Substrate conformational changes in glycoside hydrolase catalysis. A first-principles molecular dynamics study

A current issue in the understanding of β-glycoside hydrolase (β-GH) mechanisms is the conformational itinerary that the substrate follows during the reaction, in which substrate distortion is induced upon binding to the enzyme. The precise knowledge of the structure of the Michaelis complex, the covalent intermediate (in the case of retaining GHs) or the product gives hints on how to predict the transition state structures and this has an impact on the design of inhibitors for these enzymes. Here we summarize our recent work on substrate distortion in GHs using first-principles molecular dynamics. First, we show that distortion of the substrate is required for binding to 1,3-1,4-β-glucanase, a family 16 GH, and that this distortion results in electronic and structural changes in the substrate that favor cleavage of the glycosidic bond. Second, by analyzing the conformational energy landscape of β-D-glucopyranose, we demonstrate that the most stable distorted conformations (¹S₅, ^1,4B, ¹S₃, B3,_o, ²SO and ^2,5B) are pre-activated for catalysis in terms of small structural and electronic changes around the anomeric carbon. These conformations are the ones found in Michaelis complexes of GHs, suggesting that enzymesubstrate interactions have evolved to use these properties for efficient catalysis.