TY - JOUR
T1 - Plastic bioconversion
T2 - Reaction mechanism of PETases
AU - Ge, B. K.
AU - Hu, G. M.
AU - Chen, C. M.
N1 - Funding Information:
BKG conducted in silico structure prediction and ligand docking experiments and analyzed data. GMH analyzed data and contributed to writing the manuscript. CMC developed the model and contributed to writing the manuscript. We thank R.H.G. Chen for editing the manuscript and I.J. Chang for stimulating discussions. This work is supported by the Ministry of Science and Technology of Taiwan under grant no. MOST 108-2112-M-003-008 .
Publisher Copyright:
© 2021 The Physical Society of the Republic of China (Taiwan)
PY - 2021/10
Y1 - 2021/10
N2 - The enzyme IsPETase can efficiently degrade polyethylene terephthalate (PET) at room temperature and is an attractive method of plastic bioconversion. Based on mutagenesis experiments on IsPETase, we propose a physical model which predicts that its reaction mechanism can be described by the Michaelis-Menten model with a catalytic efficiency of Ka∙k2, where Ka is the association constant of substrate binding and k2 is the rate constant to form the acyl-enzyme intermediate. This model verifies the assumption of Michaelis-Menten kinetics in previous studies on PETases and has novel applications in deriving the enzyme activity using computational molecular dockings. By computationally docking bis-(2-hydroxyethyl) terephthalic acid (BHET) on the surface of IsPETase mutants, we studied the catalytic effects of various side chains and observed that their predicted activities are consistent with experimental data, with a correlation coefficient in the range of 0.79∼0.88. Based on this study, our model presents an analytical interpretation for the reaction mechanism of PETases and provides an efficient method for computing their catalytic efficiency for identifying enzymes with a better catalytic performance from numerous protein sequences in open databases.
AB - The enzyme IsPETase can efficiently degrade polyethylene terephthalate (PET) at room temperature and is an attractive method of plastic bioconversion. Based on mutagenesis experiments on IsPETase, we propose a physical model which predicts that its reaction mechanism can be described by the Michaelis-Menten model with a catalytic efficiency of Ka∙k2, where Ka is the association constant of substrate binding and k2 is the rate constant to form the acyl-enzyme intermediate. This model verifies the assumption of Michaelis-Menten kinetics in previous studies on PETases and has novel applications in deriving the enzyme activity using computational molecular dockings. By computationally docking bis-(2-hydroxyethyl) terephthalic acid (BHET) on the surface of IsPETase mutants, we studied the catalytic effects of various side chains and observed that their predicted activities are consistent with experimental data, with a correlation coefficient in the range of 0.79∼0.88. Based on this study, our model presents an analytical interpretation for the reaction mechanism of PETases and provides an efficient method for computing their catalytic efficiency for identifying enzymes with a better catalytic performance from numerous protein sequences in open databases.
KW - Catalytic efficiency
KW - Michaelis-Menten kinetics
KW - Plastic bioconversion
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U2 - 10.1016/j.cjph.2021.07.027
DO - 10.1016/j.cjph.2021.07.027
M3 - Article
AN - SCOPUS:85111937199
SN - 0577-9073
VL - 73
SP - 331
EP - 339
JO - Chinese Journal of Physics
JF - Chinese Journal of Physics
ER -