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Conservation of Protein Domains Over Different Proteins

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Implementing N-terminomics and machine learning to probe Nt-arginylation.

Shinyeong Ju1, Laxman Nawale2,3, Seonjeong Lee1

  • 1Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea.

Nature Communications
|December 9, 2025
PubMed
Summary
This summary is machine-generated.

Researchers developed a new method to detect N-terminal arginylation (Nt-arginylation), a key protein modification involved in cellular processes. This technique identifies new sites, aiding in the discovery of potential biomarkers and drug targets.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Proteomics

Background:

  • N-terminal arginylation (Nt-arginylation) is a crucial post-translational modification (PTM) impacting protein quality control, organelle homeostasis, and stress signaling.
  • Previous studies of Nt-arginylation were hindered by significant technical challenges.

Purpose of the Study:

  • To develop an integrated approach for identifying N-terminal arginylation sites in cells.
  • To overcome technical limitations in studying this important PTM.

Main Methods:

  • Combined N-terminomics with machine learning-based filtering to detect Nt-arginylation in cellulo.
  • Utilized Arg-starting missed cleavage peptides as proxies for ATE1-mediated arginylation.
  • Trained a transfer learning model to predict mass spectra and retention times, followed by statistical filtering.

Main Results:

  • Identified 134 novel Nt-arginylation sites in thapsigargin-treated HeLa cells.
  • Found arginylation enrichment in proteins involved in various organelles, particularly at caspase cleavage and signal peptide processing sites.
  • Validated interactions of eight tested proteins with the p62 ZZ domain and observed temporal changes in arginylation post-stress.

Conclusions:

  • The developed approach enables sensitive detection of rare N-terminal modifications.
  • This method holds potential for discovering novel biomarkers and drug targets related to Nt-arginylation.
  • Provides new insights into the roles of Nt-arginylation in cellular stress responses.