Comparison of and limits of accuracy for statistical analyses of vibrational and electronic circular dichroism spectra in terms of correlations to and predictions of protein secondary structure

Abstract

This work provides a systematic comparison of vibrational CD (VCD) and electronic CD (ECD) methods for spectral prediction of secondary structure. The VCD and ECD data are simplified to a small set of spectral parameters using the principal component method of factor analysis (PC/FA). Regression fits of these parameters are made to the X-ray-determined fractional components (FC) of secondary structure. Predictive capability is determined by computing structures for proteins sequentially left out of the regression. All possible combinations of PC/FA spectral parameters (coefficients) were used to form a full set of restricted multiple regressions with the FC values, both independently for each spectral data set as well as for the two VCD sets and all the data grouped together. The complete search over all possible combinations of spectral parameters for different types of spectral data is a new feature of this study, and the focus on prediction is the strength of this approach. The PC/FA method was found to be stable in detail to expansion of the training set. Coupling amide I1 to amide I' parameters reduced the standard deviations of the VCD regression relationships, and combining VCD and ECD data led to the best fits. Prediction results had a minimum error when dependent on relatively few spectral coefficients. Such a limited dependence on spectral variation is the key finding of this work, which has ramifications for previous studies as well as suggests future directions for spectral analysis of structure. The best ECD prediction for helix and sheet uses only one parameter, the coefficient of the first subspectrum. With VCD, the best predictions sample coefficients of both the amide I' and I1 bands, but error is optimized using only a few coefficients. In this respect, ECD is more accurate than VCD for a-helix, and the combined VCD (amide I'+II) predicts the P-sheet component better than does ECD. Combining VCD and ECD data sets yields exceptionally good predictions by utilizing the strengths of each. However, the residual error, its distribution, and, most importantly, the lack of dependence of the method on many of the significant components derived from the spectra leads to the conclusion that the heterogeneity of protein structure is a fundamental limitation to the use of such spectral analysis methods. The underutilization of these data for prediction of secondary structure suggests spectral data could predict a more detailed descriptor.

The optimization of protein secondary structure determination with infrared and circular dichroism spectra

“…Contrary to what would be expected, the general trend is for the error to increase with the number of proteins used (e.g [41]). For the CD analyses the relationships for FC H and FC E are well represented by straight lines (not shown).…”

“…It remains possible that these differences reflect the internal consistency of the spectra in each respective basis set rather than the expected general accuracy of the methods. In a recent paper, Sreerama & Woody [6] investigated the effect of the number of reference proteins (29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48) on the accuracy of the prediction obtained by three publicly available CD analysis software programs.…”

Papaya glutamine cyclase, a plant enzyme highly resistant to proteolysis, adopts an all‐β conformation

“…The value reported for PQC has been experimentally determined while those given for trypsin and chymotrypsin were calculated using information from the Swiss Prot Data Bank (M r ; content of the chromophores Trp, Tyr and SS bonds) and the known ε values of the various chromophores [31]. For CD samples only, the protein concentration was determined using a peptide bond absorption coefficient of 5167 mol Ϫ1 l cm Ϫ1 at 205 nm, which is based on a combination of previously published values ( [32,33] and references therein). PQC concentration determinations based on measurements of A 205 and A 279 agreed to within 1%.…”

Rett Syndrome-causing Mutations in Human MeCP2 Result in Diverse Structural Changes That Impact Folding and DNA Interactions

“…33, five from Ref. 35, and five denatured, was used. The estimated composition of the MBD calculated using LIN-COMB, CONTINLL was also compared with the known NMRderived secondary structure of the MBD (Protein Data Bank code 1QK9 (4)) using STRIDE (36).…”