Discriminating the helical forms of peptides by NMR and molecular dynamics simulation.
The HNCO NMR pulse sequence was applied to three selectively labeled (15)N and (13)C isotopic homologues of the peptide Ac-WAAAH(AAARA)(3)A-NH(2) 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 alpha-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-NH(2) in water using the potential energy parameter set CHARMM22/CMAP correctly yield an alpha-helix, in contrast to simulations with the set CHARMM22, which result in a pi-helix.
Contribution from the Laboratory of Biophysics, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852, USA.
Darón I
DI
Freedberg
Richard M
RM
Venable
Angelo
A
Rossi
Thomas E
TE
Bull
Richard W
RW
Pastor
D000409:Alanine / Q000737:chemistry; D002247:Carbon Isotopes; D002942:Circular Dichroism; D003198:Computer Simulation; D006860:Hydrogen Bonding; D009587:Nitrogen Isotopes; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D025801:Ubiquitin / Q000737:chemistry
D002247:Carbon Isotopes; D009587:Nitrogen Isotopes; D010455:Peptides; D025801:Ubiquitin; D000409:Alanine