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Related Experiment Video

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An Integrated Proteomic Strategy to Identify SHP2 Substrates.

Peipei Zhu1,2, Xiaofeng Wu1, Ruo-Yu Zhang3

  • 1Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.

Journal of Proteome Research
|September 14, 2022
PubMed
Summary

Researchers developed a new proteomics method to identify protein phosphatase substrates. This approach successfully identified 18 direct substrates for SHP2, a key enzyme in cell signaling and cancer.

Keywords:
DOK1LC-MS/MSSHP2phosphatase substratephosphoproteomicstyrosine phosphorylation

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Area of Science:

  • Molecular Biology
  • Proteomics
  • Cellular Signaling

Background:

  • Protein phosphatases are crucial for cell physiology and disease, but studying them is challenging.
  • Understanding protein phosphatase substrates and mechanisms is limited due to inherent difficulties.
  • Src homology 2 containing protein tyrosine phosphatase 2 (SHP2) is implicated in cancer development.

Purpose of the Study:

  • To develop a novel, high-throughput strategy for identifying physiological substrates of protein phosphatases.
  • To identify direct substrates of SHP2 using substrate-trapping mutants and quantitative proteomics.
  • To elucidate the role of SHP2 in epidermal growth factor receptor signaling pathways.

Main Methods:

  • Integration of three parallel mass spectrometry-based proteomics experiments.
  • Utilized substrate-trapping mutants of SHP2.
  • Employed affinity isolation, in vivo quantitative phosphoproteomics, and in vitro phosphatase assays.

Main Results:

  • Confidently identified 18 direct substrates of SHP2 within epidermal growth factor receptor signaling.
  • Included both previously known and novel SHP2 substrates.
  • Validated Docking protein 1 as a novel SHP2 substrate, revealing a mechanism for Ras activation.

Conclusions:

  • The developed workflow enhances the systemic identification of direct protein phosphatase substrates.
  • This method facilitates a deeper understanding of protein phosphatases' roles in cellular signaling.
  • The findings provide new insights into SHP2 function and its substrates in cancer-related pathways.