A microscopic view of helix propagation: N and C-terminal helix growth in alanine helices

Molecular dynamics simulations with umbrella sampling are used to perform free energy simulations of C-terminal and N-terminal helix propagation in small helices of Ace-(Ala)n-NMe, with n= (4,5,10,15), in water. From the resulting free energy surfaces, computed as a function of the terminal psi dihedral angle, the roles of length and end effects in helix propagation are explored. An energetic analysis of the helices, both formed and partially formed, is used to develop a molecular rationalization for the observed trends in helix stability. We find that the microscopic helix propagation parameters vary significantly depending on the end and length of the helix in which the terminal hydrogen bond is forming. A model which considers propagation of the helices from either end as statistically independent yields Zimm-Bragg s parameters in the range of 0.5 to 1.5, depending on helical length. Analysis of the mechanism of helix propagation suggests that 3(10)-helix plays a role in helix formation but its population should be low in the helical state of these model peptides.