Downhill Folding - Simulations

Simulations

Because downhill folding is difficult to measure experimentally, molecular dynamics and Monte Carlo simulations have been performed on fast-folding proteins to explore their folding kinetics. Proteins whose folding rate is at or near the folding "speed limit", whose timescales make their folding more accessible to simulation methods, may more commonly fold downhill. Simulation studies of the BBL protein imply that its rapid folding rate and very low energy barrier arise from a lack of cooperativity in the formation of native contacts during the folding process; that is, a low contact order. The link between lack of cooperativity and low contact order was also observed in the context of Monte Carlo lattice simulations These data suggest that the average number of "nonlocal contacts" per residue in a protein serves as an indicator of the barrier height, where very low nonlocal contact values imply downhill folding. Coarse-grained simulations by Knott and Chan also support the experimental observation of global downhill folding in BBL.