Potential-Energy Surface of Infinite Helical Polypeptides

The potential-energy surfaces of infinite polyalanine and polyglycine chains in helical conformation are studied using density-functional theory in the Perdew, Burke and Ernzerhof approximation to the exchange-correlation functional (DFT-PBE). Minima associated to a $\pi$-helix, $\alpha$-helix and $3_{10}$-helix conformations are identified for both polypeptides. For polyalanine the $\alpha$-helix minimum is the lowest in energy. However for polyglycine $\pi$-helix and $\alpha$-helix minima are degenerated within the DFT accuracy. The $\alpha$-helix is found to undergo structural transitions to a $\pi$- or $3_{10}$-helix when the length of the helix is strainend by more than 10\%. The barriers for the structural transitions mainly associated to the breaking of the hydrogen bonds are considerably affected by the side group in polyalanine. We find this effect can not be solely attributed to repulsive interactions between the side group and the helix backbone but to sizeable changes in covalent bonds in the peptide unit of polyalanine with respect to polyglycine.