Discriminating the Helical Forms of Peptides by NMR and Molecular Dynamics Simulation

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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.

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