Influence of the hydrophobic face width on the degree of association of coiled–coil proteins

A very simplistic computational model for the simulation of the association of dimeric coiled–coil proteins has been extended to permit the formation of higher order quaternary structures. The main parameter of the new model is ω, the width of the potential well representing the attraction among hydrophobic residues. For values of ω ranging from 0.5 to 3.0 Å, our Monte Carlo simulations predict the formation of trimers at low temperatures. The different structures (monomers, dimers, and trimers) which populate the simulated system at various temperatures allow us to discuss the optimum value of ω from the point of view of the thermal unfolding transition. On the other hand, the detailed analysis of the trimer structure provides a different point of view about the performance of the model, when compared with the structural information experimentally available for trimeric coiled–coils.