Helix formation in unsolvated alanine-based peptides: Helical monomers and helical dimers

High-resolution ion mobility measurements and molecular dynamics simulations have been used to examine helix formation in protonated alanine-based peptides in a solvent-free environment. Protonated polyalanines, Ala(n)H(+), with up to 20 residues do not form extended helices in a vacuum. However, experiment and theory indicate that the addition of a lysine to the C terminus (Ac-Ala(n)-LysH(+)) results in the formation of a stable monomeric helix for n greater than or equal to 7. This helix is stabilized by the protonated lysine side chain capping the C terminus and by the interaction of the charge with the helix dipole. If the lysine is moved to the N terminus (Ac-LysH(+)-Ala(n)) the helix-stabilizing factors are absent, and for n < 13 these peptides adopt globular conformations, For n > 13 only dimers are observed. The dimers appear to be helical, with the lysine from one peptide interacting with the C terminus of the other in a head-to-toe, "coiled-coil"-like arrangement of antiparallel helices. The transition from helical dimers to monomeric globules that occurs at n = 13 is partly driven by the entropy cost of dimerization. Dimers are also observed for the Ac-Ala(n)-LysH(+) peptides. These dimers also appear to be helical and linked by the lysine of one peptide interacting with the C terminus of the other. However, here the helices adopt a nearly collinear (or vee-shaped) arrangement that minimizes unfavorable electrostatic interactions.