SCAN:Identification of structural regulators for substrate selectivity in different Flavodiiron proteins

ITQB Scan Seminar

Title: Identification of structural regulators for substrate selectivity in different Flavodiiron proteins

Speaker: Bruno L. Victor

Affiliation: Protein Modeling Group-ITQB

Abstract:

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. 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. 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. To further characterize the substrate selectivity of this protein family we have carried out equivalent simulations in two other proteins of this family: the FDP from Giardia intestinalis, which is a strict O2 reducing protein, and the FDP from Escherichia coli described to be a strict NO reducing protein. Since these two proteins catalyze the reduction of a single substrate molecule we were aiming to ascertain the structural molecular basis for substrate selectivity. From our results we could conclude that the substrate selectivity is not related with the access pathways of substrate molecules to the active site, but by a still unknown factor which may be related with the singularity of the catalytic site found in these proteins.