Some problems of CD analyses of protein conformation

Abstract

The circular dichroic (CD) spectra of 16 reference proteins were analyzed by the Provencher-Glöckner method (Biochemistry 20, 31, 1981) with the lower-wavelength limit raised from 190 to 235 nm at 5-nm intervals. Fifty-one data points at 1-nm intervals were taken between 190 and 240 nm. Variations of the correlation coefficients (r) and root-mean-square (RMS) deviations between X-ray diffraction results and CD analyses showed no definite trend with shorter wavelength ranges. The CD spectra (190-240 nm) were also analyzed by assigning the secondary structure of X-ray results according to the Levitt-Greer method (J. Mol. Biol. 114, 181, 1977) and the Kabsch-Sander method (Biopolymers 22, 2577, 1983). The r and RMS values based on the Levitt-Greer assignment were good and comparable to those based on the secondary structure given by crystallographers, but the Kabsch-Sander assignment seemed to give unsatisfactory results. The choice of reference proteins remains one of the uncertainties in the CD analysis. The five most significant orthogonal spectra (190-240 nm) calculated from the 16 reference proteins and those based on another 16 proteins used by Hennessey and Johnson (Biochemistry 20, 1085, 1981) were similar to each other, but different in intensities. These methods still cannot recognize a failed analysis of unknown proteins without X-ray results to check their reliability.