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

Sündermann 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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Structure of the pentameric chlorite dismutase from Candidatus Nitrospira defluvii. The five different monomersare colored differently, and the secondary structure elements areshown in a cartoon representation, while the side chains are shownas sticks. The heme is also shown with a stick representation, andthe substrate ions in the active sites are shown with a bubble representation.
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fig1: Structure of the pentameric chlorite dismutase from Candidatus Nitrospira defluvii. The five different monomersare colored differently, and the secondary structure elements areshown in a cartoon representation, while the side chains are shownas sticks. The heme is also shown with a stick representation, andthe substrate ions in the active sites are shown with a bubble representation.

Mentions: Theatom-positional root-mean-square deviation (rmsd) with respect tothe crystal structures 3nn1 and 3nn3 was in the range between 0.16 and 0.19 nm with a statistical uncertaintyof 0.01–0.03 nm. No significant deviations from the crystalstructure were observed. Moreover, the rmsd of the mutant is comparableto wild-type NdCld. Secondary structure elements over time were analyzedusing the DSSP algorithm. The predominant α-helical structure(Figure 1) did not change significantly duringthe simulations. The percentage of amino acids that are part of ahelix over 10 ns of simulations over all five monomers ranges from42.0% to 43.5% with a statistical uncertainty of 0.5% to 1.5% determinedvia block averaging.39 In the crystal structuresof wild-type NdCld and the variant R173A 43.9% and 44.3% of the aminoacids are part of α-helical structures. The major helices didnot unfold during the various simulations. Furthermore, the β-sheetstructures at the center of each monomer were analyzed. The percentageof amino acids that are part of a β-sheet structure over thesimulation time over all five monomers was found to range from 22.4%to 23.8% with a statistical uncertainty of 0.5% to 2.8%. This compareswith 25.5% and 24.7% found in the crystal structures of the wild-typeand mutant proteins. The absence of significant changes of secondarystructure elements, as well as the low rmsd values for all simulationsclearly suggest that the monomers of NdCld are very stable duringthe simulations.


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

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

Structure of the pentameric chlorite dismutase from Candidatus Nitrospira defluvii. The five different monomersare colored differently, and the secondary structure elements areshown in a cartoon representation, while the side chains are shownas sticks. The heme is also shown with a stick representation, andthe substrate ions in the active sites are shown with a bubble representation.
© Copyright Policy
Related In: Results  -  Collection

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

fig1: Structure of the pentameric chlorite dismutase from Candidatus Nitrospira defluvii. The five different monomersare colored differently, and the secondary structure elements areshown in a cartoon representation, while the side chains are shownas sticks. The heme is also shown with a stick representation, andthe substrate ions in the active sites are shown with a bubble representation.
Mentions: Theatom-positional root-mean-square deviation (rmsd) with respect tothe crystal structures 3nn1 and 3nn3 was in the range between 0.16 and 0.19 nm with a statistical uncertaintyof 0.01–0.03 nm. No significant deviations from the crystalstructure were observed. Moreover, the rmsd of the mutant is comparableto wild-type NdCld. Secondary structure elements over time were analyzedusing the DSSP algorithm. The predominant α-helical structure(Figure 1) did not change significantly duringthe simulations. The percentage of amino acids that are part of ahelix over 10 ns of simulations over all five monomers ranges from42.0% to 43.5% with a statistical uncertainty of 0.5% to 1.5% determinedvia block averaging.39 In the crystal structuresof wild-type NdCld and the variant R173A 43.9% and 44.3% of the aminoacids are part of α-helical structures. The major helices didnot unfold during the various simulations. Furthermore, the β-sheetstructures at the center of each monomer were analyzed. The percentageof amino acids that are part of a β-sheet structure over thesimulation time over all five monomers was found to range from 22.4%to 23.8% with a statistical uncertainty of 0.5% to 2.8%. This compareswith 25.5% and 24.7% found in the crystal structures of the wild-typeand mutant proteins. The absence of significant changes of secondarystructure elements, as well as the low rmsd values for all simulationsclearly suggest that the monomers of NdCld are very stable duringthe simulations.

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