Methane bioconversion to methanol by <i>Methylotuvimicrobium buryatense</i> 5GB1C: mechanistic insights using molecular simulations

This paper reports homology modeling and molecular simulation studies of methane bioconversion to methanol by the particulate methane monooxygenase (pMMO) enzyme complex in <i>Methylotuvimicrobium buryatense</i> 5GB1C. Homology modeling predicted the 3D structures of key enzymes (PmoA, PmoB, PmoC) involved. Molecular docking studies revealed the binding energies of -1.75, -1.84 and -1.79 kcal/mol for methane and -2.13, -2.45 and -2.35 kcal/mol for methanol with PmoA, PmoB and PmoC, respectively, in the presence of cofactors of NADH, Cu cation and oxygen. Molecular dynamics simulations provided further insights to evaluate the stability of the docked complexes over a 100 ns simulation, and analyzed the trajectories to measure root mean square deviation (RMSD), root mean square fluctuation (RMSF), intermolecular hydrogen bonding (H-bond), and radius of gyration (Rg). The analyses revealed a low binding affinity of methane with the enzyme complex due to a lack of hydrogen bonding, which is a result of the small size and non-polar nature of methane. Docking analysis also indicated competition between methane and methanol for binding with proteins due to common residues of the active site. In addition, the instability of the ligand-enzyme complex consequently resulted in poor methane conversion, leading to low methanol titers, which were otherwise attributed to mass transfer limitation.