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Investigating substrate pathways in Flavodiiron proteins

Substracte specificity in Flavodiiron proteins


Collaboration between the Laboratories of Miguel Teixeira and Cláudio M. Soares.


Financed project: PTDC/BIA-PRO/67263/2006 “Microbial enzymes involved in superoxide and nitric oxide reduction”


Flavodiiron proteins


Flavodiiron proteins (FDPs) are a family of proteins acting on the detoxification of nitric oxide (NO) and dioxygen (O2) in anaerobes and microaerophiles. NO and other nitrogen reactive species are cytotoxic to microbes since they are produced by macrophages as part of the immune infection response in both mammalian and plants. In anaerobic organisms, O2 and other reactive oxygen species can also act as dangerous molecules to organism viability.



ROO crystallographic structure


Rubredoxin:Oxygen Oxidoreductase (ROO) is an example of a FDP protein found in Desulfovibrio gigas. This protein is the terminal oxidase of a soluble electron transfer chain and was described to reduce both O2 and NO molecules. In order to clarify the apparent bifunctional nature of the protein, we performed several Molecular Dynamics and Free energy simulations of the protein, in different redox states, together with O2 and NO molecules.


Molecular Density Maps of the diffusion of oxygen in the presence of ROO

With these simulations we were able to identify specific protein channels that allow the permeation of both these molecules through the protein matrix towards the catalytic centers. In accordance with its bifunctional activity, we have also found that both O2 and NO molecules show similar stabilities when placed inside the catalytic pocked of the protein (Victor, et al, 2009, JBIC).

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