Study of the Structural and Electronic Properties of the Particulate Form of the Methane Monooxygenase Enzyme (pMMO)

In this work, molecular dynamics methods based on density functional theory were used to investigate at the molecular level the structural and electronic properties of the copper mononuclear site of the pMMO enzyme, in order to assist in the interpretation of recent experimental data of electronic paramagnetic resonance (EPR). ), and in understanding how these properties can influence the enzyme's mechanism of action. The results obtained indicate that the copper mononuclear site of pMMO has its first coordination sphere sphere composed of residues His 33, His 137, His 139 and two molecules of water arising from the solution. The structural analysis of the last 50 ns of a 500 ns molecular dynamics simulation revealed that the residue Glu35, which occupies the second coordination sphere, has an important role in the composition of the catalytic site acting, through hydrogen bonds, in the stabilization of one of the water molecules coordinated to the copper ion. A systematic study, which evaluated the performance of different DFT exchange-correlation functionals in determining the RPE parameters of the investigated system against experimental data, showed that the use of hybrid functionals is more suitable than pure functionals for the calculation of RPE parameters Highlighting the functional BHANDLYP