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Protein Science (2004), 13:100-112. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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On the analysis of membrane protein circular dichroism spectra

Narasimha Sreerama and Robert W. Woody

Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA

Reprint requests to: Robert W. Woody, Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA; e-mail: rww{at}lamar.colostate.edu; fax: (970) 491-0494.

Analysis of circular dichroism spectra of proteins provides information about protein secondary structure. Analytical methods developed for such an analysis use structures and spectra of a set of reference proteins. The reference protein sets currently in use include soluble proteins with a wide range of secondary structures, and perform quite well in analyzing CD spectra of soluble proteins. The utility of soluble protein reference sets in analyzing membrane protein CD spectra, however, has been questioned in a recent study that found current reference protein sets to be inadequate for analyzing membrane proteins. We have examined the performance of reference protein sets available in the CDPro software package for analyzing CD spectra of 13 membrane proteins with available crystal structures. Our results indicate that the reference protein sets currently available for CD analysis perform reasonably well in analyzing membrane protein CD spectra, with performance indices comparable to those for soluble proteins. Soluble + membrane protein reference sets, which were constructed by combining membrane proteins with soluble protein reference sets, gave improved performance in both soluble and membrane protein CD analysis.

Keywords: protein secondary structure; reference protein set; membrane proteins; protein CD; CDPro

Abbreviations: CD, circular dichroism • CCA, the convex constraint method for protein CD analysis • CDSSTR, Johnson’s minimal basis-random selection method for protein CD analysis • CONTIN/LL, the ridge-regression method for protein CD analysis combined with the locally linearized method for variable selection • DSSP, a computer program for defining secondary structure of proteins • PDB, Protein Data Bank • SELCON3, the self-consistent method for protein CD analysis, version 3 • MP13, reference set of 13 membrane proteins • MP30, reference set of 30 membrane proteins • SP29, reference set of 29 soluble proteins • SP37, reference set of 37 soluble proteins • SP42, reference set of 42 soluble proteins • SP43, reference set of 43 soluble proteins • SP48, reference set of 48 soluble proteins • SMP50, reference set of 50 soluble + membrane proteins • SMP56, reference set of 56 soluble + membrane proteins • RMS, root mean square • NRMSD, normalized RMS deviation • {delta}, RMS deviation • r, correlation coefficient • {alpha}R, regular {alpha}-helix • {alpha}D, distorted {alpha}-helix • {alpha}, total {alpha}-helix • ßR, regular ß-strand • ßD, distorted ß-strand • ß, total ß-sheet • T, turns • U, unordered • fX, fractional content of secondary structure X, X = {alpha}, ß, T and U • {delta}X, RMS deviation between the CD-estimated and the X-ray values of the secondary structure X for a set of proteins, X = {alpha}, ß, T and U • rX, correlation between the CD-estimated and the X-ray values of the secondary structure X for a set of proteins, X = {alpha}, ß, T and U • {delta}f, RMS deviation between the CD estimates and the crystal structure values of secondary structure fractions for a given protein


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