Fig. 5.

Topological traps and model for GFP folding. (A) The wild type GFP structure in blue is superimposed onto the misfolded structure in red. Misfolding of the loop connecting β₉ and β₁₀ causes a topological trap. The arrows show the correct (folded) and incorrect (misfolded) conformation of the loop. (B) In the second misfolded structure the barrel involving the 11 β-strands form with no contact between the central α-helix and rest of the structure. (C) Folding landscape and network of connected states based on simulations. The flux through the four channels and the routes from the UBA to the NBA are indicated by arrows. Because topological traps (structures in (A) and (B)) are dead ends in the folding process they do not reach the NBA on the time scale of our simulations. Thus, the total flux to the NBA from UBA is less than 100%. Representative structures sampled along the four pathways as well as an unfolded conformation are shown.