K2D2: Estimation of protein secondary structure from circular dichroism spectra

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Abstract

Background

Circular dichroism spectroscopy is a widely used technique to analyze the secondary structure of proteins in solution. Predictive methods use the circular dichroism spectra from proteins of known tertiary structure to assess the secondary structure contents of a protein with unknown structure given its circular dichroism spectrum.

Results

We developed K2D2, a method with an associated web server to estimate protein secondary structure from circular dichroism spectra. The method uses a self-organized map of spectra from proteins with known structure to deduce a map of protein secondary structure that is used to do the predictions.

Conclusion

The K2D2 server is publicly accessible at http://www.ogic.ca/projects/k2d2/. It accepts as input a circular dichroism spectrum and outputs the estimated secondary structure content (alpha-helix and beta-strand) of the corresponding protein, as well as an estimated measure of error.

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Most cited references 23

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The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

Helen Berman, Kim Henrick, Haruki Nakamura … (2006)

The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The founding members of the wwPDB are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan) [H.M. Berman, K. Henrick and H. Nakamura (2003) Nature Struct. Biol., 10, 980]. The BMRB group (USA) joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Additionally, the wwPDB provides a variety of services to a broad community of users. The wwPDB website at provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.

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Analyzing protein circular dichroism spectra for accurate secondary structures.

Kevin C. Johnson (1999)

We have developed an algorithm to analyze the circular dichroism of proteins for secondary structure. Its hallmark is tremendous flexibility in creating the basis set, and it also combines the ideas of many previous workers. We also present a new basis set containing the CD spectra of 22 proteins with secondary structures from high quality X-ray diffraction data. High flexibility is obtained by doing the analysis with a variable selection basis set of only eight proteins. Many variable selection basis sets fail to give a good analysis, but good analyses can be selected without any a priori knowledge by using the following criteria: (1) the sum of secondary structures should be close to 1.0, (2) no fraction of secondary structure should be less than -0.03, (3) the reconstructed CD spectrum should fit the original CD spectrum with only a small error, and (4) the fraction of alpha-helix should be similar to that obtained using all the proteins in the basis set. This algorithm gives a root mean square error for the predicted secondary structure for the proteins in the basis set of 3.3% for alpha-helix, 2.6% for 3(10)-helix, 4.2% for beta-strand, 4.2% for beta-turn, 2.7% for poly(L-proline) II type 3(1)-helix, and 5.1% for other structures when compared with the X-ray structure.

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A self-consistent method for the analysis of protein secondary structure from circular dichroism.

N Sreerama, R Woody (1993)

A self-consistent procedure for estimating the secondary structure content from circular dichroism spectra of proteins is presented. In this method the spectrum of the protein to be analyzed is included in the basis set and an initial guess is made for the unknown structure as a first approximation. The resulting matrix equation is solved using the singular value decomposition algorithm and the initial guess is replaced by the solution. The process is repeated until self-consistency is attained. The best features of the variable selection and the locally linearized methods are incorporated in this procedure. We have applied this method to examine the inconsistencies in the CD data, to compare the predictions with different ranges and resolutions of the CD data, and to compare different assignments of secondary structures from X-ray structure analyses in the context of secondary structure predictions. The results are compared using the root mean square differences and correlation coefficients. The results obtained are as good as or better than the previous analyses. For most of the proteins considered the self-consistent solutions obtained with different initial guesses were similar. We find the Kabsch and Sander protein crystal structure analysis to be most suitable for our prediction method.

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Author and article information

Journal

Journal ID (nlm-ta): BMC Struct Biol

Title: BMC Structural Biology

Publisher: BioMed Central

ISSN (Electronic): 1472-6807

Publication date Collection: 2008

Publication date (Electronic): 13 May 2008

Volume: 8

Page: 25

Affiliations

[1 ]Ontario Genomics Innovation Centre, Ottawa Health Research Institute, 501 Smyth, Ottawa, ON, K1H 8L6, Canada

[2 ]Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Canada

[3 ]Computational Biology and Data Mining Group, Max Delbrück Centre for Molecular Medicine, Berlin, Germany

Article

Publisher ID: 1472-6807-8-25

DOI: 10.1186/1472-6807-8-25

PMC ID: 2397409

PubMed ID: 18477405

SO-VID: f528bf22-10c5-4ca3-a01e-101c332fff37

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date received : 17 July 2007

Date accepted : 13 May 2008

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K2D2: Estimation of protein secondary structure from circular dichroism spectra

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Most cited references 23

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

Analyzing protein circular dichroism spectra for accurate secondary structures.

A self-consistent method for the analysis of protein secondary structure from circular dichroism.

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