Methane is among the most potent of the greenhouse gases, which plays a key role in global climate change. As an excellent carbon and energy source, methane can be utilized by anaerobic methane oxidizing archaea and aerobic methane oxidizing bacteria. The previous work shows that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C4 hydrocarbon butane. However, the catalytic mechanism of butane anaerobic oxidation for alkyl-coenzyme M reductase is still unknown. Therefore, molecular dynamics (MD) simulation was used to investigate the dynamics differences of catalytic mechanism between methane coenzyme M reductase (MCR) and alkyl-coenzyme M reductase (ACR). At first, the binding pocket of ACR is larger than that of MCR. Then, the complex of butane and ACR is more stable than that of methane and ACR. Protein conformation cloud suggests that the position of methane is dynamics and methane escapes from the binding pocket of ACR during most of the simulation time, while butane tightly binds in the pocket of ACR. The hydrophobic interactions between butane and ACR are more and stronger than those between methane and ACR. At the same time, the binding free energy between butane and ACR is significantly lower than that between methane and ACR. The dynamics correlation network indicates that the transformation of information flow for ACR-butane is smoother than that for ACR-methane. The shortest pathway for ACR-butane is from Gln144, Ala141, Hie135, Ile133, Ala160, Arg206, Asp97, Met94, Tyr347 to Phe345 with synergistic effect for two butane molecules. This study can insight into the catalytic mechanism for butane/ACR complex.
Keywords: alkyl-coenzyme M reductase; butane; dynamics correlation network; molecular dynamics simulation.
© 2021 John Wiley & Sons A/S.