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Protein Science, Vol 1, Issue 8 1032-1049, Copyright © 1992 by Cold Spring Harbor Laboratory Press

ARTICLE

Differentiation between transmembrane helices and peripheral helices by the deconvolution of circular dichroism spectra of membrane proteins

K. PARK, A. PERCZEL and G. D. FASMAN
Graduate Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02154

The interpretation of the circular dichroism (CD) spectra of proteins to date requires additional secondary structural information of the proteins to be analyzed, such as X-ray or NMR data. Therefore, these methods are inappropriate for a CD database whose secondary structures are unknown, as in the case of the membrane proteins. The convex constraint analysis algorithm (Perczel, A., Hollosi, M., Tusnady, G., & Fasman, G.D., 1991, Protein Eng. 4, 669-679), on the other hand, operates only on a collection of spectral data to extract the common spectral components with their spectral weights. The linear combinations of these derived ``pure'' CD curves can reconstruct the original data set with great accuracy. For a membrane protein data set, the five-component spectra so obtained from the deconvolutio consisted of two different types of {alpha} helices (the {alpha} helix in the soluble domain and the {alpha}(T) 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 CD spectrum for the {alpha}(T) helix was characterized by a positive red-shifted band in the range 195-200 nm (+95,000 deg cm(2) 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 deg cm(2) 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 deg cm(2) dmol(-1), respectively.
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