Effects of Site-Directed Mutations on the Communicability between Local Segments and Binding Pocket Distortion of Engineered GH11 Xylanases Visualized through Network Topology Analysis

Mutations occurred within the binding pocket of enzymes directly modified interaction network between an enzyme and its substrate. However, some mutations affecting catalytic efficiency far from explanation regarding mechanisms underlying transmission mechanical signal mutated site to was lacking. In this study, topology analysis used characterize visualize changes networks caused by site-directed on a GH11 xylanase our previous study. For each structure, coordinates molecular dynamics (MD) trajectory were obtained create representative atoms all protein xylooligosaccharide substrate residues, in which edges defined pairs residues cutoff distance. Then, communicability matrices extracted provide information number possible paths any residue or local segments. The subgraph centrality clearly showed that site-direct mutagenesis at non-reducing reducing ends distortion close opposite created denser networks. both cancelled distortion, while enhancing thermostability. Therefore, tool atomistic simulations engineered proteins could play roles design for minimization correction tilting, affect functionality efficacy enzymes.