Figure 1.6.

One sequential (A) and two parallel folding pathways (B and C) used in KINSIM simulations. (A) The unfolded species folds through two intermediates before forming the native species. (B) Two unfolded and native species exist and interconvert. (C) Three unfolded species exist, where U₁ and U₂ fold to the native state and U₃ interconverts with U₁ or U₂. (D-F) Plots of an Apaf-1 CARD refolding reaction in 3.64 M urea. KINSIM simulations for each plot are shown as a continuous line. For pathway A, the concentration of I₁ was 10 μM. The extinction coefficient for U, I₁,I₂, and N were 0, 0.0007, 0.0058, and 0.0063, respectively. The rates for I₁ to I₂ and I₂ to N were 45 and 0.6 sec^-1, respectively. For pathway B, the concentrations of U₁ and U₂ were 1 and 9 μM, respectively. The extinction coefficients for N₁ and N₂ were 0.0074 and 0.0064. The rates of U₁ to N₁, U₁ to U₂, U₂ to N₂, and N₁ to N₂ were 500, 100, 50, and 0.4 sec^-1, respectively. For pathway C, the concentrations of U₁, U₂, and U₃ were 0.7, 8.3 and 1 μM. The extinction coefficient of N was 0.0086. The rates of U₁ to N, U₂ to N and U₃ to U₁ or U₂ were 5000, 37 (back rate of 13) and 0.6 (back rate of 0.01) per second.