Figure 6

Comparison of network communities (left) and structural representation (right) derived from MD analysis. Left: Active site residues network presented by spring layout using Fruchterman-Reingold algorithm from distance matrixes from 1 µs MD simulations of the parental ΔN₁₂₃-GBD-CD2, the F2163G mutant, and the double mutants W2135S-F2136L and W2135I-F2136C. Amino acid communities highlighted with orange, red, green, yellow and cyan colors were found by spin-glass algorithm. The catalytic, the transition state stabilizer, and the mutated residues are labelled respectively by “cat”, “tss” and “mut” for each corresponding graph. Right: View of active site residue clusters from the spin-glass algorithm for the parental ΔN₁₂₃-GBD-CD2 and the mutants F2136G, W2135S-F2136L, and W2135I-F2136C. The 5 communities are presented: I (orange), II (green), III (red), IV (yellow) and V (cyan). Three dimensional structures are taken from the low energy regions of the free energy landscapes of each system (Fig. 5). Graphs in figures were drawn using the R software³⁹. Molecular graphics were prepared using PYMOL 1.7 (PyMOL Molecular Graphics System, Schrödinger, LLC).