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

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 F 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/beta-strand (beta(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 similar to 195 and similar to 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 (C) 2006 John Wiley & Sons, Ltd.