Secondary structure of an isolated P-region from the voltage-gated sodium channel: A molecular modelling/dynamics study

Conformational studies of synthetic peptides corresponding to the pore-forming regions of voltage-gated sodium channels show a high tendency for β-sheet conformation when interacting with lipid vesicles, as revealed by circular dichroism and infrared spectroscopy. These observations have guided our choice of possible molecular models for the P-region peptide of domain II of voltage-gated sodium channels: three alternative β-hairpins, with differing turn assignments, or an α-helical hairpin. After generation of models by distance geometry-based methods, molecular dynamics (MD) simulations were run, in the absence of explicit solvent molecules but employing three different dielectric constants, to explore possible conformational preferences. The simulations in the different dielectric environments suggest that a 4-residue turn with the sequence LCGE yields mere stable β-hairpins. The MD results suggest that the SS1 part of the peptide may be more stable as an α-helix, whereas the SS2 part tends to adopt a β-conformation.