Infrared absorption spectra are reported for six apolipoprotein fragments in SDS/D2O. Five of the peptides correspond to proposed lipid- binding domains of human apolipoproteins [apoC-I(7-24), apoC-I(35-53), apoA- II(18-30)+, apoA-I(166-185), apoE(267-289)], and the sixth is the de novo lipid associating peptide LAP-20. The amide I infrared absorption patterns are generally consistent with predominantly helical structures (as determined previously by NMR spectroscopy and distance geometry calculations) and further suggest that apoA-I(166-185) and apoE(267-289) are hound to SDS relatively weakly in comparison to the other four peptides. The latter conclusion is also supported by the temperature dependence of the infrared spectra, as increasing temperature promotes a distinct increase in random coil structure only for apoA-I(166-185) and apoE(267-289). In addition to features readily ascribed to helices, the infrared spectra of all the peptides show absorptions in the spectral region 1630-1635 cm-1 that is usually associated with β-structure, a motif that is clearly absent from the NMR-derived structures. Parallel difficulties also arose in the analyses of the circular dichroism spectra. We suggest that both the low-frequency infrared absorptions and the ambiguities in interpreting the CD spectra may be due to unusual structures at the peptide C-termini, involving C=O groups that form hydrogen bonds simultaneously either with two solvent molecules or with donors from the backbone (NH) and the solvent (OH). Analogous absorptions may be a general feature of solvent-exposed helices, which suggests a need for caution in assigning amide I bands below 1640 cm-1.
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