Prediction of protein secondary structure from circular dichroism using theoretically derived spectra
Article first published online: 17 NOV 2011
Copyright © 2011 Wiley Periodicals, Inc.
Proteins: Structure, Function, and Bioinformatics
Volume 80, Issue 2, pages 374–381, February 2012
How to Cite
Louis-Jeune, C., Andrade-Navarro, M. A. and Perez-Iratxeta, C. (2012), Prediction of protein secondary structure from circular dichroism using theoretically derived spectra. Proteins, 80: 374–381. doi: 10.1002/prot.23188
- Issue published online: 10 JAN 2012
- Article first published online: 17 NOV 2011
- Accepted manuscript online: 14 SEP 2011 03:56PM EST
- Manuscript Accepted: 27 AUG 2011
- Manuscript Revised: 18 AUG 2011
- Manuscript Received: 20 JUL 2011
Vol. 80, Issue 12, 2818, Article first published online: 27 SEP 2012
- web tool;
Circular dichroism (CD) is a spectroscopic technique commonly used to investigate the structure of proteins. Major secondary structure types, alpha-helices and beta-strands, produce distinctive CD spectra. Thus, by comparing the CD spectrum of a protein of interest to a reference set consisting of CD spectra of proteins of known structure, predictive methods can estimate the secondary structure of the protein. Currently available methods, including K2D2, use such experimental CD reference sets, which are very small in size when compared to the number of tertiary structures available in the Protein Data Bank (PDB). Conversely, given a PDB structure, it is possible to predict a theoretical CD spectrum from it. The methodological framework for this calculation was established long ago but only recently a convenient implementation called DichroCalc has been developed. In this study, we set to determine whether theoretically derived spectra could be used as reference set for accurate CD based predictions of secondary structure. We used DichroCalc to calculate the theoretical CD spectra of a nonredundant set of structures representing most proteins in the PDB, and applied a straightforward approach for predicting protein secondary structure content using these theoretical CD spectra as reference set. We show that this method improves the predictions, particularly for the wavelength interval between 200 and 240 nm and for beta-strand content. We have implemented this method, called K2D3, in a publicly accessible web server at http://www. ogic.ca/projects/k2d3. Proteins 2012. © 2011 Wiley Periodicals, Inc.