Low entropic barrier to the hydrophobic collapse of the prion protein: Effects of intermediate states and conformational flexibility

A simple kinetic model is applied to study the folding reaction of the C-terminal domain of the murine prion protein, mPrP(121-231). The model provides an equation linking a protein's folding rate with its native topology and the conformational entropic cost of folding. The model predicts that the average conformational entropic cost per residue associated with the folding transition of mPrP(121-231) is smaller than the average for a broad sample of two-state folding proteins. The results are consistent with the native state of mPrP(121-231) being more flexible than the average protein, but the behavior could also arise from the presence of early intermediate states. The findings are in agreement with experimental and theoretical results on the prion protein conformational flexibility. The model is fully analytical and provides a simple way to obtain a quantitative measure of conformational flexibility in two-state proteins from kinetic and structural experimental data.