGoogle Scholar
  29. 29.
    Dhib M, Bouanich JP, Aroui H, Picard-Bersellini A (2001) J Quant Spectrosc Radiat Transf 68:163–178CrossRefGoogle Scholar
  30. 30.
    Eslami H, Mozaffari F, Boushehri A (2001) Int J Therm Sci 40:999–1010CrossRefGoogle Scholar
  31. 31.
    Lin ST, Hsu HW (1969) J Chem Eng Data 14:328–332Google Scholar
  32. 32.
    Pawlikowski EM, Prausnitz JM (1983) Ind Eng Chem Fund 22:86–90CrossRefGoogle Scholar
  33. 33.
    Tan ZQ, Gao GH, Yu YX, Gu C (2001) Fluid Phase Equilib 180:375–382CrossRefGoogle Scholar
  34. 34.
    Tiepel EW, Gubbins KE (1973) Ind Eng Chem Fund 12:18–25CrossRefGoogle Scholar
  35. 35.
    Berendsen HJC, Vanderspoel D, Vandrunen R (1995) Comput Phys Commun 91:43–56CrossRefGoogle Scholar
  36. 36.
    Scott WR, Hunenberger PH, Tironi IG, Marck AE, Billeter SR, Fennen J, Torda AE, Huber T, Kruger P, van Gunsteren WF (1999) J Phys Chem A 103:3596–3607CrossRefGoogle Scholar
  37. 37.
    van Gunsteren WF, Berendsen HJC (1990) Angew Chem Int Ed Engl 29:992–1023CrossRefGoogle Scholar
  38. 38.
    Hermans J, Berendsen HJC, Vangunsteren WF, Postma JPM (1984) Biopolymers 23:1513–1518CrossRefGoogle Scholar
  39. 39.
    Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) J Comput Chem 18:1463–1472CrossRefGoogle Scholar
  40. 40.
    Miyamoto S, Kollman PA (1992) J Comput Chem 13:952–962CrossRefGoogle Scholar
  41. 41.
    Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) J Chem Phys 81:3684–3690CrossRefGoogle Scholar
  42. 42.
    Shirts MR, Pitera JW, Swope WC, Pande VS (2003) J Chem Phys 119:5740–5761CrossRefGoogle Scholar
  43. 43.
    Ben-Naim A (1978) J Phys Chem 82:792–803CrossRefGoogle Scholar
  44. 44.
    Ben-Naim A (1992) Statistical thermodynamics for chemists and biochemists. Plenum Press, New YorkGoogle Scholar
  45. 45.
    Bashford D, Gerwert K (1992) J Mol Biol 224:473–486PubMedCrossRefGoogle Scholar
  46. 46.
    Baptista AB, Soares CM (2001) J Phys Chem B 105:293–309CrossRefGoogle Scholar
  47. 47.
    Teixeira VH, Cunha CA, Machuqueiro M, Oliveira AS, Victor BL, Soares CM, Baptista AM (2005) J Phys Chem B Condens Matter Mater Surf Interfaces Biophys 109:14691–14706PubMedGoogle Scholar
  48. 48.
    Lindahl E, Hess B, van der Spoel D (2001) J Mol Model 7:306–317Google Scholar
  49. 49.
    Beveridge DL, Dicapua FM (1989) Annu Rev Biophys Biophys Chem 18:431–492PubMedCrossRefGoogle Scholar
  50. 50.
    Victor BL, Baptista AM, Soares CM (2004) Biophys J 87:4316–4325PubMedCrossRefGoogle Scholar
  51. 51.
    Silaghi-Dumitrescu R, Kurtz DM, Ljungdahl LG, Lanzilotta WN (2005) Biochemistry 44:6492–6501PubMedCrossRefGoogle Scholar
  52. 52.
    Seedorf H, Hagemeier CH, Shima S, Thauer RK, Warkentin E, Ermler U (2007) FEBS J 274:1588–1599PubMedCrossRefGoogle Scholar
  53. 53.
    Di Matteo A, Scandurra FM, Testa F, Forte E, Sarti P, Brunori M, Giuffre A (2008) J Biol Chem 283:4061–4068PubMedCrossRefGoogle Scholar

Copyright information

© SBIC 2009

Authors and Affiliations

  • Bruno L. Victor
    • 1
  • António M. Baptista
    • 1
  • Cláudio M. Soares
    • 1
    Email author
  1. 1.Instituto de Tecnologia Química e BiológicaUniversidade Nova de LisboaOeirasPortugal

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