Estimation of Protein Secondary Structure from Circular Dichroism Spectra: Comparison of CONTIN, SELCON, and CDSSTR Methods with an Expanded Reference Set

Publisher Summary Circular dichroism (CD) is a spectroscopic method which depends on the fact that certain molecules interact differently with right and left circularly polarized light. Circularly polarized light is chiral—that is, it occurs in two nonsuperimposable forms that are mirror images of one another. To discriminate between the two chiral forms of light, a molecule must be chiral, including the vast majority of biological molecules. A method that can discern the subtle differences between non superimposable mirror image molecules (enantiomers) must be highly sensitive to the three-dimensional features of molecules—that is, to conformation. Binding of ligands or protein-protein and protein–DNA interactions can also alter the circular dichroism spectrum of the protein and/or nucleic acid. These changes in CD can be used to determine equilibrium constants, and they can also provide evidence for conformational changes. Thus, CD can provide information about the secondary structure of proteins and nucleic acids and about the binding of ligands to these types of macromolecule.

[4] Circular dichroism

Quantitative studies of the structure of proteins in solution by fourier-transform infrared spectroscopy

Theoretical descriptions of two-dimensional (2D) vibrational and electronic spectroscopy are presented By using a coupled multi-chromophore model, some examples of 2D spectroscopic studies of peptide solution structure determination and excitation transfer process in electronically coupled multi-chromophore system are discussed A few remarks on perspectives of this research area are given

Coherent Two-Dimensional Optical Spectroscopy

Circular dichroism spectroscopy is a widely used technique to analyze the secondary structure of proteins in solution. Predictive methods use the circular dichroism spectra from proteins of known tertiary structure to assess the secondary structure contents of a protein with unknown structure given its circular dichroism spectrum. We developed K2D2, a method with an associated web server to estimate protein secondary structure from circular dichroism spectra. The method uses a self-organized map of spectra from proteins with known structure to deduce a map of protein secondary structure that is used to do the predictions. The K2D2 server is publicly accessible at http://www.ogic.ca/projects/k2d2/
 . It accepts as input a circular dichroism spectrum and outputs the estimated secondary structure content (alpha-helix and beta-strand) of the corresponding protein, as well as an estimated measure of error.

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K2D2: Estimation of protein secondary structure from circular dichroism spectra

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 II 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 II bands, but error is optimized using only a few coefficients. In this respect, ECD is more accurate than VCD for alpha-helix, and the combined VCD (amide I' + II) predicts the beta-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.

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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.

The conformation of the milk protein alpha-lactalbumin has been studied using vibrational circular dichroism (VCD) and compared to parallel studies on lysozyme. These proteins have been shown by Acharya et al. [(1989) J. Mol. Biol. 208, 99-127] to have very similar three-dimensional crystal structures. However, their VCD spectra in D2O solution are quite different. The VCD of lysozyme in D2O more resembles that of alpha-lactalbumin in 33% propanol/D2O, under which conditions alpha-lactalbumin has conformationally transformed to a structure with increased helical fraction. These results can be seen to be consistent with UVCD and resolution-enhanced FTIR spectra of alpha-lactalbumin and lysozyme in both D2O and H2O environments. The solvent sensitivity of the alpha-lactalbumin spectra and hence of its conformation contrasted with the lack of such sensitivity for lysozyme suggest that the alpha-lactalbumin crystal structure represents a conformation different from that which is dominant in aqueous solution.

Comparison of alpha-lactalbumin and lysozyme using vibrational circular dichroism. Evidence for a difference in crystal and solution structures.

The amide II vibrational CD (VCD) spectra of poly (L-glutamic acid) and poly (L-lysine) in various conformational forms and those of several proteins in H2O have been measured. Characteristic VCD patterns have been observed in the amide II region due to helix, beta-sheet, and coil conformations in polypeptides. Based on their x-ray crystal structures, the proteins studied have been assigned to six categories. Proteins in the same category give rise to similar amide II VCD. While the protein conformational type is indicated using the amide II VCD, discrimination between types is less characteristic than with the previously studied amide I' VCD in D2O.

Vijai P. Gupta

Papers

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.

Comparison of alpha-lactalbumin and lysozyme using vibrational circular dichroism. Evidence for a difference in crystal and solution structures.

Vibrational CD of the amide II band in some model polypeptides and proteins.

Determination of Secondary Structures of Proteins Using Vibrational Circular Dichroism