Density functional studies of oxidized and reduced methane monooxygenase. Optimized geometries and exchange coupling of active site clusters.
The conflicting protein crystallography data for the oxidized form (MMOH(ox)) of methane monooxygenase present a dilemma regarding the identity of the solvent-derived bridging ligands within the active site: do they comprise a diiron unit bridged by 1H2O and 1OH(-) as postulated for Methylococcus capsulatus or 2OH(-) ligands as suggested for Methylosinus trichosporium? Using models derived explicitly from the M. capsulatus and M. trichosporium protein data, spin-unrestricted density functional methods have been used to study two structurally characterized forms of the hydroxylase component of methane monooxygenase. The active site geometries of the oxidized (MMOH(ox)) and two-electron-reduced (MMOH(red)) states have been geometry optimized using several quantum cluster models which take into account the antiferromagnetic (AF) and ferromagnetic (F) coupling of electron spins. Trends in cluster geometries, energetics, and Heisenberg J values have been evaluated. For the majority of models, calculated geometries are in good agreement with the X-ray analyses and appear relatively insensitive to the F or AF alignment of electron spins on adjacent Fe sites. Discrepancies between calculation and experiment appear in the orientation of the coordinated His and Glu amino acid side chains for both MMOH(ox) and MMOH(red) and also in unexpected intramolecular proton transfer in the MMOH(ox) cluster models. There is additional dispersion between (and among) calculated and experimental Fe(3+)-OH(-) distances with relevance to the correct protonation state of the solvent-derived ligands. In an accompanying paper (Lovell, T.; Li, J.; Noodleman, L. Inorg. Chem. 2001, 40, 5267), a comparison of the related energetics of the active site models examined herein is further evaluated in the full protein and solvent environment.
Lovell
T
T
Department of Molecular Biology TPC-15, The Scripps Research Institute, La Jolla, California 92037, USA. tlovell@scripps.edu
Li
J
J
Noodleman
L
L
D001665:Binding Sites; D020619:Methylococcus capsulatus / Q000201:enzymology; D008956:Models, Chemical; D008958:Models, Molecular; D010084:Oxidation-Reduction; D010105:Oxygenases / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory
D010105:Oxygenases; C021555:methane monooxygenase