Figure 1. Experimental structure and MD simulations of native Trp-cage miniprotein.

(A) Cartoon representation of the folded experimental structure of Trp-cage mini protein [1]. A subset of side chains important for folding are labeled (stick representation). (B) Root-mean –square deviation (RMSD) of C_α–atoms with respect to native structure and (C) distance between Asp9-Arg16 (salt bridge) of sampled Trp-cage conformations in explicit solvent starting from the native structure (1^st entry of pdb 1L2Y) versus simulation time. Simulations were performed with four different force fields encoded as different line colors (black:ff03, red:ff99SB, green:ff99SB_ILDN,blue:ff99SB_NMR). (D) Partially unfolded Trp-cage structures sampled during simulation starting from native state (with the C-terminal PolyPro_II motive transiently dissociated from the central Trp6 residue).