Fig. 6: Binding of the G4OG3OG natural substrate in the HvExoI active site calculated via cMD and QM/MM MD metadynamics simulations, plotted as a function of θ and φ puckering coordinates.
From: The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases
a Conformational FEL map of the Glc moiety at the −1 subsite in WT; Glc moieties of G4OG3OG in the subsites −1 to +2 are indicated along with the key residues; b conformational behaviour (Mercator projection) of the G3OG product after the −1 Glc moiety is hydrolysed from G4OG3OG and removed from the −1 subsite in WT; c conformational behaviour (Mercator projection) of the G3OG product after the −1 Glc moiety is hydrolysed from G4OG3OG and removed from the −1 subsite in W434A. Colour gradients from purple at 0 ns to yellow at 150 ns in Mercator projections are shown. In b, c, respective cluster analyses of trajectories (populations in %) indicate two modes of G3OG binding in WT and W434A, where each saccharide binds in the +1 and +2 subsites or Glc moieties bind in intermediary positions between those subsites and the −1 subsite.
