Conformational study of sequential Lys and Leu based polymers and oligomers using vibrational and electronic CD spectra

Abstract

Vibrational CD (VCD) and electronic CD (ECD) spectra of some sequential Lys and Leu based oligo- and polypeptides were studied as a function of added salt and (for ECD) as a function of concentration in aqueous solution. For these samples, the VCD spectra can only be measured at relatively high concentrations under which the well-known salt-induced transition to a beta-sheet form can be observed for the KL based species, but only the end-state alpha-helical conformation is obvious for the LKKL based samples. ECD concentration dependence demonstrates that, at high concentration with no added or with added salt, LKKL based oligomers and polymers give alpha-helical spectra. These data provide evidence of aggregation induced secondary structure formation in an exceptionally simple peptide system. Similarly, the KL based oligomers and polymers give beta-sheet like spectra at high concentration or at high salt. These systems further provide model systems under "normal" aqueous conditions that yield VCD band shapes that correlate to the major secondary structural types of polypeptides. They are in substantial agreement with those spectra obtained on homopolypeptides and on proteins, confirming the relative independence of the VCD technique from side-chain and solvent effects.

Comparison of and limits of accuracy for statistical analyses of vibrational and electronic circular dichroism spectra in terms of correlations to and predictions of protein secondary structure

“…For FC values corresponding to the Levitt and Greer (1977) definition we wrote our own program following their algorithm and chose the categories: helix (H), sheet (S), left-turn (LT), right-turn (RT), and "other" (C). It should be noted that C is simply what is left over and is not equivalent to a "random coil" though it may have spectral characteristics in common with that structure (Yasui & Keiderling, 1986;Dukor & Keiderling, 1991;Baumruk et al, 1994).…”

“…It is precisely due to this lack of dimensionality in ECD structural response, first noted in our qualitative comparisons (Pancoska et al, 1989;Keiderling, 1993Keiderling, , 1994, that the VCD studies were designed. However, despite all of the improvement found in the regressions by inclusion of both amide I' and I1 VCD data, the predictions d o not show the hoped-for large improvement in accuracy when aimed at determining just fractional secondary structure.…”

“…Some more recent studies have utilized band-shape methods for FTIR spectra (Dousseau & Pezolet, 1990;Leeet al, 1990;Sarver & Krueger, 1991a, 1991bPribic et al, 1993). Somewhat between these two approaches is the use of vibrational C D (VCD), a hybrid of CD and IR, to predict protein conformation (Keiderling, 1993(Keiderling, , 1994. VCD, like IR or Raman, can be used to sense several different spectrally resolved transitions involving different localized vibrations of the molecule, which, like ECD, have a distinct dependence on molecular stereochemistry.…”

?-Hairpin stabilization in a 28-residue peptide derived from the ?-subunit sequence of human chorionic gonadotropin hormone

“…22 FTIR, another commonly used spectroscopic technique for secondary structure analysis, gives rise to multiple, relatively resolved spectral bands whose frequencies shift for different structural motifs. [23][24][25] The disadvantages of FTIR are that all bands are the same sign and yield very similar band shapes for different peptides and proteins. Furthermore, the commonly used frequency assignments for the specific secondary structural types have been shown to be nonunique and influenced by the environment, which can pose problems for peptide studies employing a variety of solvents.…”

“…29 -31 As a result, VCD has the ability to distinguish among structures that are not easily separated by FTIR or ECD, and is particularly useful for following environmentally induced changes in peptide conformation. 23,32,33 In the present work we attempt to gain insight into the earliest stages of hCG␤ protein folding by studying the conformational preferences of a 28-residue peptide corresponding to the H3-␤ hairpin in the mature fully folded hormone. …”