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1 Department of Crystallography, Birkbeck College, University of London, London WC1E 7HX, UK
2 Centre for Protein and Membrane Structure and Dynamics, Daresbury Laboratory, Warrington WA4 4AD, UK
3 School of Biological Sciences, Queen Mary, University of London, London E1 4NS, UK
Reprint requests to: B.A. Wallace, Department of Crystallography, Birkbeck College, University of London, London WC1E 7HX, UK; e-mail: ubcg25a{at}mail.cryst.bbk.ac.uk; fax: 44-(0)-207-631-6803.
Circular dichroism (CD) spectroscopy is a valuable technique for the determination of protein secondary structures. Many linear and nonlinear algorithms have been developed for the empirical analysis of CD data, using reference databases derived from proteins of known structures. To date, the reference databases used by the various algorithms have all been derived from the spectra of soluble proteins. When applied to the analysis of soluble protein spectra, these methods generally produce calculated secondary structures that correspond well with crystallographic structures. In this study, however, it was shown that when applied to membrane protein spectra, the resulting calculations produce considerably poorer results. One source of this discrepancy may be the altered spectral peak positions (wavelength shifts) of membrane proteins due to the different dielectric of the membrane environment relative to that of water. These results have important consequences for studies that seek to use the existing soluble protein reference databases for the analyses of membrane proteins.
Keywords: Membrane protein; secondary structure; circular dichroism spectroscopy; synchrotron radiation; databases; bioinformatics
Abbreviations: CD, circular dichroism • SRCD, synchrotron radiation circular dichroism • Mb, myoglobin • ConA, concanavalanA • BR, bacteriorhodopsin • MscL, mechanosensitive channel • cox, cytochrome oxidase • cytbc1, cytochrome bc1 • FepA, ferric enterobactin receptor • FhuA, ferric hydroxamate uptake receptor • LamB, maltoporin • OmpF, matrix porin • NRMSD, normalized root-mean-square deviation (goodness-of-fit parameter) • PDB, Protein Data Bank
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