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Protein Science (2005), 14:368-374. Published by Cold Spring Harbor Laboratory Press. Copyright © 2005 The Protein Society
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Spectral magnitude effects on the analyses of secondary structure from circular dichroism spectroscopic data

Andrew J. Miles1, Lee Whitmore1 and B.A. Wallace1,2

1 Department of Crystallography, Birkbeck College, University of London, London, WC1E 7HX United Kingdom
2 Centre for Protein and Membrane Structure and Dynamics, Daresbury Laboratory, Warrington, WA4 4AD United Kingdom

(RECEIVED July 29, 2004; FINAL REVISION October 20, 2004; ACCEPTED October 29, 2004)

The effects of spectral magnitude on the calculated secondary structures derived from circular dichroism (CD) spectra were examined for a number of the most commonly used algorithms and reference databases. Proteins with different secondary structures, ranging from mostly helical to mostly {beta}-sheet, but which were not components of existing reference databases, were used as test systems. These proteins had known crystal structures, so it was possible to ascertain the effects of magnitude on both the accuracy of determining the secondary structure and the goodness-of-fit of the calculated structures to the experimental data. It was found that most algorithms are highly sensitive to spectral magnitude, and that the goodness-of-fit parameter may be a useful tool in assessing the correct scaling of the data. This means that parameters that affect magnitude, including calibration of the instrument, the spectral cell pathlength, and the protein concentration, must be accurately determined to obtain correct secondary structural analyses of proteins from CD data using empirical methods.

Keywords: circular dichroism (CD) spectroscopy; calibration; secondary structure analyses; synchrotron radiation circular dichroism (SRCD)

Abbreviations: CD, circular dichroism • cCD, conventional circular dichroism • CSA, camphor sulfonic acid • NRMSD, normalized root-mean-square deviation • QAA, quantitative amino acid analysis • SRCD, synchrotron radiation circular dichroism

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041019905.

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: +44-207-631-6803.


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