物理化学学报Issue(6)：1169-1178,10.DOI:10.3866/PKU.WHXB201504151
保留型与反转型β-木糖苷酶活性位点的分子动力学模拟
Molecular Dynamics Simulation of Active-Sites of Retaining and Invertingβ-Xylosidases
摘要
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 typicalβ-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 ofβ-xylosidases, and wil therefore be useful in improving the efficiency and applications ofβ-xylosidases.关键词
β-木糖苷酶/催化机制/分子建模/质子供体/pKa值Key words
β-Xylosidase/Catalytic mechanism/Molecular model ing/Proton donor/pKa value分类
化学化工引用本文复制引用
张俊威,周峻岗,吕红,黄强..保留型与反转型β-木糖苷酶活性位点的分子动力学模拟[J].物理化学学报,2015,(6):1169-1178,10.基金项目
The project was supported by the Shanghai Natural Science Foundation, China (13ZR1402400) and National Natural Science Foundation of China (31200022).上海市自然科学基金(13ZR1402400)及国家自然科学基金(31200022)资助项目 （13ZR1402400）
