Biodegradation mechanism of polycaprolactone by a novel esterase MGS0156: a QM/MM approach,Environmental Science: Processes & Impacts

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Biodegradation mechanism of polycaprolactone by a novel esterase MGS0156: a QM/MM approach
Environmental Science: Processes & Impacts ( IF 4.3 ) Pub Date : 2020-10-07 , DOI: 10.1039/d0em00340a
Shanshan Feng _{1,

2,

3,

4} , Yue Yue _{1,

2,

3,

4} , Jinfeng Chen _{1,

2,

3,

4} , Jie Zhou _{1,

2,

3,

4} , Yanwei Li _{1,

2,

3,

4} , Qingzhu Zhang _{1,

2,

3,

4}

Affiliation

Nowadays micro-plastic pollution has become one of the most serious global environmental problems. A potential strategy in managing micro-plastic waste is enzyme-catalyzed degradation. MGS0156 is a hydrolase screened from environmental metagenomes, which can efficiently degrade commercial plastics such as polycaprolactone, polylactide, etc. Here a combined molecular dynamics, molecular mechanics Poisson–Boltzmann surface area, and quantum mechanics/molecular mechanism method was used to reveal the enzymatic depolymerization mechanism. By systematically analyzing the binding processes of nine oligomers (from a monomer to tetramer), we found that longer oligomers have relatively stronger binding energy. The degradation process involves two concerted elementary steps: triad-assisted nucleophilic attack and C–O bond cleavage. C–O bond cleavage is the rate determining step with an average barrier of 15.7 kcal mol⁻¹, which is consistent with the experimentally determined k_cat (1101 s⁻¹, corresponds to 13.3 kcal mol⁻¹). The electrostatic influence analysis of twenty amino acids highlights His231 and Asp237 as potential mutation targets for designing more efficient MGS0156 mutants.

中文翻译：

新型酯酶MGS0156对聚己内酯的生物降解机理：QM / MM方法

如今，微塑料污染已成为全球最严重的环境问题之一。处理微塑料废物的潜在策略是酶催化的降解。MGS0156是从环境基因组中筛选的水解酶，可有效降解商业塑料，例如聚己内酯，聚丙交酯等。这里结合了分子动力学，分子力学泊松-玻尔兹曼表面积和量子力学/分子机理方法来揭示酶解聚机理。通过系统地分析九种低聚物（从单体到四聚物）的结合过程，我们发现较长的低聚物具有相对较强的结合能。降解过程涉及两个共同的基本步骤：三联体辅助的亲核攻击和C-O键裂解。C–O键断裂是速率确定步骤，平均壁垒为15.7 kcal mol ^-1，与实验确定的k _cat（1101 s ^-1对应于13.3 kcal mol ^-1）。二十种氨基酸的静电影响分析突显出His231和Asp237作为潜在突变目标，可用于设计更有效的MGS0156突变体。

更新日期：2020-11-04

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