Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling
Figure 1
(A) Probability distributions of VMMCG, P(VMMCG), defined in Eq. 1 for 12 replicas of MSES simulation. (B) Time course of VMMCG for a representative model replica, i.e., the replica fixed not by kMMCG, but by the configuration. (C–E) Quantities from the unbiased MSES ensemble (with kMMCG = 0) as a function of simulation time: Root-mean-square displacement for Cα atoms (Cα RMSD) of barstar after fitting to barnase, RMSDbs (C), center-of-mass (COM) distance between two COMs for barstar and barnase, respectively, dCOM (D), and number of polar contacts found in eight inter-molecular pairs, #3, 4, 6, 7, 8, 11, 12, and 13, listed in Table 1 (E). In (D), dCOM in conventional equilibrium MD simulation starting from complex structure (MM simulation) is also shown by red. In (F) and (G), arrangements of barstar observed in the unbiased MSES ensemble and in MM simulation are shown, respectively. Both coordinates were superimposed on barnase.