Computational Studies on Enzyme-Substrate Complexes of Methanogenesis for Revealing their Substrate Binding Affinities to Direct the Reverse Reactions

In the present work, a combined approach of molecular modeling and systems biology was used to reveal how structural dynamics of enzymes involving in methanogenesis contributed to do reverse methanogenic reactions in methanotrophic archaea. The binding energies and molecular interaction distances of homology models and crystallographic structures of each enzyme with corresponding substrates were computed and its binding affinity compared with experimental enzyme kinetic data. The binding energies of enzyme model-substrate complexes in each reaction were favored to reverse reactions compared to PDB structure-substrate complexes, supporting the existence of structural motions to direct substrate specificities in reverse order. Based on these, a proposed metabolic pathway for reverse methanogenesis in methanotrophic archaea was constructed, and its metabolic flux balance analyzed with experimental data of each enzyme reaction step. Methyl CoM reductase and methylene tetrahydromethanopterin reductase were assumed to determine the rate of the reverse methanogenesis reactions. Pathway model of this study should be concerned on understanding the cellular behavior of reverse methanogenesis in response to methane consumption from environment. Binding mode analysis of enzymes is thus directly correlated to molecular conservation and functional divergence of reverse methanogenesis, which lends strong support to reveal the molecular evolutionary hypothesis for methanotrophic archaea.