Searching for a Better Match between Protein Secondary Structure Definitions and Protein FTIR Spectra
| Autor: | Erik Goormaghtigh, Joëlle De Meutter |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
Chemistry
010401 analytical chemistry Protein Array Analysis Proteins Chemical structure Fourier transform infrared spectroscopy Nucleic acid structure Peptides and proteins Protein structure 010402 general chemistry 01 natural sciences Protein Structure Secondary 0104 chemical sciences Analytical Chemistry symbols.namesake Protein structure Fourier transform Spectroscopy Fourier Transform Infrared symbols Sensitivity (control systems) Fourier transform infrared spectroscopy Biological system Spectroscopy Protein secondary structure DSSP (hydrogen bond estimation algorithm) |
| Zdroj: | Analytical Chemistry. 93:1561-1568 |
| ISSN: | 1520-6882 0003-2700 |
| DOI: | 10.1021/acs.analchem.0c03943 |
| Popis: | Obtaining protein secondary structure content from high-resolutionstructures requires definitions and thresholds for the various parameters involved, typicallyhydrogen bond energy or length/angle and backbone φ/ψ angles. Several definitions arecurrently used and can have a profound impact on secondary structure content. Fouriertransform infrared (FTIR) spectroscopy has its own sensitivity to molecular geometry. Itis, therefore, important to select a set of definitions that matches this sensitivity. Here, weused a new protein set consisting of 92 proteins designed for the calibration ofspectroscopic methods. Spectra have been obtained from protein microarrays in a highthroughput process. The potential for improving secondary structure predictions fromFTIR spectra has been tested using 71 structures determined according to different definitions. The paper demonstrates thatdifferent secondary structure definitions result in large variations in secondary structure content that are not equivalent in view of theprotein FTIR spectra. The prediction quality factor ζ can be improved by ca. 20−50% by selecting an adequate definition set. Theresults also indicate that the dictionary of secondary structure of proteins (DSSP) algorithm, which is currently widely used toevaluate protein secondary structure content, is a good choice when dealing with FTIR spectra. |
| Databáze: | OpenAIRE |
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