Computer Simulation and Modeling Laboratory and Institut de Química Teòrica i Computacional (IQTCUB), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
J Am Chem Soc. 2010 Nov 17;132(45):16058-65. doi: 10.1021/ja105520h. Epub 2010 Oct 25.
The mechanism of glycosidic bond cleavage by glycosidases involves substrate ring distortions in the Michaelis complex that favor catalysis. Retaining β-mannosidases bind the substrate in a (1)S(5) conformation, and recent experiments have proposed an unusual substrate conformational pathway ((1)S(5) → B(2,5) → (O)S(2)) for the hydrolysis reaction. By means of Car-Parrinello metadynamics simulations, we have obtained the conformational free-energy surface (FES) of a β-d-mannopyranose molecule associated with the ideal Stoddart conformational diagram. We have found that (1)S(5) is among the most stable conformers and simultaneously is the most preactivated conformation in terms of elongation/shortening of the C1-O1/C1-O5 bonds, C1-O1 orientation, and charge development at the anomeric carbon. Analysis of the computed FES gives support to the proposed (1)S(5) → B(2,5) → (O)S(2) catalytic itinerary, showing that the degree of preactivation of the substrate in glycoside hydrolases (GHs) is related to the properties of an isolated sugar ring. We introduce a simple preactivation index integrating several structural, electronic, and energetic properties that can be used to predict the conformation of the substrate in the Michaelis complex of any GH.
糖苷酶通过糖昔键断裂的机制涉及米歇利斯复合物中底物环的扭曲，有利于催化。保留的β-甘露糖苷酶以（1）S（5）构象结合底物，最近的实验提出了水解反应的一种不寻常的底物构象途径（（1）S（5）→B（2，5）→（O）S（2））。通过 Car-Parrinello 元动力学模拟，我们获得了与理想的 Stoddart 构象图相关的β-d-甘露吡喃糖分子的构象自由能表面（FES）。我们发现（1）S（5）是最稳定的构象之一，同时也是在 C1-O1/C1-O5 键的伸长/缩短、C1-O1 取向和端基碳原子上电荷发展方面最具预激活构象。计算 FES 的分析为所提出的（1）S（5）→B（2，5）→（O）S（2）催化途径提供了支持，表明糖苷水解酶（GHs）中底物的预激活程度与孤立糖环的性质有关。我们引入了一个简单的预激活指数，它整合了几个结构、电子和能量性质，可以用于预测任何 GH 的米歇利斯复合物中底物的构象。
