The effects of non-native interactions on protein folding rates: Theory and simulation

Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free energy barrier. We present an analytic theory to account for the modification on the free energy landscape upon introduction of non-native contacts, added as a perturbation to the strong native interactions driving folding. Our theory predicts a rate-enhancement regime at fixed temperature, under the introduction of weak, non-native interactions. We have thoroughly tested this theoretical prediction with simulations of a coarse-grained protein model, by employing an off-lattice $C_\alpha$ model of the src-SH3 domain. The strong agreement between results from simulations and theory confirm the non trivial result that a relatively small amount of non-native interaction energy can actually assist the folding to the native structure.