Yao Jianzhuang, Luo Haixia, Wang Xia
School of Biological Science and Technology, University of Jinan , Jinan 250022, P. R. China.
Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, Life Science School, Ningxia University , Yinchuan 750021, P. R. China.
J Chem Inf Model. 2017 May 22;57(5):1179-1186. doi: 10.1021/acs.jcim.7b00167. Epub 2017 May 9.
Celiac sprue, also known as gluten-sensitive enteropathy, is a chronic disease suffered by approximately 1% of the world's population. Engineered enzymes have been emerging to treat celiac disease by hydrolyzing the pathogenic peptides of gluten. For example, Kuma010 has been studied experimentally and proved to be a promising gluten hydrolase under gastric conditions. However, the detailed catalytic mechanism and the substrate specificity are still unclear. In this paper, quantum-mechanical/molecular-mechanical (QM/MM) molecular dynamics (MD) and free energy simulations were performed to determine the catalytic mechanism, the substrate specificity, and the role of the active-site residues during the reaction. The results given here demonstrate that the Kuma010 has a similar catalytic mechanism but different substrate specificity as wild-type kumamolisin-As. Binding properties of the enzyme (especially mutated residues) and substrate complex are discussed, and activation free energy barriers toward different substrates have also been examined. The computational free energy results are in reasonable agreement with the experimental data. The strategy for developing next-generation gluten hydrolases is discussed.
乳糜泻，也称为麸质敏感性肠病，是一种慢性病，全球约1%的人口受其影响。工程酶已逐渐出现，通过水解麸质的致病肽来治疗乳糜泻。例如，Kuma010已通过实验研究，被证明是一种在胃部条件下有前景的麸质水解酶。然而，其详细的催化机制和底物特异性仍不清楚。本文通过量子力学/分子力学（QM/MM）分子动力学（MD）和自由能模拟来确定催化机制、底物特异性以及反应过程中活性位点残基的作用。此处给出的结果表明，Kuma010与野生型库马莫利辛 - As具有相似的催化机制，但底物特异性不同。讨论了酶（特别是突变残基）与底物复合物的结合特性，还研究了针对不同底物的活化自由能垒。计算得到的自由能结果与实验数据合理吻合。讨论了开发下一代麸质水解酶的策略。
