Figure 4

Opening and closing of the Man5B catalytic pocket. A. Illustration of the key principal component analysis (PCA) mode involved in the opening and closing motion of the Man5B catalytic pocket. B. Motional amplitude of each amino acid in the PCA for Man5B without substrate (black), with cellohexaose (red) and mannohexaose (green). For the simulations with substrates the amplitude shown is the average amplitude of the three sample simulations performed for each substrate. C. Enlargement showing amplitude and deviation in the main amplitude peak region in B. This region corresponds to flaps that open and close, giving access to the catalytic pocket. The reduction of the peak amplitude values indicates that cellohexaose is inhibiting the opening and closing motion of the enzyme’s catalytic pocket.