Role of explicitly cooperative interactions in protein folding funnels: A simulation study

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Abstract
We discuss an off-lattice simulation of a model protein containing nonpairwise-additive interactions. The effect of varying the strength of nonadditivity within a physically reasonable range on the folding funnel topography, i.e., free energy profiles as a function of global and local order parameters, is determined. A critical comparison is made with existing theories of free energy profiles based on energy landscape ideas. While the global mean-field theory gives the correct trends for the essential simulation results, its barriers are not quantitatively accurate for short range interactions. Variational approximations that allow spatial variation of the order parameter provide quite accurate barriers and accurate pictures of the localization of order.