A set of constructed type spectra for the practical estimation of peptide secondary structure from circular dichroism

While reliable methods have been developed for the estimation of globular protein secondary structure content from their far UV circular dichroism spectra, these are not suitable for the analysis of simple peptides. Model peptides have been measured in purely alpha-helical, beta-sheet, and coil form, and are often used for fitting the CD spectra of peptides, but these are mainly derived from homopolymers and exhibit side-chain-dependent characteristics that do not accurately represent the situation in natural sequences. We have attempted to reduce the side chain bias inherent in these spectra by constructing a series of frequency-weighted ''average'' spectra from all available data on model peptides. These have proved quite satisfactory in estimating the secondary structure of a number of peptides, A computer program incorporating these spectra has been developed for practical use. (C) 1997 Academic Press.