Convex constraint analysis: a natural deconvolution of circular dichroism curves of proteins

Abstract

A new algorithm, called convex constraint analysis, has been developed to deduce the chiral contribution of the common secondary structures directly from experimental CD curves of a large number of proteins. The analysis is based on CD data reported by Yang, J.T., Wu, C.-S.C. and Martinez, H.M. [Methods Enzymol., 130, 208-269 (1986)]. Application of the decomposition algorithm for simulated protein data sets resulted in component spectra [B (lambda, i)] identical to the originals and weights [C (i, k)] with excellent Pearson correlation coefficients (R) [Chang, C.T., Wu, C.-S.C. and Yang, J.T. (1978) Anal. Biochem., 91, 12-31]. Test runs were performed on sets of simulated protein spectra created by the Monte Carlo technique using poly-L-lysine-based pure component spectra. The significant correlational coefficients (R greater than 0.9) demonstrated the high power of the algorithm. The algorithm, applied to globular protein data, independent of X-ray data, revealed that the CD spectrum of a given protein is composed of at least four independent sources of chirality. Three of the computed component curves show remarkable resemblance to the CD spectra of known protein secondary structures. This approach yields a significant improvement in secondary structural evaluations when compared with previous methods, as compared with X-ray data, and yields a realistic set of pure component spectra. The new method is a useful tool not only in analyzing CD spectra of globular proteins but also has the potential for the analysis of integral membrane proteins.

Conformational intermediates in the folding of a coiled‐coil model peptide of the N‐terminus of tropomyosin and αα‐tropomyosin

“…In assessing factors that affect the stability of a-helices and coiled coils, it is important to realize that they are different structures and that their conformational transitions are not necessarily linked. The results also emphasize the utility of the convex constraint algorithm of Perczel et al (1991) for evaluating the contribution of different secondary structures to CD spectra.…”

Preparation and characterization of toxic Aβ aggregates for structural and functional studies in Alzheimer's disease research

“…3e) (monomeric Aβ is not detectable by TEM). Circular dichroism (CD) analysis followed by spectra deconvolution using CCA + software Lincomb algorithm 81,82 was carried out to assess the secondary structure elements of the Aβ fractions. CD analysis of this preparation showed a spectrum with minima at ~195-205 nm, consistent with a predominantly random coil conformtion (supplementary Fig.…”

“…CD spectra deconvolution, carried out using the CCA + software Lincomb algorithm 81,82 , showed that the protofibrils, obtained using this protocol, consisted of 43% β-sheet, 38% α-helix and 5% random coil as secondary structure elements (supplementary Fig. 1a).…”

Circular Dichroism and Its Application to the Study of Biomolecules

“…The deconvoluted basis curves, each of which has a unique shape, can be associated with a known mixture of secondary structures and can therefore be used to analyze the conformation of an unknown sample. Convex constraint analysis (CCA) has also been used to extract basis spectra (Perczel et al, 1991).…”