An integrated approach of bioassay and molecular docking to study the dihydroxylation mechanism of pyrene by naphthalene dioxygenase in Rhodococcus sp ustb-1
An integrated approach of bioassay and molecular docking to study the dihydroxylation mechanism of pyrene by naphthalene dioxygenase in Rhodococcus sp ustb-1
复制标题
生物测定和分子对接一体化方法研究红球菌ustb-1萘双加氧酶对芘的二羟基化机制
DOI：
10.1016/j.chemosphere.2015.02.012
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发表时间：
2015-06-01
期刊：
影响因子：
8.8
通讯作者：
Choi, Martin M. F.
中科院分区：
文献类型：
--
作者：
Jin, Jing-Nan;Yao, Jun;Choi, Martin M. F.
萘双加氧酶（NDO）是催化芳香族化合物生物降解的起始酶，在污染场地的微生物修复中起着关键作用。本研究以原油源红球菌ustb-1为研究对象，采用生物测定和分子对接相结合的方法，研究了该菌对芘的生物降解特性和双羟基化机理。生物降解实验表明，菌株ustb-1对芘具有高效的生物降解性，第28天降解率为70.8%，其代谢产物芘cis-4，分子对接的结果表明，芘的周围区域由疏水氨基酸限定，有利于芘的C4和C5位上的双氧分子结合在侧链上。在mode。分子氧的结合位置与代谢产物芘顺式-4，5-二氢二醇的质谱分析一致。综上所述，本研究为芘与NDO活性位点之间可能的结合行为提供了一个有希望的解释。(C)2015爱思唯尔有限公司版权所有。
Naphthalene dioxygenase (NDO) is the initial enzyme catalyzing the biodegradation of aromatic compounds, and it plays a key role in microbial remediation of polluting sites. In this study, Rhodococcus sp. ustb-1 derived from crude oil was selected to investigate the biodegradation characters and dihydroxylation mechanism of pyrene by an integrated approach of bioassay and molecular docking. The biodegradation experiment proved that the strain ustb-1 shows high effective biodegradability to pyrene with a 70.8% degradation on the 28th day and the metabolite pyrene cis-4,5-dihydrodiol was found. The results of molecular docking indicated that the regions surrounding pyrene are defined by hydrophobic amino acids which are favorable for the binding of dioxygen molecule at C4 and C5 positions of pyrene in a side-on mode. The binding positions of dioxygen are in agreement with the mass spectral analysis of the metabolite pyrene cis-4,5-dihydrodiol. In summary, this study provides a promising explanation for the possible binding behavior between pyrene and active site of NDO. (C) 2015 Elsevier Ltd. All rights reserved.