Coarse-grained protein model, cooperativity of folding and subdomain structure

We investigate how does the range of attraction of a coarse-grained protein model affect cooperativity of folding transition. Free-energy landscapes of chymotrypsin inhibitor 2 (CI2) and bovine pancreatic trypsin inhibitor (BPTI) are obtained by a lattice protein model with Gō-like interaction. With the range of attraction being varied as a parameter, we find that a short-range nature of interaction is important for cooperativity. BPTI exhibits a folding intermediate whose structure is similar to that observed experimentally, when the range of attractions is appropriately set. Thus subdomain structure is determined mainly by the native topology.