Monitoring peptide tyrosine nitration by spectroscopic methods
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ORIGINAL ARTICLE
Monitoring peptide tyrosine nitration by spectroscopic methods Petr Niederhafner1,2 · Martin Šafařík1 · Jitka Neburková1 · Timothy A. Keiderling3 · Petr Bouř1 · Jaroslav Šebestík1 Received: 25 August 2020 / Accepted: 4 November 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract Oxidative stress can lead to various derivatives of the tyrosine residue in peptides and proteins. A typical product is 3-nitroL-tyrosine residue (Nit), which can affect protein behavior during neurodegenerative processes, such as those associated with Alzheimer’s and Parkinson’s diseases. Surface enhanced Raman spectroscopy (SERS) is a technique with potential for detecting peptides and their metabolic products at very low concentrations. To explore the applicability to Nit, we use SERS to monitor tyrosine nitration in Met-Enkephalin, rev-Prion protein, and α-synuclein models. Useful nitration indicators were the intensity ratio of two tyrosine marker bands at 825 and 870 cm−1 and a bending vibration of the nitro group. During the SERS measurement, a conversion of nitrotyrosine to azobenzene containing peptides was observed. The interpretation of the spectra has been based on density functional theory (DFT) simulations. The CAM-B3LYP and ωB97XD functionals were found to be most suitable for modeling the measured data. The secondary structure of the α-synuclein models was monitored by electronic and vibrational circular dichroism (ECD and VCD) spectroscopies and modeled by molecular dynamics (MD) simulations. The results suggest that the nitration in these peptides has a limited effect on the secondary structure, but may trigger their aggregation. Keywords Nitration · Oxidative stress · Surface-enhanced Raman spectroscopy (SERS) · Vibrational circular dichroism (VCD) · Electronic circular dichroism (ECD) · Density functional theory (DFT) Abbreviations ACN Acetonitrile Bn Benzyl CCT Cartesian coordinate-based tensor transfer method CPCM Conductor-like polarizable continuum model DFT Density functional theory Handling editor: D. Tsikas. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00726-020-02911-7) contains supplementary material, which is available to authorized users. * Jaroslav Šebestík [email protected] 1
Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic
2
Department of Chemistry of Natural Compounds, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
3
Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St., Chicago, IL 60607‑7061, USA
DIC N,N′-Diisopropylcarbodiimide DMF N,N-Dimethylmethanamide ECD Electronic circular dichroism EDT 1,2-Ethanedithiol ESI Electrospray ionization Fmoc 9-Fluorenylmethoxycarbonyl FWHH Full width (of a spectral peak) at half height GSH Glutathione HF Hartree Fock HOBt N-Hydroxybenzotriazole HPLC
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