Circular dichroic analysis of protein conformation: Inclusion of the β-turns

The mean residue ellipticity, [θ], at any wavelength, λ, of a protein in aqueous solution is expressed as [θ] λ = f H [θ] H x (1 − k n ) + f β[θ] β + f t [θ] t + f R [θ] R with two constraints: 1 ≥ f j ≥ 0 and Σf j = 1. The subscripts H, β, t, and R refer to the helix, β-form, β-turn, and unordered form. The fractions, f j ′s, of 15 proteins are based on X-ray crystallography, f t refers to the net β-turn after cancelling those residues having dihedral angles of opposite sign. The [ θ] H x of an infinite helix and its chain-length dependence factor, k, were computed from the myoglobin data (Chen et al., 1974, Biochemistry, 13, 3350). The average number of residues per helical segment, n , for 15 proteins was about 10, which can be used for proteins of unknown structure. The reference spectra of other three structural elements are computed by a least-squares method. Once the reference spectra are chosen, the same equation above can be used to estimate the fractions of the secondary structure of a portein from its CD data points between 190 and 240 nm at 1-nm intervals. The computed helical content is usually good to excellent (concanavalin A is a notable exception). Inclusion of the β-turn in the analysis improves the correlation for the estimates of the β-form, but the computed β t values are not significantly correlated with the X-ray results. Matrix formulation proves the equivalence of the least-squares method and the integral curve-fitting.