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Nuclear Magnetic Resonance Spectroscopy for the Identification of Multiple Phosphorylations of Intrinsically Disordered Proteins

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Temporal Profiling of Peroxynitrite-Mediated Protein Nitration and Phosphorylation Using Proteomics Analysis.

Yating Yao^1,2, Shuang Wang³, Jingyi Li²

¹State Key Laboratory of Metabolic Dysregulation & Prevention and Treatment of Esophageal Cancer, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China.

Journal of Proteome Research

|December 23, 2025

Summary

Peroxynitrite exposure causes protein nitration and alters protein phosphorylation in cells. This study reveals distinct temporal changes in protein profiles and modification sites, offering insights into cellular signaling.

Keywords:

mass spectrometry peroxynitrite post-translational modifications protein nitration protein phosphorylation temporal profiling

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Area of Science:

Biochemistry
Cellular Biology
Proteomics

Background:

Peroxynitrite induces protein nitration, impacting cellular structure and phosphorylation-dependent signaling pathways.
Understanding the interplay between nitration and phosphorylation is crucial for elucidating cellular responses to oxidative stress.

Purpose of the Study:

To investigate the effects of peroxynitrite-induced nitration and phosphorylation on proteins in HEK293T cells.
To analyze the temporal dynamics of protein expression, nitration, and phosphorylation following peroxynitrite exposure.

Main Methods:

Label-free quantitative mass spectrometry was employed to identify and quantify over 5,000 proteins.
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to map nitration and phosphorylation sites.
Proteins were analyzed from HEK293T cell extracts at five time points (0, 2, 15, 30, and 60 minutes) post-peroxynitrite exposure.

Main Results:

Protein expression profiles at 2-60 minutes post-exposure differed significantly from the baseline (0 min).
Distinct temporal profiles were observed for protein nitration and phosphorylation.
Analysis suggests that nitration may influence the phosphorylation status of proteins or their interactors.

Conclusions:

Peroxynitrite exposure induces significant changes in protein expression and post-translational modifications.
The temporal dynamics of nitration and phosphorylation indicate a potential crosstalk between these modification pathways.
This research provides a foundation for further mechanistic studies on peroxynitrite-mediated cellular signaling.