Structural Determinants of Misfolding in Multidomain Proteins
Fig 6
Illustration of relation between folding funnels for native and domain-swapped domains. (A) Example native contact map, highly coarse-grained for simplicity. (B) Map of all possible native-like contacts for a two-domain protein, showing native contacts in black and domain-swapped contacts in blue. (C) In the context of the two-domain sequence, the folding funnels for a single native domain (green broken line) and domain-swapped domain (red broken line) are interconnected, forming part of a single global funnel (black line). States are considered part of the native funnel if all contacts formed belong to the native state, and to the domain-swap funnel if all contacts formed belong to the domain-swapped structure. Note that only a subset of possible states are shown, for clarity (e.g. other domain-swapped species are possible). Only states with a single native-like stretch of residues are considered, whose length does not exceed that of a single folded domain. Arrows connect states differing by a single coarse grained residue flipping between native and non-native.