ArticleNature chemical biology2024
Massively parallel measurement of protein-protein interactions by sequencing using MP3-seq.
Article in Nature chemical biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Aligning protein-generative models to experimental fitness with ProteinDPO.Nature methods · 2026Article
- Accelerating protein design by scaling experimental characterization.Nature communications · 2026Article
- Amplicon/Protein Bead Display enables quantitativebioRxiv : the preprint server for biology · 2026Article
- PPIscreenML is a method for structure-based screening of protein-protein interactions using AlphaFold.eLife · 2026Article
- Backbone Thioamidation of a Ribosomal Subunit Protein in Pseudomonadota.Biochemistry · 2026Article
- Experimental assessment of AI-based interactome mapping.Nature communications · 2026Article
- Interrelational Proteomic Sequence Features Enhance Predictive Modeling: Application to COVID-19 Severity.Biomedicines · 2026Article
- Quantifying cytoskeletal protein interactions with far Western blotting.Frontiers in molecular biosciences · 2026Article
- Click-linking: a cell-compatible protein crosslinking method based on click chemistry.Nature communications · 2025Article
- Article
- PANCS-Binders: a rapid, high-throughput binder discovery platform.Nature methods · 2025Article
- Recent progress and future challenges in structure-based protein-protein interaction prediction.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Beyond Dimerization: Harnessing Tetrameric Coiled-Coils for Nanostructure Assembly.Angewandte Chemie (International ed. in English) · 2025Article
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
- The Application of Machine Learning on Antibody Discovery and Optimization.Molecules (Basel, Switzerland) · 2024Review
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7 authors.
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Abstract
Protein-protein interactions (PPIs) regulate many cellular processes and engineered PPIs have cell and gene therapy applications. Here, we introduce massively parallel PPI measurement by sequencing (MP3-seq), an easy-to-use and highly scalable yeast two-hybrid approach for measuring PPIs. In MP3-seq, DNA barcodes are associated with specific protein pairs and barcode enrichment can be read by sequencing to provide a direct measure of interaction strength. We show that MP3-seq is highly quantitative and scales to over 100,000 interactions. We apply MP3-seq to characterize interactions between families of rationally designed heterodimers and to investigate elements conferring specificity to coiled-coil interactions. Lastly, we predict coiled heterodimer structures using AlphaFold-Multimer (AF-M) and train linear models on physics-based energy terms to predict MP3-seq values. We find that AF-M-based models could be valuable for prescreening interactions but experimentally measuring interactions remains necessary to rank their strengths quantitatively.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.