3(10)-HELIX VERSUS ALPHA-HELIX - A MOLECULAR-DYNAMICS STUDY OF CONFORMATIONAL PREFERENCES OF AIB AND ALANINE

The alpha-helix and the 3(10) helix are two common constituents of protein architecture. Spectroscopy and crystallography indicate that short peptides containing alanine tend to assume alpha-helical conformations while short peptides containing Aib (alpha-aminoisobutyric acid) tend to assume 3(10)-helical conformations. Here we have used molecular dynamics simulations to study the equilibrium between helix types both in vacuo and in water and found that decaalanine prefers the alpha-helix over the 3(10) helix by 16 kcal/mol in water, or 8.0 kcal/mol in vacuo, while Aib(10) shows no clear preference in water, and prefers the 3(10) helix by 4.3 kcal/mol in vacuo. In either medium, introduction of a single Aib residue in the middle of a 14-residue 3(10) helix containing only Ala (alanine) residues very much stabilizes the 3(10)-helical conformation (Delta Delta G degrees = -2.6 kcal/mol, in water), while in the alpha-helical conformation the effect of the introduction is quite small (Delta Delta G degrees = -0.7 kcal/mol, in water). We argue that the conformation of the Aib residue predisposes this residue to helix formation, in terms of both entropy and energy, and that the low propensity for alpha-helix formation comes from unfavorable interactions between the methyl groups of an Aib residue in position i and the Ala residue in position i + 3, interactions which are absent in the 3(10) helix. This is supported by results of simulations with oligomers with Aib in position i and glycine (Gly) in position i + 3, which show that the Aib/Gly pair makes as stable an alpha-helix as does the Ala/Ala pair, entirely suppressing the inherent helix destabilizing effect of Gly.