Numerous publications report the establishment of a mathematical relationship between protein FTIR spectra and secondary structure content (Lee et al. To deal with the large number of proteins present, we worked on protein microarrays deposited on BaF 2 slides and FTIR spectra were acquired with an imaging system.įourier transform infrared (FTIR) spectroscopy has become a global tool for the study of protein structure (Barth 2007 Wang et al. The study was performed on a large protein set. It must be concluded that side chain contribution subtraction benefit for the evaluation of other secondary structure contents is limited by the very rough description of side chain absorbance which does not take into account the variations related to their environment. We also show that, even though based on different criteria, secondary structures defined by DSSP and XTLSSTR both arrive at the same conclusion: only the β-sheet structure clearly benefits from side chain subtraction. We show that co-linearity between secondary structure content and amino acid composition is not a main limitation for improving secondary structure prediction.

The other structures such as α-helix do not significantly benefit from side chain contribution subtraction, in some cases prediction is even degraded. Other methods tested such as partial least square regression and support vector machine have also improved accuracy for β-sheet content evaluation. Improvement is relatively important, for instance, the error of prediction of β-sheet content decreases from 5.42 to 4.97% when evaluated by ascending stepwise regression. We show that the β-sheet content prediction is improved upon subtraction of amino acid side chain contributions in the amide I–amide II spectral range. The present paper evaluates the contribution of amino acid side chains in this spectral region and the potential to improve secondary structure prediction after correcting for their contribution. Yet, it is accepted that, on the average, about 20% of the absorbance is due to amino acid side chains. It assumes that the absorbance in this spectral region, i.e., roughly 1700–1500 cm −1 is solely arising from amide contributions. Prediction of protein secondary structure from FTIR spectra usually relies on the absorbance in the amide I–amide II region of the spectrum.

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