CORRECTING THE CIRCULAR-DICHROISM SPECTRA OF PEPTIDES FOR CONTRIBUTIONS OF ABSORBING SIDE-CHAINS

The aromatic and sulfur-containing side chains Trp, Tyr, Phe, Cys, and Met contribute to the CD spectra of peptides and proteins in the amid e region, interfering with the analysis for secondary structure. We pr opose a method to correct the CD spectra of peptides undergoing the he lix-coil transition for contributions due to absorbing side chains usi ng singular value decomposition, The method uses the common basis vect ors obtained from an analysis of the CD spectra of related peptides wi thout the aromatic and sulfur-containing amino acids, The common basis vectors are fitted to a portion of the CD spectrum of the peptide bei ng corrected, in the range that is unaffected by its sidechain contrib utions. Then the resulting coefficients from the fitting are used alon g with the common basis vectors to regenerate the entire corrected spe ctrum. The method is illustrated for the CD spectra of the peptide seq uence acetyl-Y-VAXAK-VAXAK-VAXAK-amide, where X is substituted with th e 20 naturally occurring amino acids. This peptide model adopts a rand om-coil conformation in 2 mM sodium phosphate buffer, pH 5.5, and beco mes an alpha helix in methanol/buffer solutions. The difference betwee n the original and corrected spectra shows the contribution from the a romatic and sulfur-containing side chains. (C) 1997 Academic Press.