title: Discrimination between peptide 3(10)- and alpha-helices. Theoretical analysis of the impact of alpha-methyl substitution on experimental spectra.
abstract: Detailed spectral simulations based on ab initio density functional theory computations of the amide I and II infrared (IR) and vibrational circular dichroism (VCD) spectra for Ac-(Ala)(4)-NH(2), Ac-(Aib-Ala)(2)-NH(2), and Ac-(Aib)(4)-NH(2) constrained to 3(10)- and alpha-helical conformations are presented. Parameters from these ab initio calculations are transferred onto corresponding larger oligopeptides to simulate the spectra for dodecamers. The differences between conformations and for different Aib substitution patterns within a conformation are reflected in observable spectral patterns where data are available. Simulated IR spectra show small frequency shifts in the amide I maxima between 3(10)- and alpha-helices, but the same magnitude shifts occur within one conformation upon Aib substitution. Thus, from a computational basis, the frequency of the amide I maximum does not discriminate between the 3(10)- or alpha-helical conformations. Calculated VCD band shapes for 3(10)-helices showed more significant changes in amplitude, with change in the fraction of Aib, than those for alpha-helices. Generally, with increasing Aib content, the overall amide I VCD intensity becomes weaker and the amide I couplet becomes more conservative, while the amide II VCD is less affected. Although the detailed band shape is shown to be sensitive to alpha-Me substitution, the basic pattern of amide I and II relative VCD intensities still differs between alpha- and 3(10)-helices and, as a consequence, successfully discriminates between them. These predictions are all borne out in experimental spectra of Aib, mixed Aib-Ala, and Ala-based helical peptides, where available.
authors: Department of Chemistry (M/C 111), University of Illinois at Chicago, 60607-7061, USA.
authors: Jan
authors: J
authors: Kubelka
authors: R A Gangani D
authors: RA
authors: Silva
authors: Timothy A
authors: TA
authors: Keiderling
mesh_terms: D000409:Alanine / Q000031:analogs & derivatives* / Q000737:chemistry; D002942:Circular Dichroism; D008745:Methylation; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013055:Spectrophotometry, Infrared; D013329:Structure-Activity Relationship
chemical_list: D009842:Oligopeptides; C024933:acetyltrialanine; D000409:Alanine