Fig. 5

MD simulations of the XynA–XBP271 chimera. a Representation of the final xylose-bound XynA–XBP271 structure after molecular dynamics simulations. Details of the inter-domain interface are illustrated, where the XynA domain is shown as a cartoon and transparent surface and XBP is shown in a space-filling representation. Hot-spot residues at the protein–protein interface between XBP and XynA are shown in blue (XBP residues) and red (XynA residues). The catalytic site of the XynA is located between the palm and fingers domains, and access to the active site cleft is determined by the orientation of the thumb domain. b Comparison of the inter-domain interaction potential energy (IPE) as a function of simulation time in the presence (black line) and absence (red line) of xylose in the chimera enzyme. c Local fluctuations (RMSF) of parental XynA (green line) and the XynA–XBP271 chimera in the presence (black line) and absence (red line) of xylose. d Essential dynamics of the chimeras represented by arrows on an equilibrated representative 3D structure from MDS. The arrows indicate the direction of the local movements of the polypeptide chain in the XynA domain in chimera in the presence and absence of xylose