Analyzing protein circular dichroism spectra for accurate secondary structures

Analyzing protein circular dichroism spectra for accurate secondary structures 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 ॅ‐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 ॅ‐helix, 2.6% for 310‐helix, 4.2% for ॆ‐strand, 4.2% for ॆ‐turn, 2.7% for poly(L‐proline) II type 31‐helix, and 5.1% for other structures when compared with the X‐ray structure. Proteins 1999;35:307–312. © 1999 Wiley‐Liss, Inc. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Proteins: Structure Function and Bioinformatics Wiley

Analyzing protein circular dichroism spectra for accurate secondary structures

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Publisher
Wiley
Copyright
Copyright © 1999 Wiley‐Liss, Inc.
ISSN
0887-3585
eISSN
1097-0134
DOI
10.1002/(SICI)1097-0134(19990515)35:3<307::AID-PROT4>3.3.CO;2-V
Publisher site
See Article on Publisher Site

Abstract

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 ॅ‐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 ॅ‐helix, 2.6% for 310‐helix, 4.2% for ॆ‐strand, 4.2% for ॆ‐turn, 2.7% for poly(L‐proline) II type 31‐helix, and 5.1% for other structures when compared with the X‐ray structure. Proteins 1999;35:307–312. © 1999 Wiley‐Liss, Inc.

Journal

Proteins: Structure Function and BioinformaticsWiley

Published: May 15, 1999

Keywords: circular dichroism; secondary structure; proteins

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