Computer simulation of protein refolding pathways and intermediates

Computer simulation studies of refolding pathways and the formation of intermediates for a simple, 2–D lattice protein model are presented. The sequence of the 20–bead model protein chain is chosen so that hydrophobic beads will reside in the protein interior in the native state. Nonbonded hydrophobic beads attract each other with strength ϵ decreasing the |ϵ/kT| mimics increasing the concentration of the denaturant. Dynamic Monte Carlo simulations and exhaustive conformational searches have been performed on an isolated model protein sequence at different levels of |ϵ| (different denaturant concentrations). As the denaturant is withdrawn, the model protein exhibits a transition from a random coil state to a compact native state with a hydrophobic core. The refolding process is observed to be cooperative in that the chain does not start folding until the middle section has folded correctly, and proceeds along preferred pathways that are populated by distinct, partially folded intermediates.