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Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Updated: Jun 7, 2025

Peptide-based Identification of Functional Motifs and their Binding Partners

Peptide-based Identification of Functional Motifs and their Binding Partners

Published on: June 30, 2013

Generating and validating renewable affimer protein binding reagents targeting SH2 domains.

Sophie J Heseltine¹, Gregory J Billenness¹, Heather L Martin¹

¹School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.

Scientific Reports

|November 16, 2024

Summary

This summary is machine-generated.

Researchers developed novel Affimer reagents to target specific SH2 domains, crucial in diseases like cancer. These tools enable new screening methods and show potential for developing domain-specific inhibitors.

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Last Updated: Jun 7, 2025

Peptide-based Identification of Functional Motifs and their Binding Partners

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Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Published on: January 14, 2020

Area of Science:

Biochemistry
Molecular Biology
Drug Discovery

Background:

SH2 domains are critical for protein interactions implicated in diseases such as cancer.
Existing research tools lack specificity for intracellular assays targeting individual SH2 domains.
Affimer reagents offer potential for domain-specific targeting, but their application to the SH2 domain family is underexplored.

Purpose of the Study:

To identify Affimer reagents that selectively bind to SH2 domains.
To evaluate the utility of these Affimers in medium-throughput screening.
To assess the potential of Affimers as domain-specific inhibitors for SH2-mediated interactions.

Main Methods:

Selection of Affimer reagents against 41 SH2 domains.
Development of a medium-throughput screening assay.
Characterization of Affimer binding affinities and inhibitory potential.
Assessment of Affimer-mediated inhibition of pERK nuclear translocation.
Validation of Affimer binding to endogenous Grb2 in cell lysates.

Main Results:

Identified Affimer reagents binding selectively to 22 out of 41 SH2 domains.
Demonstrated Affimers' utility in a medium-throughput screening approach.
Showcased Affimer-mediated inhibition of pERK nuclear translocation, targeting Grb2.
Quantified competitive inhibition by Grb2-specific Affimers with IC50s from 270.9 nM to 1.22 µM and low nanomolar binding affinities.
Confirmed Affimers' ability to precipitate endogenous Grb2 from cell lysates.

Conclusions:

Affimer reagents can be developed as domain-specific inhibitors for SH2 domains.
These Affimers are effective tools for medium/high-throughput phenotypic screening.
The study highlights a promising strategy for identifying and characterizing novel drug targets within the SH2 domain family.