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

doi:10.11949/0438-1157.20190278

Abstract

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.

Key words: protein denaturation, urea, dimethyl sulfoxide, molecular dynamics simulation

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。

关键词: 蛋白质变性, 尿素, 二甲基亚砜, 分子动力学模拟

CLC Number:

O 629.73

He ZHENG, Shengjiang YANG, Yongchao ZHENG, Yan CUI, Xuan GUO, Jinyi ZHONG, Jian ZHOU. 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.

Figures/Tables 10

Fig.1 Native three dimensional structure of DhaA(red beads represent catalytic sites)

Fig.2 RMSD evolutions of DhaA as a function of time in different simulation systems

Fig.3 Secondary structure evolutions of DhaA as a function of time in different simulation systems

Fig.4 Snapshots of tunnel of DhaA in different simulation systems

Table 1 Main tunnel parameters of DhaA in different simulation systems

DhaA模拟体系	通道长度/?	通道曲率	瓶颈尺寸/?	通过成本
纯水	12.55	1.25	1.16	0.45
尿素	22.48	1.45	1.10	0.54
DMSO	10.27	1.27	1.26	0.19

Fig.5 Numbers of H-bonds in DhaA in simulation systems(blue bar represents H-bond between DhaA and water molecules, red bar represents H-bond between DhaA and organic molecules, black bar represents intramolecular H-bond of DhaA molecules)

Fig.6 Snapshots of solution molecules distribution within 3.5 ? around catalytic sites in DhaA in different simulation systems(blue beads represent water molecules, red beads represent urea molecules, green beads represent DMSO molecules)

Fig.7 Radial distribution functions (RDFs) of solvent molecules around catalytic sites

Fig.8 Structural change of catalytic sites of DhaA in different simulation systems(blue part represents DhaA in water, red part represents DhaA in urea solution, orange part represents DhaA in DMSO solution)

Fig.9 Gibbs free energies landscapes of DhaA in different simulation systems (F indicated folding state)

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