Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain.
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark.
J Phys Chem B. 2022 Feb 3;126(4):802-812. doi: 10.1021/acs.jpcb.1c09536. Epub 2022 Jan 24.
Glycoside hydrolases and glycosyltransferases are the main classes of enzymes that synthesize and degrade carbohydrates, molecules essential to life that are a challenge for classical chemistry. As such, considerable efforts have been made to engineer these enzymes and make them pliable to human needs, ranging from directed evolution to rational design, including mechanism engineering. Such endeavors fall short and are unreported in numerous cases, while even success is a necessary but not sufficient proof that the chemical rationale behind the design is correct. Here we review some of the recent work in CAZyme mechanism engineering, showing that computational simulations are instrumental to rationalize experimental data, providing mechanistic insight into how native and engineered CAZymes catalyze chemical reactions. We illustrate this with two recent studies in which (i) a glycoside hydrolase is converted into a glycoside phosphorylase and (ii) substrate specificity of a glycosyltransferase is engineered toward forming -, -, or -glycosidic bonds.
糖苷水解酶和糖基转移酶是合成和降解碳水化合物的主要酶类，碳水化合物是生命必需的分子，对经典化学来说是一个挑战。因此，人们付出了相当大的努力来设计这些酶，使它们能够满足人类的需求，从定向进化到合理设计，包括机制工程。在许多情况下，这些努力都没有成功，也没有报道，即使成功了，也不能证明设计背后的化学原理是正确的。在这里，我们回顾了一些最近在 CAZyme 机制工程方面的工作，表明计算模拟对于合理化实验数据是至关重要的，为了解天然和工程 CAZymes 如何催化化学反应提供了机制上的见解。我们用最近的两项研究来说明这一点，（i）将糖苷水解酶转化为糖苷磷酸化酶，（ii）工程化糖基转移酶的底物特异性以形成 α-、β-或 γ-糖苷键。
