Molecular dynamics simulation of denaturation of DhaA induced by urea and dimethyl sulfoxide

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Molecular dynamics simulation of denaturation of DhaA induced by urea and dimethyl sulfoxide

Biochemical engineering and technology | 更新时间：2020-06-24

- Molecular dynamics simulation of denaturation of DhaA induced by urea and dimethyl sulfoxide
- CIESC Journal Vol. 70, Issue 11, Pages: 4337-4345(2019)
- 作者机构：
  
  1.国民核生化灾害防护国家重点实验室，北京 102205
  2.华南理工大学化学与化工学院，广东广州 510640
- 作者简介：
- 基金信息：
- DOI：10.11949/0438-1157.20190278
  CLC： O 629.73;Q 518.4
- Received：22 March 2019，
  
  Revised：2019-07-10，
  
  Published：05 November 2019
- 稿件说明：
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郑禾, 杨盛江, 郑永超, 崔燕, 郭旋, 钟近艺, 周健. 尿素和二甲基亚砜诱导DhaA变性的分子动力学模拟[J]. 化工学报, 2019, 70(11): 4337-4345

ZHENG He, YANG Shengjiang, ZHENG Yongchao, CUI Yan, GUO Xuan, ZHONG Jinyi, ZHOU Jian. Molecular dynamics simulation of denaturation of DhaA induced by urea and dimethyl sulfoxide[J]. CIESC Journal, 2019, 70(11): 4337-4345
郑禾, 杨盛江, 郑永超, 崔燕, 郭旋, 钟近艺, 周健. 尿素和二甲基亚砜诱导DhaA变性的分子动力学模拟[J]. 化工学报, 2019, 70(11): 4337-4345 DOI： 10.11949/0438-1157.20190278.

ZHENG He, YANG Shengjiang, ZHENG Yongchao, CUI Yan, GUO Xuan, ZHONG Jinyi, ZHOU Jian. Molecular dynamics simulation of denaturation of DhaA induced by urea and dimethyl sulfoxide[J]. CIESC Journal, 2019, 70(11): 4337-4345 DOI： 10.11949/0438-1157.20190278.

摘要

DhaA能够有效降解化学毒剂芥子气，而环境耐受性差影响了其在军事洗消中的应用。虽然已有研究表明定向进化、化学修饰、固定化有利于提高DhaA在尿素、二甲基亚砜(DMSO)溶液中的稳定性，但DhaA在尿素、DMSO下的变性过程尚不清晰。利用分子动力学(MD)模拟方法研究了DhaA在尿素和DMSO两种体系中的变性过程，结果表明尿素分子通过取代水分子与DhaA形成氢键的方式诱导其变性，并且能够与催化位点形成氢键，造成DhaA底物进出口通道长度增加、通道曲率增大、瓶颈尺寸减小；DMSO分子通过范德华作用进入DhaA疏水空腔，从而诱导DhaA变性，使得DhaA通道长度缩短、瓶颈尺寸增大，造成DhaA发生构象变化。该研究结果揭示了DhaA在两种体系中变性过程的区别，能够为DhaA的进一步稳定化提供理论指导。

Abstract

DhaA can effectively degrade the chemical poison mustard gas

and poor environmental tolerance affects its application in military decontamination. However

the molecular denaturation processes of DhaA induced by urea and dimethyl sulfoxide (DMSO) remain unclear

although it is reported that directed evolution

chemical modification and immobilization were helpful to the stabilization of DhaA. In this study

molecular dynamics (MD) simulations are used to investigate the denaturation processes of DhaA in urea and DMSO solutions. The results show that urea molecules can replace water to form H-bonds with DhaA and its catalytic active sites

which made main tunnel lengthened

curvature enhanced and bottleneck radius reduced. Whereas DMSO molecules can enter into hydrophobic cavity of DhaA by van der Waals interaction

which made main tunnel shortened

bottleneck radius enlarged and conformation changed. These findings reveal the differences of molecular denaturation process of DhaA in two systems

which could provide theoretical guidance for the stabilization of DhaA.

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references

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