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Monitoring peptide tyrosine nitration by spectroscopic methods

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Abstract

Oxidative stress can lead to various derivatives of the tyrosine residue in peptides and proteins. A typical product is 3-nitro-L-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.

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Abbreviations

ACN:

Acetonitrile

Bn:

Benzyl

CCT:

Cartesian coordinate-based tensor transfer method

CPCM:

Conductor-like polarizable continuum model

DFT:

Density functional theory

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:

High-performance liquid chromatography

IR :

Infrared absorption

MALDI:

Matrix-assisted laser desorption/ionization

MS:

Mass spectrometry

Nit:

3-Nitro-L-tyrosine

PDB id.:

Four letter identification code of a structure deposited in the RCSB Protein Data Bank

PTM:

Posttranslational modification

ROA:

Raman optical activity

SERS:

Surface-enhanced Raman spectroscopy

tBu:

tert-Butyl

TEM :

Transmission electron microscopy

TFA:

Trifluoroacetic acid

TOF:

Time of flight (detection)

TIS:

Triisopropyl silane

VCD:

Vibrational circular dichroism

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Acknowledgements

This work was supported by the Czech Science Foundation (14-00431S, 17-00121S, 20-10144S), Research Project RVO 61388963, by European Regional Development Fund; OP RDE; Project: "Chemical biology for drugging undruggable targets (ChemBioDrug)" (No. CZ.02.1.01/0.0/0.0/16_019/0000729), and computational grants of CESNET (LM2015042) and the CERIT-SC (LM2015085).

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Authors and Affiliations

  1. Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic

    Petr Niederhafner, Martin Šafařík, Jitka Neburková, Petr Bouř & Jaroslav Šebestík

  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

    Petr Niederhafner

  3. Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St., Chicago, IL, 60607-7061, USA

    Timothy A. Keiderling

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  1. Petr Niederhafner
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Correspondence to Jaroslav Šebestík.

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Niederhafner, P., Šafařík, M., Neburková, J. et al. Monitoring peptide tyrosine nitration by spectroscopic methods. Amino Acids 53, 517–532 (2021). https://doi.org/10.1007/s00726-020-02911-7

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