The optimization of protein secondary structure determination with infrared and circular dichroism spectra

Authors

  • Keith A. Oberg,

    1. Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Free University of Brussels (ULB), Belgium
    Search for more papers by this author
  • Jean-Marie Ruysschaert,

    1. Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Free University of Brussels (ULB), Belgium
    Search for more papers by this author
  • Erik Goormaghtigh

    1. Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Free University of Brussels (ULB), Belgium
    Search for more papers by this author

E. Goormaghtigh, Structural Biology and Bioinformatics Center, Structure and Function of Biological Membranes Laboratory, CP 206/2, Free University of Brussels (ULB), Bld du triomphe, Accès 2 B-1050 Brussels, Belgium. Fax: + 32 2650 53 82, Tel.: + 32 2650 53 86, E-mail: egoor@ulb.ac.be

Abstract

We have used the circular dichroism and infrared spectra of a specially designed 50 protein database [Oberg, K.A., Ruysschaert, J.M. & Goormaghtigh, E. (2003) Protein Sci. 12, 2015–2031] in order to optimize the accuracy of spectroscopic protein secondary structure determination using multivariate statistical analysis methods. The results demonstrate that when the proteins are carefully selected for the diversity in their structure, no smaller subset of the database contains the necessary information to describe the entire set. One conclusion of the paper is therefore that large protein databases, observing stringent selection criteria, are necessary for the prediction of unknown proteins. A second important conclusion is that only the comparison of analyses run on circular dichroism and infrared spectra independently is able to identify failed solutions in the absence of known structure. Interestingly, it was also found in the course of this study that the amide II band has high information content and could be used alone for secondary structure prediction in place of amide I.

Ancillary