TY - JOUR
T1 - Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from Desulfovibrio gigas
AU - Soares, Claudio Manuel
AU - Baptista, Antonio Manuel
AU - Victor, Bruno Lourenco
PY - 2009/1/1
Y1 - 2009/1/1
N2 - 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 O-2 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 O-2 and/or NO at the active site. By using free-energy simulations, we did not find any significant preference for ROO to accommodate both O-2 and NO. Also, from our molecular dynamics simulations we were able to identify similar diffusion profiles for both O-2 and NO molecules. These two conclusions are in good agreement with previous experimental works stating that ROO is able to catalyze both O-2 and NO.
AB - 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 O-2 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 O-2 and/or NO at the active site. By using free-energy simulations, we did not find any significant preference for ROO to accommodate both O-2 and NO. Also, from our molecular dynamics simulations we were able to identify similar diffusion profiles for both O-2 and NO molecules. These two conclusions are in good agreement with previous experimental works stating that ROO is able to catalyze both O-2 and NO.
KW - Diffusion
KW - escherichia-coli
KW - oxygen
KW - o-2
KW - electron-transfer
KW - Rubredoxin:oxygen oxidoreductase
KW - active-site
KW - free-energy
KW - Oxygen
KW - in-vivo
KW - Nitric oxideMolecular dynamics
KW - flavodiiron proteins
KW - simulation
U2 - 10.1007/s00775-009-0497-5
DO - 10.1007/s00775-009-0497-5
M3 - Article
VL - 14
SP - 853
EP - 862
JO - Journal Of Biological Inorganic Chemistry
JF - Journal Of Biological Inorganic Chemistry
SN - 0949-8257
IS - 6
ER -