Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR
Figure 3
(A) Comparison of the all-Cα atom RMSDs calculated from the MD trajectories for the folding element group, nonfolding element group, and the native DHFR at 300 °K during the 5-ns simulation (red: folding elements, green: nonfolding elements, blue: native DHFR).
(B) Comparison of the all-Cα atom RMSDs calculated from the MD trajectories for five folding element variants (a01, a02, a08, a08, and a10), five nonfolding element variants (b01, b04, b05, b08, and b09), and native DHFR at 300 °K during the 10-ns simulations (red: folding elements, green: nonfolding elements, blue: native DHFR).
(C) The comparison of RMSF for the folding element group, nonfolding element group, and the native DHFR averaged over 2.5- to 5.0-ns simulations (red: folding elements group, green: nonfolding elements group, blue: native DHFR). The blocks and numbers along the x-axis indicate the folding element region; see Figure 2 and Table 1 for reference.