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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Screening Intrinsically Disordered Regions for Short Linear Binding Motifs.

Muhammad Ali¹, Leandro Simonetti¹, Ylva Ivarsson²

¹Department of Chemistry, BMC, Uppsala, Sweden.

Methods in Molecular Biology (Clifton, N.J.)

|July 23, 2020

Summary

This study presents a high-throughput proteomic peptide phage display (ProP-PD) protocol to screen for short linear motifs (SLiMs) in intrinsically disordered protein regions, enabling large-scale interaction discovery.

Keywords:

Data management High-throughput purification IDP Interactions Next-generation sequencing Phage display SLiM

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Identifying Protein-protein Interaction Sites Using Peptide Arrays

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Published on: November 18, 2014

Area of Science:

Molecular Biology
Biochemistry
Bioinformatics

Background:

Intrinsically disordered regions (IDRs) of proteins are rich in short linear motifs (SLiMs).
SLiMs mediate low-to-mid micromolar affinity interactions with peptide-binding proteins, which are difficult to screen experimentally.
Recent advancements offer methods for large-scale screening of SLiM-based interactions.

Purpose of the Study:

To describe a complete high-throughput protocol for screening IDRs for SLiMs.
To enable large-scale discovery of SLiM-based interactions.
To provide a standardized method for researchers in standard biochemistry labs.

Main Methods:

Utilizes a variant of phage display termed proteomic peptide phage display (ProP-PD).
Involves library construction, high-throughput bait protein expression and purification, phage selection, and next-generation sequencing.
Requires basic bioinformatics for library design and data analysis.

Main Results:

Demonstrates a comprehensive ProP-PD protocol for SLiM screening in IDRs.
Generates large datasets, highlighting the importance of data management and storage.
Facilitates the identification of binding-enriched phage pools.

Conclusions:

The described high-throughput ProP-PD protocol is effective for screening intrinsically disordered regions for SLiMs.
This method facilitates large-scale discovery of protein-protein interactions mediated by SLiMs.
The protocol is accessible to standard biochemistry labs with basic bioinformatics support.