Nearly symmetrical proteins: Folding pathways and transition states

The folding pathways of the B domain of protein A have been the subject of many experimental and computational studies. Based on a statistical mechanical model, it has been suggested that the native state symmetry leads to multiple pathways, highly dependent on temperature and denaturant concentration. Experiments, however, have not confirmed this scenario. By considering four nearly symmetrical proteins, one of them being the above molecule, here we show that, if contact energies are properly taken into account, a different picture emerges from kinetic simulations of the above-mentioned model. This is characterized by a dominant folding pathway, which is consistent with the most recent experimental results. Given the simplicity of the model, we also report on a direct sampling of the transition state.