Insights into the Lactonase Mechanism of Serum Paraoxonase 1 (PON1): Experimental and Quantum Mechanics/Molecular Mechanics (QM/MM) Studies

• Published in: The journal of physical chemistry. B 2015-07, Vol.119 (30), p.9571-9585
• Main Authors: Le, Quang Anh Tuan, Kim, Seonghoon, Chang, Rakwoo, Kim, Yong Hwan
• Format: Article
• Language: English
• Subjects: 4-Butyrolactone - metabolism; Accuracy; Aryldialkylphosphatase - blood; Aryldialkylphosphatase - chemistry; Aryldialkylphosphatase - metabolism; Barriers; Biocatalysis; Enzymes; Kinetics; Lactones; Lactones - metabolism; Mathematical analysis; Molecular Dynamics Simulation; Platforms; Protein Conformation; Quantum mechanics; Quantum Theory; Serums; Thermodynamics
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/acs.jpcb.5b03184

Serum paraoxonase 1 (PON1) is a versatile enzyme for the hydrolysis of various substrates (e.g., lactones, phosphotriesters) and for the formation of a promising chemical platform γ-valerolactone. Elucidation of the PON1-catalyzed lactonase reaction mechanism is very important for understanding the enzyme function and for engineering this enzyme for specific applications. Kinetic study and hybrid quantum mechanics/molecular mechanics (QM/MM) method were used to investigate the PON1-catalyzed lactonase reaction of γ-butyrolactone (GBL) and (R)-γ-valerolactone (GVL). The activation energies obtained from the QM/MM calculations were in good agreement with the experiments. Interestingly, the QM/MM energy barriers at MP2/3-21G­(d,p) level for the lactonase of GVL and GBL were respectively 14.3–16.2 and 11.5–13.1 kcal/mol, consistent with the experimental values (15.57 and 14.73 kcal/mol derived from respective k cat values of 36.62 and 147.21 s–1). The QM/MM energy barriers at MP2/6-31G­(d) and MP2/6-31G­(d,p) levels were also in relatively good agreements with the experiments. Importantly, the difference in the QM/MM energy barriers at MP2 level with all investigated basis sets for the lactonase of GVL and GBL were in excellent agreement with the experiments (0.9–3.1 and 0.8 kcal/mol, respectively). A detailed mechanism for the PON1-catalyzed lactonase reaction was also proposed in this study.