Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe–NO Ligand Orientations in Myoglobin Distal Pockets

Abstract

The globular dioxygen binding heme protein myoglobin (Mb) is present in several species. Its interactions with the simple nitrogen oxides, namely, nitric oxide (NO) and nitrite, have been known for decades, but the physiological relevance has only recently become more fully appreciated. We previously reported the O-nitrito mode of binding of nitrite to ferric horse heart wild-type (wt) Mb and human hemoglobin. We have expanded on this work and report the interactions of nitrite with wt sperm whale (sw) Mb and its H64A, H64Q, and V68A/I107Y mutants whose dissociation constants increase in the following order: H64Q < wt < V68A/I107Y < H64A. We also report their X-ray crystal structures that reveal the O-nitrito mode of binding of nitrite to these derivatives. The Mb-mediated reductions of nitrite to NO and structural data for the wt and mutant Mb-NOs are described. We show that their FeNO orientations vary with distal pocket identity, with the FeNO moieties pointing toward the hydrophobic interiors when the His64 residue is present but toward the hydrophilic exterior when this His64 residue is absent in this set of mutants. This correlates with the nature of H-bonding to the bound NO ligand (nitrosyl O vs N atom). Quantum mechanics and hybrid quantum mechanics and molecular mechanics calculations help elucidate the origin of the experimentally preferred NO orientations. In a few cases, the calculations reproduce the experimentally observed orientations only when the whole protein is taken into consideration.

Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2ndsphere interactions in catalysis

“…Several studies revealed that both haemoglobin (Hb) and myoglobin (Mb) have nitrite reductase activity with the capability to generate NO. [276][277][278] Such heme based nitrite reduction generally proceeds through N-bound nitrite complex as the starting point, similar to that observed for bacterial NiRs. Mechanistic studies revealed that such reduction pathway proceeds to the formation of {FeNO} 7 complexes of Hb or Mb (eqn ( 7) and ( 8)).…”

“…Mechanistic studies revealed that such reduction pathway proceeds to the formation of {FeNO} 7 complexes of Hb or Mb (eqn ( 7) and ( 8)). 277 An alternative possible reduction pathway through O-bound complex was first explored by Radu Silaghi-Dumitrescu in Cd 1 NiR. 279 Theoretical calculations suggested that this reaction proceeded through a protonation from distal histidine residue leading to formation of hydroxo-Fe(III) complex and NO.…”

Redesign of a Copper Storage Protein into an Artificial Hydrogenase

“…In addition, the average Ni-Cys bond length ( R Ni–S ) of 2.31 Å in 1 NBP-SP is in excellent agreement with the experimental average value of 2.29 Å and has much better agreement with experiment than the average Ni-Cys bond lengths of 2.35 and 2.44 Å for 1 NBP-TH and 3 NBP-TH, respectively. Additional computational results in Supporting Information (Figure S9) suggest that the protein environment plays a significant role in determining the final electronic and geometric structure for Ni center here, and the full protein QM/MM calculations are needed to reproduce experimental protein results as reported recently …”

“…Additional computational results in Supporting Information (Figure S9) suggest that the protein environment plays a significant role in determining the final electronic and geometric structure for Ni center here, and the full protein QM/MM calculations are needed to reproduce experimental protein results as reported recently. 49 Photoinduced H + Reduction by NBP. We next tested whether Ni(II)-NBP can generate H 2 gas under photochemical conditions, employing Ru(bpy) 3 2+ as a photosensitizer and ascorbate as a sacrificial electron donor.…”

Biological and Bioinspired Inorganic N–N Bond-Forming Reactions

“…denitrificans cNOR (PdNOR) with NO that occurred within 2 μs upon photolysis . The reconstructed spectrum was similar to that of the reduced myoglobin NO adduct, with a trough at 430 nm and a peak at 410 nm, overall characteristic of ligand binding to reduced high-spin hemes. Time- and temperature-dependent rapid freeze quench (RFQ) EPR studies identified two Fe–nitrosyl signals within 0.5 ms after NO addition .…”