Journal of the American Chemical Society, Vol.126, No.33, 10478-10484, 2004
Discriminating the helical forms of peptides by NMR and molecular dynamics simulation
The HNCO NMR pulse sequence was applied to three selectively labeled N-15 and C-13 isotopic homologues of the peptide Ac-WAAAH(AAARA)(3)A-NH2 to probe directly for hydrogen bonds between residues 8 and 11 (characteristic of a 3(10)-helix), 8 and 12 (alpha-helix), and 8 and 13 (pi-helix). The experiments demonstrate conclusively, and in agreement with circular dichroism studies, that the center of the peptide is a-helical; there is no discernible 3(10)-or pi-helix at these specific positions. Molecular dynamics simulations of the preceding peptide and Ac-(AAAAK)(3)A-NH2 in water using the potential energy parameter set CHARMM22/CMAP correctly yield an a-helix, in contrast to simulations with the set CHARMM22, which result in a pi-helix.