How the all-atom simulation and the Ising-based theory reconcile with each other on the helix-coil transition

In this report, we addressed a somewhat basic question about how the two extreme models, the all-atom model and the Ising-based model, can be consistent with each other regarding the polypeptide helix-coil transition. Comparisons of several physical properties were made between the results of the all-atom simulations and those of the Ising-based theories. From the equilibrium point of view, the two models were found to exhibit a qualitatively similar trend, which is significant considering the extreme difference in precision between the two models. On the other hand, from the kinetic viewpoint, there appeared a difference in relaxation behavior between the two models; i.e., so-called stretched exponential relaxation was observed in the all-atom simulation whereas the kinetic Ising model showed simple exponential relaxation. A plausible source of the observed difference is briefly discussed.