Study of the Helical Protein Ace-(Ala)<SUB>10</SUB>-NMe in Solvent by Conformational Space Annealing

Abstract

Using conformational space annealing (CSA), a powerful global optimization method, and the allatom CHARMM force field (param27) with the GB/SA continuum solvation potential, the energy landscape of the polyalanine Ace-(Ala) 10 -NMe in solvent (one of the standard models for the study of helix folding) is investigated. The native helical conformation is obtained for all 45 CSA runs. Gathering all conformations in the banks (final banks) of 45 independent CSA runs, we collect a total of 5588 (1045) distinct local minima, enabling us to investigate the energy landscape of Ace-(Ala) 10 -NMe in solvent. Our results show a funnel-shaped energy landscape leading to the native helical conformation. This kind of funnel-shaped landscape for Ace-(Ala) 10 -NMe in solvent is obtained for the first time.