Fig. 2. α3D folding transition path at neutral pH from MD simulation (13).
Exemplar structures from the unfolded state, the folded state, and the transition path are shown. The side chains of charged residues are represented in sticks and colored in red if they are involved in a non-native salt bridge, or in blue if the salt bridge is native. All other side chains are omitted for the sake of clarity. The transition path is defined as the region of the free energy surface (black) enclosed between the two dashed lines that separates the unfolded from the folded basin. The average number of native (blue) and non-native (red) salt bridges is also reported as a function of an optimized reaction coordinate. Salt bridges are determined using the stable-state picture (24) with cutoff distances of 4.5 and 8.0 Å between the Cγ of Asp or the Cδ of Glu and the Nζ of Lys or the Cζ of Arg. Salt bridges are considered native if they are within the longest cutoff distance in the experimentally determined structure 20. Note that due to the large number of highly flexible charged side chains present, ~2 non-native salt bridges can be transiently formed, on average, even in the folded state.