ArticleMethods in molecular biology (Clifton, N.J.)2020
Screening Intrinsically Disordered Regions for Short Linear Binding Motifs.
Article in Methods in molecular biology (Clifton, N.J.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 27 citations in OpenAlex.
- SPPIDER-seq: sequence-based partner-aware predictor of protein-protein interaction sites.Bioinformatics (Oxford, England) · 2026Article
- SPPIDER-seq: Sequence-based partner-aware predictor of protein-protein interaction sites.bioRxiv : the preprint server for biology · 2026Article
- A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3.The Journal of biological chemistry · 2026Article
- Elucidation of short linear motif-based interactions of the MIT and rhodanese domains of the ubiquitin-specific protease 8.Biology direct · 2025Article
- A comparative analysis of sequence composition in different lots of a phage display peptide library during amplification.Virology journal · 2025Article
- Selection of Nucleotide-Encoded Mass Libraries of Macrocyclic Peptides for Inaccessible Drug Targets.Chemical reviews · 2024Review
- Proteome-scale characterisation of motif-based interactome rewiring by disease mutations.Molecular systems biology · 2024Article
- ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers.Nature communications · 2024Article
- MLL4 binds TET3.Structure (London, England : 1993) · 2024Article
- ELM-the Eukaryotic Linear Motif resource-2024 update.Nucleic acids research · 2024Article
- Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets.Nature communications · 2023Article
- Large-scale phosphomimetic screening identifies phospho-modulated motif-based protein interactions.Molecular systems biology · 2023Article
- Assessing structure and disorder prediction tools forF1000Research · 2023Article
- Heterologous expression of naturally evolved putative de novo proteins with chaperones.Protein science : a publication of the Protein Society · 2022Article
- The Eukaryotic Linear Motif resource: 2022 release.Nucleic acids research · 2022Article
- Proteome-scale mapping of binding sites in the unstructured regions of the human proteome.Molecular systems biology · 2022Article
- Structural Insights into Protein Regulation by Phosphorylation and Substrate Recognition of Protein Kinases/Phosphatases.Life (Basel, Switzerland) · 2021Review
- Tandem domain structure determination based on a systematic enumeration of conformations.Scientific reports · 2021Article
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3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The intrinsically disordered regions of the proteome are enriched in short linear motifs (SLiMs) that serve as binding sites for peptide binding proteins. These interactions are often of low-to-mid micromolar affinities and are challenging to screen for experimentally. However, a range of dedicated methods have been developed recently, which open for screening of SLiM-based interactions on large scale. A variant of phage display, termed proteomic peptide phage display (ProP-PD), has proven particularly useful for the purpose. Here, we describe a complete high-throughput ProP-PD protocol for screening intrinsically disordered regions for SLiMs. The protocol requires some basic bioinformatics skills for the design of the library and for data analysis but can be performed in a standard biochemistry lab. The protocol starts from the construction of a library, followed by the high-throughput expression and purification of bait proteins, the phage selection, and the analysis of the binding-enriched phage pools using next-generation sequencing. As the protocol generates rather large data sets, we also emphasize the importance of data management and storage.
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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.