Experimental and Computational Investigation of pH-Dependent Urease Conformational Dynamics and Its Impact on MICP Efficiency
10.13865/j.cnki.cjbmb.2025.05.1071
- VernacularTitle:pH调控脲酶构象影响微生物诱导碳酸盐沉淀效能及模拟研究
- Author:
Qiu-Cai ZHANG
1
;
Yi-Fei ZHENG
;
Mei-Zhong HUANG
;
Xiu-Kang SHEN
;
Ling-Ling WU
;
Zhi-Jun ZHANG
Author Information
1. 南华大学资源环境与安全工程学院实验中心,湖南衡阳 421001;湖南省矿山岩土工程灾害预测与控制工程技术研究中心,湖南衡阳 421001
- Publication Type:Journal Article
- Keywords:
microbially induced carbonate precipitation(MICP);
enzyme induced calcium carbonate precipitation(EICP);
urease;
molecular dynamics
- From:
Chinese Journal of Biochemistry and Molecular Biology
2025;41(6):879-894
- CountryChina
- Language:Chinese
-
Abstract:
The engineering application of microbially induced carbonate precipitation(MICP)is limited by pH-dependent conformational dynamics of urease.Focusing on the α-subunit urease from Sporosarcina pasteurii,this study integrated conductivity experiments and constant-pH molecular dynamics simulations to analyze active site conformational dynamics and catalytic function across pH 3-11.Results showed that under neutral conditions(pH 7-8),key histidine residues(HIS139/HIS249)exhibited minimal dis-placement(＜0.5 ?),the longest hydrogen bond lifetime(＞8 ps),highest conformational stability(root mean square deviation,RMSD:0.15-0.18 nm),and optimal catalytic activity(conductivity change rate:0.03 mS/cm·min-1,CaCO3 precipitation:3.84 g).Extreme pH(pH 3/11)induced structural collapse(displacement up to 1.8 ?)and complete activity loss.Simulations revealed that neutral pH sta-bilizes a protonation-dependent cooperative allosteric network by maintaining active site cavity volume(～120 ?3)and moderate conformational coherence(correlation coefficient～0.8).This work deciphers the molecular mechanism of pH-regulated urease dynamics through protonation states,providing theoreti-cal support for MICP applications in acidic mine tailing remediation and alkaline soil stabilization.
