4.4 Article

Catalytic mechanism of butane anaerobic oxidation for alkyl-coenzyme M reductase

期刊

CHEMICAL BIOLOGY & DRUG DESIGN
卷 98, 期 5, 页码 701-712

出版社

WILEY
DOI: 10.1111/cbdd.13931

关键词

alkyl-coenzyme M reductase; butane; dynamics correlation network; molecular dynamics simulation

资金

  1. Center for HPC at Shanghai Jiao Tong University
  2. National Key Research and Development Program of China [2018YFC0310803, 2020YFA0907700]
  3. National Natural Science Foundation of China [31770771, 21977068, 31620103901]

向作者/读者索取更多资源

The study compared the catalytic mechanisms of butane coenzyme M reductase (ACR) and methane coenzyme M reductase (MCR) using molecular dynamics simulation. Results showed that the binding of butane with ACR is more stable, with stronger hydrophobic interactions compared to methane binding. The dynamics correlation network also indicated a smoother flow of information for ACR-butane compared to ACR-methane.
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.

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