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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Related Experiment Video

Updated: Jan 8, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
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Multiplex mapping of protein-protein interaction interfaces.

Jingxuan He1, Ling-Nan Zou1, Vidhi Pareek2

  • 1Department of Chemistry, The Pennsylvania State University, University Park, PA 16802.

Proceedings of the National Academy of Sciences of the United States of America
|December 22, 2025
PubMed
Summary
This summary is machine-generated.

We developed Split Antibiotic Resistance Complementation (SpARC-map), a novel method for identifying protein-protein interaction (PPI) interfaces. This technique uses bacterial hosts and DNA sequencing to map interactions, even weak ones, without specialized equipment.

Keywords:
protein complexprotein interaction interfaceprotein–protein interactionpurinosome

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Identifying protein-protein interactions (PPIs) is crucial for understanding cellular functions.
  • Existing methods often require specialized equipment or in vitro reconstitution.
  • Mapping interaction interfaces, especially for weak or transient complexes, remains challenging.

Purpose of the Study:

  • To introduce Split Antibiotic Resistance Complementation (SpARC-map), a novel in vivo method for peptide mapping and PPI interface identification.
  • To demonstrate SpARC-map's ability to detect PPIs across a broad affinity range, including weak interactions.
  • To validate SpARC-map's utility in identifying functional interfaces and constraining structural predictions.

Main Methods:

  • SpARC-map employs in vivo affinity selection within a bacterial host.
  • High-throughput DNA sequencing is utilized to infer protein-protein interaction (PPI) interfaces.
  • The method relies on routine microbiology techniques, avoiding specialized reagents or in vitro complex reconstitution.

Main Results:

  • SpARC-map successfully identified known PPI interfaces in p21-PCNA, p53-MDM2, and MYC-MAX complexes.
  • The method revealed potential functional interfaces within the purinosome complex, supporting substrate channeling.
  • SpARC-map results were validated using site-specific photocrosslinking and demonstrated utility in constraining machine learning-based structure prediction.

Conclusions:

  • SpARC-map is a versatile and sensitive method for identifying protein-protein interaction interfaces in vivo.
  • The technique is adaptable for various affinities, multiplexing, and precise background measurement.
  • SpARC-map provides valuable insights into complex formation, substrate channeling, and aids in computational structure prediction.