ONIOM Study of the Mechanism of the Enzymatic Hydrolysis of Biodegradable Plastics

DOI PDF Web Site 被引用文献4件 参考文献68件
  • Sakae Yoshitake
    Center for Quantum Life Sciences and Graduate School of Science, Hiroshima University
  • Matsubara Toshiaki
    Center for Quantum Life Sciences and Graduate School of Science, Hiroshima University
  • Aida Misako
    Center for Quantum Life Sciences and Graduate School of Science, Hiroshima University
  • Kondo Hidemasa
    Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology
  • Masaki Kazuo
    National Research Institute of Brewing
  • Iefuji Haruyuki
    National Research Institute of Brewing

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A cutinase-like enzyme (CLE), which is purified experimentally from the yeast Cryptococcus sp. strain S-2, has been recently found to degrade biodegradable plastics very efficiently. In this study, we theoretically examine the mechanism of hydrolysis of biodegradable plastics by the CLE by means of the ONIOM method. We optimize all the intermediates and the transition states involved in the considered enzymatic reaction and determine the energy surface of the entire catalytic cycle. The calculations show that the amino acid residues inside the pocket of the active site, Thr17 and Gln86, which stabilize the tetrahedral intermediates, and Gly115 in addition to Ser85, His180, and Asp165, which compose the catalytic triad, significantly contribute to the catalytic reaction. This is similar to the case of serine protease reported to date. Moreover, we have newly found that the energy barrier of the catalytic cycle is significantly lowered by the electronic effect of the OH group in the side-chain of Thr17 and bound water. The calculated potential energy surface of the reaction shows that the cleavage of the ester bond is a rate-determining step.

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