Discriminating the helical forms of peptides by NMR and molecular dynamics simulation

Abstract

The HNCO NMR pulse sequence was applied to three selectively labeled 15N and 13C isotopic homologues of the peptide Ac-WAAAH(AAARA)3A-NH2 to probe directly for hydrogen bonds between residues 8 and 11 (characteristic of a 310-helix), 8 and 12 (α-helix), and 8 and 13 (π-helix). The experiments demonstrate conclusively, and in agreement with circular dichroism studies, that the center of the peptide is α-helical; there is no discernible 310- or π-helix at these specific positions. Molecular dynamics simulations of the preceding peptide and Ac-(AAAAK)3A-NH2 in water using the potential energy parameter set CHARMM22/CMAP correctly yield an α-helix, in contrast to simulations with the set CHARMM22, which result in a π-helix.