Estimation of the number of alpha-helical and beta-strand segments in proteins using circular dichroism spectroscopy

A simple approach to estimate the number of alpha-helical and beta-strand s egments from protein circular dichroism spectra is described. The alpha-hel ix and beta-sheet conformations in globular protein structures, assigned by DSSP and STRIDE algorithms, were divided into regular and distorted fracti ons by considering a certain number of terminal residues in a given alpha-h elix or beta-strand segment to be distorted. The resulting secondary struct ure fractions far 29 reference proteins were used in the analyses of circul ar dichroism spectra by the SELCON method. From the performance indices of the analyses, we determined that, on an average, four residues per alpha-he lix and two residues per beta-strand may be considered distorted in protein s. The number of alpha-helical and beta-strand segments and their average l ength in a given protein were estimated from the fraction of distorted alph a-helix and beta-strand conformations determined from the analysis of circu lar dichroism spectra. The statistical test for the reference protein set s hows the high reliability of such a classification of protein secondary str ucture. The method was used to analyze the circular dichroism spectra of fo ur additional proteins and the predicted structural characteristics agree w ith the crystal structure data.