Energy landscape of the small protein Ace-(Ala) 10 -NMe

The energy landscape of the polyalanine Ace-(Ala) 10 -NMe, one of the standard models for the study of α -helix folding, is investigated using conformational space annealing (CSA) and the all-atom CHARMM force field (param22). The native α -helical conformation is obtained for all 100 CSA runs. Gathering all conformations in the final banks of 100 independent CSA runs, we collect a total of 1933 distinct local minima, enabling us to investigate the energy landscape. Our results clearly indicate a funnel-shaped energy landscape leading to the native helical conformation. To the best of our knowledge, this kind of funnel-shaped landscape for Ace-(Ala) 10 -NMe is obtained for the first time. Also, we find that the conformations of low-energy local minima are classified approximately into five groups according to their secondary structures: native-like α -helix conformations, partially α -helical conformations, conformations with an α -helix and a β -sheet, β -sheet conformations, and coil conformations.