The conformations adopted by the octamer peptide (AAKA)₂ in aqueous solution probed by FTIR and polarized Raman spectroscopy

Abstract

In an effort to further elucidate the chain length dependence of the poly-L-proline 3₁ helical structure (PPII) in short alanine-based polypeptides, we utilize FTIR, isotropic and anisotropic Raman, and electronic circular dichroism (ECD) spectroscopies to probe the amide I′ band of the unblocked octamer H-Ala-Ala-Lys-Ala-Ala-Ala-Lys-Ala-OD in D₂O. Our results are in disagreement with recent notions suggesting that the 3₁ helical structure increases with an increase in the number of alanine residues.1, 2 Simulations of the spectra were carried out and found to best reproduce experimental spectra using parameters that suggest a 40/60% PPII/β-strand (ß_s) mixture. The amount of PPII in the octamer is found to be significantly lower than what was determined for unblocked alanine-based peptides of comparable or even larger size. This is confirmed by the relatively weak ECD minimum and maximum at ∼195 and ∼220 nm, respectively, for the octamer relative to tri- and tetraalanine.3 In this paper we also address a recent issue concerning the validity of the delocalized character of the amide I mode in unfolded polypeptides containing a significant amount of PPII structure. We conclude that experimental evidence strongly supports the vibrational coupling model used to interpret the amide I mode in unfolded polypeptides. Copyright © 2006 John Wiley & Sons, Ltd.