Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

Abstract

Background: A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available.

Results: In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements.

Conclusion: Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.

Figure 1

Composite FTIR and CD spectra. The CD spectra are in Δε units (y-axis) with wavelengths in nm (x-axis). The FTIR spectra are in arbitrary intensity units scaled as described in the methods (y-axis), with the wavenumbers in cm^-1 (x-axis). A pair of hashed lines indicates the discontinuity point for the axes, and the black circle indicates the join between the CD and FTIR spectra.