物理化学学报 >> 2015, Vol. 31 >> Issue (6): 1169-1178.doi: 10.3866/PKU.WHXB201504151

生物物理化学 上一篇    下一篇

保留型与反转型β-木糖苷酶活性位点的分子动力学模拟

张俊威1, 周峻岗1, 吕红1,2, 黄强1,2   

  1. 1 复旦大学生命科学学院, 遗传工程国家重点实验室, 上海工业菌株工程技术研究中心, 上海200433;
    2 上海生物制造技术协同创新中心, 上海200237
  • 收稿日期:2015-02-16 修回日期:2015-04-13 发布日期:2015-06-05
  • 通讯作者: 周峻岗, 黄强 E-mail:zhoujg@fudan.edu.cn;huangqiang@fudan.edu.cn
  • 基金资助:

    上海市自然科学基金(13ZR1402400)及国家自然科学基金(31200022)资助项目

Molecular Dynamics Simulation of Active-Sites of Retaining and Inverting β-Xylosidases

ZHANG Jun-Wei1, ZHOU Jun-Gang1, Lü Hong1,2, HUANG Qiang1,2   

  1. 1 State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200433, P. R. China;
    2 Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai 200237, P. R. China
  • Received:2015-02-16 Revised:2015-04-13 Published:2015-06-05
  • Contact: ZHOU Jun-Gang, HUANG Qiang E-mail:zhoujg@fudan.edu.cn;huangqiang@fudan.edu.cn
  • Supported by:

    The project was supported by the Shanghai Natural Science Foundation, China (13ZR1402400) and National Natural Science Foundation of China (31200022).

摘要:

木聚糖是潜在的重要可再生能源, 如何提高其降解效率已成为近年来的研究热点. β-木糖苷酶是木聚糖降解过程中的关键酶之一, 按其水解机制可分为保留型与反转型酶. 目前虽然对于这两种催化机制的研究不断深入, 但很少有工作从溶液环境的角度出发探究它们的差异. 本文采用分子动力学模拟方法, 对4 个典型的β-木糖苷酶进行了显式溶剂模拟研究, 详细分析了酶的催化氨基酸间的距离和质子供体氨基酸pKa值的动态变化. 结果显示, 反转型酶催化氨基酸间的距离约为0.8-1.0 nm, 大于保留型的0.5-0.6 nm, 与先前对糖苷酶晶体结构的统计分析结果一致. 令人意外的是, 保留型酶的质子供体通过与其附近组氨酸的相互作用, 其pKa在两个不同的高、低值之间交替变换, 使保留型酶的双取代反应得以发生; 而反转型酶的质子供体则由附近的天冬氨酸调节, 其pKa稳定在某个较高值, 这可能有利于其在反应pH值下获得水溶液中的氢离子, 进行反转型酶特有的单取代反应. 因此, 本工作加深了人们对β-木糖苷酶保留型与反转型水解机制的认识, 并为后续酶的理性改造与高效利用提供具有指导价值的结构与机理信息.

关键词: β-木糖苷酶, 催化机制, 分子建模, 质子供体, pKa

Abstract:

Xylans are important as potential renewable energy sources. In recent years, there has therefore been interest in improving their degradation efficiencies. β-Xylosidases are key enzymes for xylan degradation; these enzymes are classified, based on their hydrolysis mechanisms, as retaining or inverting enzymes. Although much research has been devoted to understanding retaining and inverting mechanisms, little is known about their differences in solution. We used molecular dynamics (MD) simulations with explicit solvent representation to study the dynamic behaviors of the active-sites of four typical β-xylosidases by analyzing the distances between two catalytic amino acids and the pKa values of proton-donor amino acids. The results show that the distance between the catalytic amino acids with inverting enzymes is about 0.8-1.0 nm, which is greater than that for retaining enzymes, i.e., 0.5-0.6 nm. This is consistent with previous results based on the crystal structures of glycosidases. We found that the pKa of the retaining proton donors are modulated by interactions with neighboring amino acids, enabling switching between low and high values. Such a pKa switch is needed for the double-displacement mechanism of retaining enzymes. In contrast, inverting proton donors, modulated by interactions with neighboring glutamic acids, have only high pKa values. This may be important in proton capture from the solvent by donors, and may facilitate the single-displacement mechanism of inverting enzymes. This study provides new insights into the hydrolysis mechanisms of β-xylosidases, and will therefore be useful in improving the efficiency and applications of β-xylosidases.

Key words: β-Xylosidase, Catalytic mechanism, Molecular modelling, Proton donor, pKa value

MSC2000: 

  • O643