title: The effects of nonnative interactions on protein folding rates: theory and simulation.
abstract: Proteins are minimally frustrated polymers. However, for realistic protein models, nonnative interactions must be taken into account. In this paper, we analyze the effect of nonnative 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 nonnative 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, nonnative interactions. We have thoroughly tested this theoretical prediction with simulations of a coarse-grained protein model, by using an off-lattice C(alpha)model of the src-SH3 domain. The strong agreement between results from simulations and theory confirm the nontrivial result that a relatively small amount of nonnative interaction energy can actually assist the folding to the native structure.
authors.affiliation: Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA. cecilia@rice.edu
authors.forename: Cecilia
authors.initials: C
authors.lastname: Clementi
authors.forename: Steven S
authors.initials: SS
authors.lastname: Plotkin
mesh_terms: D003198:Computer Simulation; D007700:Kinetics; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins