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. Author manuscript; available in PMC: 2012 Dec 7.
Published in final edited form as: Structure. 2011 Dec 7;19(12):1837–1845. doi: 10.1016/j.str.2011.09.014

Figure 1. Analysis of flexible side-chain simulation of PDZ-peptide complex.

Figure 1

(A) RMSD values of peptide conformations with respect to the crystallographic pose of the peptide for peptide-bound (black) and peptide-unbound (gray) states from a representative replica. If any atom of the peptide is within 5.5 Å of any atom of the protein in the trajectory, then that snapshot is considered as a peptide-bound conformation. (B) The backbone of PDZ domain is fixed during simulation, and we reconstruct all peptide-bound states from the simulation trajectories. The positions of the peptide in each peptide-bound frame are displayed in ribbon diagrams. The hit map of peptide interactions with the protein corresponds to the frequency with which the peptide atoms interact with the protein atoms, and these interactions range from very frequent (red) to very infrequent (blue). (C) Energy landscape with the interface energy between the peptide and protein in terms of MedusaScore. (D) The lowest energy conformation (magenta) of the peptide from the largest cluster and its experimental pose (black). See also Figure S1.