Statistical behaviour and suitability of protein-derived circular dichroic-basis spectra for the determination of globular protein conformation

Underlying assumptions in the estimation of secondary structure content in proteins by circular dichroism spectroscopy--a critical review

Recombinant DNA technology has made possible the large-scale production of proteins for pharmaceutical applications. As a result, there has been a renaissance in methodology which can provide information on the structural stability and character of these materials. Circular dichroism (CD) spectroscopy, with its sensitivity to the secondary structure adopted by the polypeptide chain, is a powerful tool in this regard. Quantitative analysis of the CD spectra of proteins is now wide-spread, aided by the availability of such algorithms on commercial instrumentation. However, there are basic assumptions made when conducting these calculations, many of which have not been addressed or summarized. Some of these assumptions are independent of the selection of basis spectra and the algorithm employed. These assumptions are listed and the available data concerning their validity is presented and discussed.

Secondary structure prediction and determination of proteins--a review

The rapid increase in sequence data in combination with a greater understanding of the forces regulating protein structure has been the impetus for an upsurge in the development of theoretical prediction methods. These methods have afforded protein chemists the ability to identify and quantify the various secondary structures along the protein chain. Concurrently, various physico-chemical techniques have been developed such as nuclear Overhauser enhancement n.m.r. and laser Raman spectroscopy. In addition, traditional methods such as infrared and circular dichroism spectroscopy have been refined. Although both predictive and physico-chemical techniques are limited in the types of secondary structure they are capable of determining, they have provided valuable information with regards to protein folding and topology in the absence of X-ray data, and have formed the basis for the development of improved methods for secondary structure determination. This paper reviews some of the predictive and physico-chemical methods presently used to determine protein secondary structure.

CD-resolved secondary structure of bovine plasma albumin in acid-induced isomerization

Bovine plasma albumin (BPA) showed the acid-induced two-step transition, the N-F transition and acid-expansion. Changes in fractions of alpha-helix (f alpha), beta-form (f beta) and unordered form (fR) in the acid-induced isomerization of BPA were studied using the method of Chen et al. (1972) with two constraints: sigma fi = 1, 0 less than or equal to fi less than or equal to 1. pH-profiles of f alpha and fR showed the two-step change, one corresponding to the N-F transition and the other to the acid-expansion in 0.10 M KCl and in 0.02 M NaClO4. pH-profile of f beta showed one-step change, correlating to the later part (lower pH side) of the N-F transition. The N-F transition might thus involve the helix leads to beta and helix leads to coil transitions.

Circular dichroic analysis of protein conformation: inclusion of the beta-turns

The mean residue ellipticity, [theta], at any wavelength, lambda, of a protein in aqueous solution is expressed as [theta]lambda = fH[theta]H infinity(1-k/n) + f beta[theta]beta + ft[theta]t + fR[theta]R with two constraints: 1 > or = fj > or = 0 and sigma fj = 1. The subscripts H, beta, t, and R refer to the helix, beta-form, beta-turn, and unordered form. The fractions, fj's, of 15 proteins are based on X-ray crystallography, ft refers to the net beta-turn after cancelling those residues having dihedral angles of opposite sign. The [theta]H infinity 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 protein 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 beta-turn in the analysis improves the correlation for the estimates of the beta-form, but the computed beta 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.

Circular dichroism of insulin A chain in water: trifluoroethanol mixtures. Use of linear and nonlinear least squares analysis

Circular dichroic spectra obtained for S-carboxymethylated insulin A chain in water: trifluoroethanol mixtures show that a marked conformational transition occurs as the concentration of trifluoroethanol is increased to (v/v) 83% to give a polypeptide containing about 43% of the residues in the alph-helical conformation. Several proposed methods of analysis, including both linear and two nonlinear lest squares methods, were unable to quantitate the amount of beta-structure present in the polypeptide in 83% trifluoroethanol. Examination of the methods of analysis lead to the conclusion that the current models for far UV CD analysis are not adequare for the data obtained in this study and shows that nonlinear least squares procedures may lead to erroneous conclusions.

Least-squares analysis of circular dichroic spectra of proteins

It is shown that the method proposed by Baker and Isenberg [Biochemistry, 15, 629 (1976)] for estimating secondary structure composition of proteins from circular dichroic spectra is a least-squares fitting technique. Estimates obtained by this method for myoglobin, lysozyme, lactate dehydrogenase, papain, and ribonuclease are not substantively different from those obtained using unconstrained linear least squares.

On the optical activity of ionized tyrosyl residues in ovine lutropin

The effect of alkali on the circular dichroic (CD) spectra of ovine lutropin and its subunits has been studied. Mild alkaline pH induces the appearance of a new optically active band in the 250-nm region of the spectra of lutropin without any detectable alteration in the secondary structure of the protein. This change is reversible and can be correlated with ionization of 2--3 exposed tyrosyl residues in the intact hormone. In a previous report from this laboratory it was concluded that the three exposed tyrosyl residues are located in the alpha subunit, in positions 21, 92 and 93 [Burleigh, B.D., Liu, W.-K, and Ward, D.M. (1976) J. Biol. Chem. 251, 308--315]. Nitration of these residues lowers the pH at which the intensity of the 250-nm band is maximal. The importance of the tyrosyl residues of lutropin alpha (as opposed to those of lutropin beta) is also supported by the similarity of the effect of alkali on the CD spectra of lutropin and lutropin alpha. Further evidence for this involvement was also obtained by a comparison of the alkali-induced changes of refolded lutropin (alpha + beta recombinant) and the product obtained by recombination of des-(92--96)-lutropin alpha (obtained from carboxypeptidase treatment of the alpha-subunit) and lutropin beta. The results indicate that removal of tyrosines alpha 92 and alpha 93 results in a decrease of the intensity of the 235-nm band of ovine lutropin (at pH7.5) as well as that of the 250-nm band observed under alkaline conditions. It is therefore concluded that the 250-nm band observed in alkaline solutions of lutropin arises (at least partially) from the red shift produced in the short-wavelength optically active band of tyrosines alpha 21, alpha 92, and alpha 93 upon ionization.