The effects of chain length and thermal denaturation on helix-forming peptides: A mode-specific analysis using 2D FT-IR

The major goal of this project was to use FT-IR spectroscopy to monitor the effects of chain length and temperature on small, helix-forming peptides of the general form, Ac-W(EAAAR)(n)A-NH2, where n = 1, 3, 5, and 7, in aqueous solutions. FT-IR spectra were collected in D2O as a function of temperature in the range of -4 to 95 degrees C. The spectral range of interest, 1500-1725 cm(-1), contains the amide-I' band of the fully-exchanged H-->D peptide bond. Even in these simple peptides, the amide-I' region of the IR spectra is complex and congested, composed of features derived from the conformation of the peptide backbone and from the contributions of amino acid side chains. Unambiguous resolution of peak positions and intensities is thus extremely difficult, particularly when assessing subtle differences between two data sets. Two-dimensional correlation analysis (Noda, I. J. Am. Chem. Soc. 1989, 111, 8116. Noda, I. Applied Spectrosc. 1990, 44, 550) was used to guide and verify the results of the peak-fitting procedure and thereby facilitate physical interpretation of the temperature-dependent spectra. The results of the two-dimensional analysis and fitting procedure show that the spectral bands, particularly those of the amide-I' band, exhibit significant frequency shifts and bandwidth and intensity changes as a function of temperature and chain length. For the amide-I' modes arising from the helical and random conformations of the peptide bond, the normalization of peak intensities to units of molar absorptivity is discussed in terms of different models. Two different molar absorptivity calculations are presented, the first using the length-dependence of alpha-helical frequencies as predicted by perturbation theory, and the second assuming a more rigorous two-state transition. The results from each are discussed in terms of the effects of chain length on alpha-helix stabilization and in terms of a mechanism of helix unfolding.