803535.fig.002a
(a)
803535.fig.002b
(b)
Figure 2: (a) Top: lowest energy conformation of the subtype C V3 loop crown from V3 loop amino acid positions 10 to 22. The structure is shown in ribbon representation colored in a gradient from the N-terminal residue at position 10 (dark blue) to the C-terminal residue at position 22 (colored dark red). The side chain conformations of Ile12, Arg13, and Ile14 are shown in full-atom wire representation. Their backbone curvature and fanned orientation are inconsistent with β-strand secondary structure. Bottom: plot of 180 lowest energy conformations from the folding simulation. -axis (ENER): energy score ranging from lowest at the left to higher at the right. -axis (NVIS): number of visits by the simulation to the indicated conformation. For example, the lowest energy conformation was found again and again by the search over 150 times. The presence of a 4 kcal simulation energy unit gap in the subtype C simulation indicates a rigid structure as a 4 kcal energy barrier prevents exit from the lowest energy conformation most of the time on the biological time scale. (b) Top: lowest energy conformation of the subtype B V3 loop crown from positions 10–22 depicted as in A. The extended linear conformation of Ile12, Arg13, and Ile14 with alternating directions for the side chains is typical of canonical β-strand structure. Bottom: plot of 180 lowest energy conformations from the folding simulation as in A. Many conformations are present near the lowest energy conformation in this subtype B simulation predicting a flexible structure that flickers between ~10 conformations all the time (is flexible) on the biological timescale.