Multiscale Coarse-Graining of the Protein Energy Landscape
Figure 5
CG-REMD folding landscapes collected at 0.6 .
The Cα RMSD from the native state is shown versus composite simulation time (A–C) or potential energy (D–F) for independent simulations (different colors) of Trpzip (A,D), Trp-cage (B,E) and AdK (C,F). Simulations were started from extended and native structures as well as their common final configuration in the case of Trp-cage. AdK simulations were started from extended, closed, open and a mixture of open and extended states; RMSD is computed from the closed crystal structure. Large structural changes between snapshots, such as folded to misfolded transitions, correspond to conformational exchanges between replicas of similar energy.