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Investigation of ion binding in chlorite dismutases by means of molecular dynamics simulations.

S√ľndermann A, Reif MM, Hofbauer S, Obinger C, Oostenbrink C - Biochemistry (2014)

Bottom Line: Chlorite dismutases are prokaryotic heme b oxidoreductases that convert chlorite to chloride and dioxygen.We report the parametrization for the GROMOS force field of the anions ClO(-), ClO2(-), ClO3(-), and ClO4(-) and describe spontaneous binding, unbinding, and rebinding events of chlorite and hypochlorite, as well as the dynamics of the conformations of Arg173 during simulations.The simulation data is discussed in comparison with experimental data on catalysis and inhibition of chlorite dismutase.

View Article: PubMed Central - PubMed

Affiliation: Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna , Muthgasse 18, A-1190 Vienna, Austria.

ABSTRACT
Chlorite dismutases are prokaryotic heme b oxidoreductases that convert chlorite to chloride and dioxygen. It has been postulated that during turnover hypochlorite is formed transiently, which might be responsible for the observed irreversible inactivation of these iron proteins. The only charged distal residue in the heme cavity is a conserved and mobile arginine, but its role in catalysis and inactivation is not fully understood. In the present study, the pentameric chlorite dismutase (Cld) from the bacterium Candidatus Nitrospira defluvii was probed for binding of the low spin ligand cyanide, the substrate chlorite, and the intermediate hypochlorite. Simulations were performed with the enzyme in the ferrous, ferric, and compound I state. Additionally, the variant R173A was studied. We report the parametrization for the GROMOS force field of the anions ClO(-), ClO2(-), ClO3(-), and ClO4(-) and describe spontaneous binding, unbinding, and rebinding events of chlorite and hypochlorite, as well as the dynamics of the conformations of Arg173 during simulations. The findings suggest that (i) chlorite binding to ferric NdCld occurs spontaneously and (ii) that Arg173 is important for recognition and to impair hypochlorite leakage from the reaction sphere. The simulation data is discussed in comparison with experimental data on catalysis and inhibition of chlorite dismutase.

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Normalized distributionsof the position of the substrate ion. The substrate ion was consideredinside the active site when the distance between the substrate ionand the heme iron was 0.8 nm or less. This threshold is shown by avertical black bar in all graphs. Tiles A and B show the simulationswith the R173A mutant structure and compound I and hypochlorite (MC)and ferric state and chlorite (MO), respectively. Tiles C and D showthe simulations with compound I and hypochlorite with the conservedarginine 173 pointing toward the substrate channel entry (CC) or towardthe heme iron (CI), respectively. Tiles E and G show the simulationswith Fe(III) state and chlorite (OC) and cyanide (ON), respectively.Tiles F and H show the simulations with Fe(II) state and chlorite(RC) and cyanide (RN), respectively. Tiles I and J show the simulationswith chlorite ions free in solution and ferric (OF) and ferrous (RF)NdCld, respectively.
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fig3: Normalized distributionsof the position of the substrate ion. The substrate ion was consideredinside the active site when the distance between the substrate ionand the heme iron was 0.8 nm or less. This threshold is shown by avertical black bar in all graphs. Tiles A and B show the simulationswith the R173A mutant structure and compound I and hypochlorite (MC)and ferric state and chlorite (MO), respectively. Tiles C and D showthe simulations with compound I and hypochlorite with the conservedarginine 173 pointing toward the substrate channel entry (CC) or towardthe heme iron (CI), respectively. Tiles E and G show the simulationswith Fe(III) state and chlorite (OC) and cyanide (ON), respectively.Tiles F and H show the simulations with Fe(II) state and chlorite(RC) and cyanide (RN), respectively. Tiles I and J show the simulationswith chlorite ions free in solution and ferric (OF) and ferrous (RF)NdCld, respectively.

Mentions: Figure 3 depicts the distribution of the distance between the heme iron andthe anions, whereas Table 5 summarizes therespective fraction being either in the heme cavity or outside. Withferric NdCld, both cyanide and chlorite remained close to the hemeiron for 100% of the simulation time (Figure 3E,G, simulations OC and ON). In comparison, in the ferrous state,cyanide spent only 11% and chlorite 30% of the time in the activesite. Figure 3F,H (simulations RC and RN) showthat some ions moved as far as into the bulk water.


Investigation of ion binding in chlorite dismutases by means of molecular dynamics simulations.

S√ľndermann A, Reif MM, Hofbauer S, Obinger C, Oostenbrink C - Biochemistry (2014)

Normalized distributionsof the position of the substrate ion. The substrate ion was consideredinside the active site when the distance between the substrate ionand the heme iron was 0.8 nm or less. This threshold is shown by avertical black bar in all graphs. Tiles A and B show the simulationswith the R173A mutant structure and compound I and hypochlorite (MC)and ferric state and chlorite (MO), respectively. Tiles C and D showthe simulations with compound I and hypochlorite with the conservedarginine 173 pointing toward the substrate channel entry (CC) or towardthe heme iron (CI), respectively. Tiles E and G show the simulationswith Fe(III) state and chlorite (OC) and cyanide (ON), respectively.Tiles F and H show the simulations with Fe(II) state and chlorite(RC) and cyanide (RN), respectively. Tiles I and J show the simulationswith chlorite ions free in solution and ferric (OF) and ferrous (RF)NdCld, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4116397&req=5

fig3: Normalized distributionsof the position of the substrate ion. The substrate ion was consideredinside the active site when the distance between the substrate ionand the heme iron was 0.8 nm or less. This threshold is shown by avertical black bar in all graphs. Tiles A and B show the simulationswith the R173A mutant structure and compound I and hypochlorite (MC)and ferric state and chlorite (MO), respectively. Tiles C and D showthe simulations with compound I and hypochlorite with the conservedarginine 173 pointing toward the substrate channel entry (CC) or towardthe heme iron (CI), respectively. Tiles E and G show the simulationswith Fe(III) state and chlorite (OC) and cyanide (ON), respectively.Tiles F and H show the simulations with Fe(II) state and chlorite(RC) and cyanide (RN), respectively. Tiles I and J show the simulationswith chlorite ions free in solution and ferric (OF) and ferrous (RF)NdCld, respectively.
Mentions: Figure 3 depicts the distribution of the distance between the heme iron andthe anions, whereas Table 5 summarizes therespective fraction being either in the heme cavity or outside. Withferric NdCld, both cyanide and chlorite remained close to the hemeiron for 100% of the simulation time (Figure 3E,G, simulations OC and ON). In comparison, in the ferrous state,cyanide spent only 11% and chlorite 30% of the time in the activesite. Figure 3F,H (simulations RC and RN) showthat some ions moved as far as into the bulk water.

Bottom Line: Chlorite dismutases are prokaryotic heme b oxidoreductases that convert chlorite to chloride and dioxygen.We report the parametrization for the GROMOS force field of the anions ClO(-), ClO2(-), ClO3(-), and ClO4(-) and describe spontaneous binding, unbinding, and rebinding events of chlorite and hypochlorite, as well as the dynamics of the conformations of Arg173 during simulations.The simulation data is discussed in comparison with experimental data on catalysis and inhibition of chlorite dismutase.

View Article: PubMed Central - PubMed

Affiliation: Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna , Muthgasse 18, A-1190 Vienna, Austria.

ABSTRACT
Chlorite dismutases are prokaryotic heme b oxidoreductases that convert chlorite to chloride and dioxygen. It has been postulated that during turnover hypochlorite is formed transiently, which might be responsible for the observed irreversible inactivation of these iron proteins. The only charged distal residue in the heme cavity is a conserved and mobile arginine, but its role in catalysis and inactivation is not fully understood. In the present study, the pentameric chlorite dismutase (Cld) from the bacterium Candidatus Nitrospira defluvii was probed for binding of the low spin ligand cyanide, the substrate chlorite, and the intermediate hypochlorite. Simulations were performed with the enzyme in the ferrous, ferric, and compound I state. Additionally, the variant R173A was studied. We report the parametrization for the GROMOS force field of the anions ClO(-), ClO2(-), ClO3(-), and ClO4(-) and describe spontaneous binding, unbinding, and rebinding events of chlorite and hypochlorite, as well as the dynamics of the conformations of Arg173 during simulations. The findings suggest that (i) chlorite binding to ferric NdCld occurs spontaneously and (ii) that Arg173 is important for recognition and to impair hypochlorite leakage from the reaction sphere. The simulation data is discussed in comparison with experimental data on catalysis and inhibition of chlorite dismutase.

Show MeSH
Related in: MedlinePlus