The complete conformational free energy landscape of ?-xylose reveals a two-fold catalytic itinerary for ?-xylanases.

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. ?-xylanases are responsible for the hydrolysis of glycosidic bonds in ?-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 ?-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 ?-xylose to predict the most likely catalytic itineraries followed by ?-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, 2SO ? [2,5B]? ? 5S1 and 1S3 ? [4H3]? ? 4C1, which clearly appear in low energy regions of the FEL. Consistently, 2SO and 1S3 are conformations preactivated for catalysis in terms of free energy/anomeric charge and bond distances. The results however exclude the OE ? [OS2]? ? 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 OE 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.

SUBMITTER: Iglesias-Fernandez J 

PROVIDER: S-EPMC5811086 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature