tailieunhanh - Báo cáo khoa học: The optimization of protein secondary structure determination with infrared and circular dichroism spectra

We have used the circular dichroismand infrared spectra of a specially designed 50 protein database [Oberg, ., Ruysschaert, . & Goormaghtigh, E. (2003)Protein Sci. 12, 2015–2031] in order to optimize the accuracy of spectroscopic protein secondary structure determination using multivariate statisticalanalysis 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 | Eur. J. Biochem. 271 2937-2948 2004 FEBS 2004 doi The optimization of protein secondary structure determination with infrared and circular dichroism spectra Keith A. Oberg Jean-Marie Ruysschaert and Erik Goormaghtigh Center for Structural Biology and Bioinformatics Laboratory for the Structure and Function of Biological Membranes Free University of Brussels ULB Belgium We have used the circular dichroism and infrared spectra of a specially designed 50 protein database Oberg . Ruysschaert . 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. Keywords circular dichroism FTIR PLS protein secondary structure. Multivariate statistical analysis methods have proved to be powerful tools for the analysis of component concentrations in chemical mixtures. Because of their effectiveness in systems where there are strongly overlapping bands these chemometric methods have also proved effective in the analysis of protein spectra 1-12 . In contrast to most typical applications of statistical analysis methods the reported accuracy in protein studies especially .