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Prediction of protein secondary structure from FTIR spectra usually relies on the absorbance in the amide I–amide II region of the spectrum. It assumes that the absorbance in this spectral region, i.e., roughly 1700–1500 cm−1 is solely arising from amide contributions. Yet, it is accepted that, on the average, about 20% of the absorbance is due to amino acid side chains. 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. 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. 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. Other methods tested such as partial least square regression and support vector machine have also improved accuracy for β-sheet content evaluation. The other structures such as α-helix do not significantly benefit from side chain contribution subtraction, in some cases prediction is even degraded. We show that co-linearity between secondary structure content and amino acid composition is not a main limitation for improving secondary structure prediction. 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. 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. The study was performed on a large protein set. To deal with the large number of proteins present, we worked on protein microarrays deposited on BaF2 slides and FTIR spectra were acquired with an imaging system. [ABSTRACT FROM AUTHOR]

The current paper contributes new evidence to the ongoing discussion of the location and organisation of production of Hellenistic colour-coated ware (CCW), through interdisciplinary investigation of morphological style, technology and provenance of relevant pottery from a Late Hellenistic deposit found in a well in the Agora of Nea Paphos on Cyprus. Through naked eye examination, four major macroscopic groups were identified based on vessel typology and fabrics. Subsequently, 53 representative samples were selected and analysed through a combination of refiring tests, chemical analysis, thin section petrography and scanning electron microscopy. The results indicated that the sheer majority of this pottery, despite some compositional and technological variability, reflects the use of similar raw materials compatible with the geology of Paphos. Therefore, during the Late Hellenistic period, most of the CCW consumed in Paphos were locally produced. The observed variation in the assemblage can be associated with several factors, such as natural diversity of raw materials, a number of co-existing pottery workshops, technological choices made by the potters and to a lesser extent post-depositional processes. This integrated research has a profound impact on studies of production and consumption of the Late Hellenistic pottery on Cyprus. [ABSTRACT FROM AUTHOR]