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Nitrite binding to globins: linkage isomerism, EPR silence and reductive chemistry.

Silaghi-Dumitrescu R, Svistunenko DA, Cioloboc D, Bischin C, Scurtu F, Cooper CE - Nitric Oxide (2014)

Bottom Line: We have used EPR (electron paramagnetic resonance) and DFT (density functional theory) to explore these binding modes to myoglobin and hemoglobin.The EPR and DFT data show that both nitrite linkage isomers can be present at the same time and that the two isomers are readily interconvertible in solution.The millisecond-scale process of nitrite reduction by Hb is investigated in search of the elusive Fe(II)-nitrite adduct.

View Article: PubMed Central - PubMed

Affiliation: "Babeş-Bolyai" University, 1 Mihail Kogalniceanu str., RO-400084 Cluj-Napoca, Romania; Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK. Electronic address: rsilaghi@chem.ubbcluj.ro.

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Left: extended models for the nitrite adducts of hemoglobin, taking into account sterical and hydrogen bonding conditions at the distal pocket around the nitrite. Right: views of the heme, perpendicular to the macrocyclic plane from a direction trans to the proximal histidine, obtained from crystal structures of Hb in the deoxy and in the ferric nitrite-bound forms (only the atoms included in our computational models are shown). These structures were employed as starting points in our calculations. Color code: carbon – gray, hydrogen – white, iron – green, porphyrin nitrogen – blue. The nitrite is shown in orange.
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f0030: Left: extended models for the nitrite adducts of hemoglobin, taking into account sterical and hydrogen bonding conditions at the distal pocket around the nitrite. Right: views of the heme, perpendicular to the macrocyclic plane from a direction trans to the proximal histidine, obtained from crystal structures of Hb in the deoxy and in the ferric nitrite-bound forms (only the atoms included in our computational models are shown). These structures were employed as starting points in our calculations. Color code: carbon – gray, hydrogen – white, iron – green, porphyrin nitrogen – blue. The nitrite is shown in orange.

Mentions: Basic models consisted of a laterally-unsubstituted heme, ligated axially by an imidazole ligand mimicking the proximal histidine, trans to a nitrite ligand bound to the iron with Fe-N distances as indicated in Fig. 1. Additionally, two sets of larger models were also constructed, starting from the α and β subunits of deoxy hemoglobin (pdb entry 2DN2). As indicated in Fig. 4, these contain the laterally-unsubstituted heme coordinated axially with protonated imidazole and nitrite respectively; to simulate the steric effect that the protein may impose, the imidazole ring of the distal histidine and the side-chain of valine 62 (cf. 2DN2 numbering) were included, and during the optimization all heavy atoms except for iron and nitrite were frozen. For each of these models both Fe(II) and Fe(III) oxidation states and low and high spin states were analyzed. Optimized structures were compared with the one described in literature for the Hb-nitrite adducts (pdb entry 3D7O).


Nitrite binding to globins: linkage isomerism, EPR silence and reductive chemistry.

Silaghi-Dumitrescu R, Svistunenko DA, Cioloboc D, Bischin C, Scurtu F, Cooper CE - Nitric Oxide (2014)

Left: extended models for the nitrite adducts of hemoglobin, taking into account sterical and hydrogen bonding conditions at the distal pocket around the nitrite. Right: views of the heme, perpendicular to the macrocyclic plane from a direction trans to the proximal histidine, obtained from crystal structures of Hb in the deoxy and in the ferric nitrite-bound forms (only the atoms included in our computational models are shown). These structures were employed as starting points in our calculations. Color code: carbon – gray, hydrogen – white, iron – green, porphyrin nitrogen – blue. The nitrite is shown in orange.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4256065&req=5

f0030: Left: extended models for the nitrite adducts of hemoglobin, taking into account sterical and hydrogen bonding conditions at the distal pocket around the nitrite. Right: views of the heme, perpendicular to the macrocyclic plane from a direction trans to the proximal histidine, obtained from crystal structures of Hb in the deoxy and in the ferric nitrite-bound forms (only the atoms included in our computational models are shown). These structures were employed as starting points in our calculations. Color code: carbon – gray, hydrogen – white, iron – green, porphyrin nitrogen – blue. The nitrite is shown in orange.
Mentions: Basic models consisted of a laterally-unsubstituted heme, ligated axially by an imidazole ligand mimicking the proximal histidine, trans to a nitrite ligand bound to the iron with Fe-N distances as indicated in Fig. 1. Additionally, two sets of larger models were also constructed, starting from the α and β subunits of deoxy hemoglobin (pdb entry 2DN2). As indicated in Fig. 4, these contain the laterally-unsubstituted heme coordinated axially with protonated imidazole and nitrite respectively; to simulate the steric effect that the protein may impose, the imidazole ring of the distal histidine and the side-chain of valine 62 (cf. 2DN2 numbering) were included, and during the optimization all heavy atoms except for iron and nitrite were frozen. For each of these models both Fe(II) and Fe(III) oxidation states and low and high spin states were analyzed. Optimized structures were compared with the one described in literature for the Hb-nitrite adducts (pdb entry 3D7O).

Bottom Line: We have used EPR (electron paramagnetic resonance) and DFT (density functional theory) to explore these binding modes to myoglobin and hemoglobin.The EPR and DFT data show that both nitrite linkage isomers can be present at the same time and that the two isomers are readily interconvertible in solution.The millisecond-scale process of nitrite reduction by Hb is investigated in search of the elusive Fe(II)-nitrite adduct.

View Article: PubMed Central - PubMed

Affiliation: "Babeş-Bolyai" University, 1 Mihail Kogalniceanu str., RO-400084 Cluj-Napoca, Romania; Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK. Electronic address: rsilaghi@chem.ubbcluj.ro.

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