Peptide length dependence of a simplified model for the folding of regular two-stranded coiled-coils

Abstract

In this work we study a simplified model for the folding of dimeric coiled-coil proteins with regular sequences. The model keeps the individual peptides in rigid straight helical conformations. This situation makes the model bad suited for its application to long peptide chains. We have thus used Monte Carlo simulations to explore how the expected limitations of the model reflect in its thermodynamic and structural behavior. We find that, for long chains, the model shows a vague definition of the folded state which is only appreciated after a careful analysis, but can become otherwise unnoticed. The formal similarity of this situation to the possible presence of intermediate states and its meaning in the cooperativity character of the folding/unfolding transition is briefly discussed.