MOE Key Laboratory of Green Chemistry, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064 PR China.
J Phys Chem B. 2012 Sep 13;116(36):11166-72. doi: 10.1021/jp306754a. Epub 2012 Aug 30.
Hyaluronate lyase from Spectrococcus pneumonia can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. The major functions of hyaluronan are to regulate water balance and osmotic pressure and act as an ion-exchange resin. In this work, we focus on the prerequisite issue of the enzymatic reaction, i.e., the initial reactive conformer. Based on the quantum mechanical and molecular mechanical molecular dynamic simulations and free energy profiles, a near attack conformer was obtained for the degradation of hyaluronan catalyzed by the hyaluronate lyase. Along with the substrate binding, the phenylhydroxyl hydrogen atom of Tyr408 will transfer to nearby His399 via a near barrierless transition state, which results in a negatively charged Tyr408 and positively charged His399. The Tyr408, rather than the previously proposed His399, was suggested to act as the general base for the subsequent β-elimination reaction. The His399 was suggested to have the function of neutralizing the C5-carboxyl group.
肺炎链球菌透明质酸裂解酶能够降解透明质酸，透明质酸是细胞外基质的主要成分之一。透明质酸的主要功能是调节水合平衡和渗透压，并作为离子交换树脂。在这项工作中，我们专注于酶反应的前提问题，即初始反应构象。基于量子力学和分子力学分子动力学模拟和自由能曲线，我们获得了透明质酸裂解酶催化的透明质酸降解的近攻击构象。随着底物的结合，Tyr408 的苯羟氢原子将通过近无势垒过渡态转移到附近的 His399，导致带负电荷的 Tyr408 和带正电荷的 His399。Tyr408 而不是之前提出的 His399，被认为是随后的β消除反应的通用碱。His399 被认为具有中和 C5-羧基的功能。
