Computer simulation studies of finite temperature conformational equilibrium in alanine-based peptides

Computer simulations were used in observing the conformational equilibria in the poly-alanine peptides, (Ala(sub 8)(super +)), (Ala(sub 16)(super +)) and the lysine-doped poly-alanine peptide (Ac-(AAAAK)(sub 3)A-NH(sub 2)(super 3+)). Two-dimensional umbrella sampling techniques along with multiple time step molecular dynamics were used in carrying out the computer simulations. Results indicated that the 3K peptide has a helical structure in vacuum and in solution. The poly-alanine peptides form compact complexes in vacuum so that solvation will occur on the N-terminus.