Large differences in the helix propensities of alanine and glycine

Abstract

THE standard view of a helix formation in water, based on helix propensities determined by the host–guest method^1,2, is that differences in helix propensity among the amino acids are small, except for proline³, and that the average value of the helix propaga-tion parameter s is near 1. A contradictory view of α helix formation in water is emerging from substitution experiments with short, unique-sequence peptides that contain only naturally occurring amino acids^4–9. Short peptides that contain only alanine and lysine, or alanine and glutamate, form surprisingly stable monomeric helices in water⁹ and substitution of a single alanine residue by another amino acid in these or related peptides produces a wide range of changes in helix content, depending on which amino acid is substituted for alanine^4–6,8. We show here that the ratio of the helix propensities of alanine to glycine is large, about 100, in substitution experiments with a 17-residue reference peptide containing alanine and lysine. The helix propensity is identified with s, the helix propagation parameter of the statistical mechanics model for α helix formation, and the results are interpreted by the Lifson–Roig theory¹⁰. Single alanine → glycine substitutions have been made at a series of positions in individual peptides. The helix-destabilizing effect of an Ala → Gly substitution depends strongly on its position in the helix, as predicted by the Lifson–Roig theory if the ratio of s values for Ala: Gly is large.