Rate Determining Factors in Protein Model Structures

Previous research has shown a strong correlation of protein folding rates to the native state geometry, yet a complete explanation for this dependence is still lacking. Here we study the rate-geometry relationship with a simple statistical physics model, and focus on two classes of model geometries, representing ideal parallel and antiparallel structures. We find that the logarithm of the rate shows an almost perfect linear correlation with the “absolute contact order”, but the slope depends on the particular class considered. We discuss these findings in the light of experimental results.

Figure 1

Logarithm of equilibration rate vs absolute contact order for parallel structures. Symbols explained in text.

Figure 2

(a) Logarithm of equilibration rate vs absolute contact order for antiparallel structures at the denaturation temperature $T_m$. Symbols explained in text. (b) Absolute value of the slope in (a) as a function of $s$.