The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases. Issue 2 (21st November 2014) - Iglesias-Fernández, Javier
Abstract : Ab initio conformational free energy landscapes, together with molecular dynamics simulations, enable to predict the catalytic itineraries of β-xylanase enzymes. Abstract : Unraveling the conformational catalytic itinerary of glycoside hydrolases (GHs) is a growing topic of interest in glycobiology, with major impact in the design of GH inhibitors. β-xylanases are responsible for the hydrolysis of glycosidic bonds in β-xylans, a group of hemicelluloses of high biotechnological interest that are found in plant cell walls. The precise conformations followed by the substrate during catalysis in β-xylanases have not been unambiguously resolved, with three different pathways being proposed from structural analyses. In this work, we compute the conformational free energy landscape (FEL) of β-xylose to predict the most likely catalytic itineraries followed by β-xylanases. The calculations are performed by means of ab initio metadynamics, using the Cremer–Pople puckering coordinates as collective variables. The computed FEL supports only two of the previously proposed itineraries, 2 SO → [ 2, 5 B] ǂ → 5 S1 and 1 S3 → [ 4 H3 ] ǂ → 4 C1, which clearly appear in low energy regions of the FEL. Consistently, 2 SO and 1 S3 are conformations preactivated for catalysis in terms of free energy/anomeric charge and bond distances. The results however exclude the O E → [ O S2 ] ǂ → B2, 5 itinerary that has been recently proposed for a family 11 xylanase. Classical and ab initio QM/MM molecular dynamics simulations reveal that, in this case, the observed O E conformation has been enforced by enzyme mutation. These results add a word of caution on using modified enzymes to inform on catalytic conformational itineraries of glycoside hydrolases.