Post date: Oct 11, 2016 2:29:48 PM
Energetics of infinite homopolypeptide chains
In a recent paper in The Journal of Physical Chemistry B, we present a novel method for comparing the long-range part of force fields in the presence of a maximally cooperative network of nonbonded interactions. The method is based on mapping the potential energy surface of an infinite polypeptide chain in the gas phase by using cylindrical coordinates (the twist and pitch) as geometry descriptors.
We apply our method to an infinite polyalanine chain and consider the AMBER99, AMBER99SB, CHARMM27, and OPLS-AA/L fixed partial-charge force fields and the protein-specific version of the AMOEBA polarizable force field. Results from our analysis are compared to those obtained from high-level density-functional theory (DFT) calculations. We find that all force fields produce stronger stabilization of the helical conformations as compared to DFT, with only
AMBER99/AMBER99SB satisfactorily reproducing all three helical conformations (π, α, and 310).
The animation shows a fragment of the infinite Ala chain in the right-handed α-helical conformation: Hydrogen bonds are indicated by dashed lines (only amide hydrogens are shown). Helix axis is shown by a long green arrow, and the red arrows indicate two consecutive backbone Cα atoms.