Protein Folding in the Landscape Perspective:
figure gallery

If you see a jpeg image you like, you can download the corresponding PostScript file. Please cite Hue Sun Chan and Ken A. Dill, Protein Folding in the Landscape Perspective: Chevron Plots and Non-Arrhenius Kinetics, Proteins: Structure, Function, and Genetics, Volume 30, No. 1, January 1998, pp 2--33.

Figure 5. General shapes of landscapes: (a) The HP landscape is shown pictorially as having a kinetic trap, A is a throughway folding trajectory whereas path B passes through the trap; (b) the HP+ landscape is smooth, unfolding paths are simply the reverses of the folding paths shown (from From Levinthal to pathways to funnels). (a) and (b) are schematic representations of Fig. 4. (c) shows a landscape on which all folding molecules must pass through an obligatory folding intermediate, represented by the "moat" in the figure. Download pocket funnel, smooth funnel, or moat funnel PostScript files.

Figure 12. Different folding scenarios. The vertical axis is internal free energy. Each conformation is represented as a point on the landscape. The two horizontal axes represent the many chain degrees of freedom. (a) shows a rugged landscape with hills and traps, folding kinetics is likely multi-exponential (from From Levinthal to pathways to funnels). (b) shows a landscape in which folding is faster than unfolding. A is a throughway folding path, whereas unfolding chains (path B) must surmount a barrier in order to reach the most stable denatured conformations. (c) shows a landscape in which folding is slower than unfolding. Most folding paths (path A) pass through a kinetic trap, whereas some low-lying denatured conformations are readily accessible from the native state during unfolding (path B). Download bumpy bowl, pocket funnel, or sluice moat funnel, PostScript files.

Figure 14. Funnelscape for a fast folding protein Folding is limited by the rate of meandering downhill. Download bumpy pit PostScript file.

Figure 15. (a) Champagne glass landscape, to illustrate how conformational entropy can cause "free energy barriers" to folding. The "bottleneck" or rate limit to folding is the aimless wandering on the flat plateau as the chain tries to find its way downhill (From From Levinthal to pathways to funnels) (b) Serpin scenario shows a landscape with a deep kinetic trap on the left (A), which is easily accessible from the open conformations. Chain trapped in this deep local minima anneal to the global minimum (B, in the middle) only very slowly. This corresponds to the folding of some serpins such as PAI-1. Download champagne, or pitted moat PostScript files.

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