Distinguishing transmembrane helices from peripheral helices by circular dichrosim

The interpretation of the circular dichroism (c.d.) spectra of proteins to date requires additional secondary structural information of the proteins to be analysed (e.g., X-ray or n.m.r. data). Therefore these methods are inappropriate for a c.d. database whose secondary structures are unknown, as in the case of the membrane proteins. The Convex Constraint Analysis algorithm [Perczel, Hollósi, Tusnady, and Fasman (1991) Convex constraint analysis: a natural deconvolution of circular dichroism curves of proteins. Protein Eng. 4, 669-679] operates on a collection of c.d. spectral data to extract the common spectral components with their spectral weights. The linear combinations of these derived 'pure' c.d. curves can reconstruct the original data set with great accuracy. For a membrane protein data set, the five-component spectra so obtained from the deconvolution consisted of two different types of alpha-helices (the alpha-helix in the soluble domain and the alpha1-helix, for the transmembrane alpha-helix), a beta-pleated sheet, a class-C-like spectrum related to beta-turns and a spectrum correlated with the unordered conformation. The deconvoluted c.d. spectrum for the alpha1-helix was characterized by a positive red-shifted band in the range 195-200 nm (+95,000 degrees.cm2-dmol-1), with the intensity of the negative band at 208 nm being slightly less negative than that of the 222 nm band (-50,000 and -60,000 degrees.cm2.dmol-1 respectively) in comparison with the regular alpha-helix, with a positive band at 190 nm and two negative bands at 208 and 222 nm with magnitudes of +70,000, -30,000 and -30,000 degrees.cm2.dmol-1 respectively.