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Protein-protein Interfaces

Protein-protein Interfaces

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 polypeptide...

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Updated: Jun 27, 2026

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

iPEP: peptides designed and selected for interfering with protein interaction and function.

Jody M Mason¹, Kristian M Müller, Katja M Arndt

¹Department of Biology, Albert-Ludwigs University of Freiburg, Freiburg, Germany. katja@biologie.unifreiburg.de

Biochemical Society Transactions

|November 22, 2008

Summary

This summary is machine-generated.

Semi-rational design created novel interfering peptides (iPEPs) with enhanced stability against therapeutic targets. Improved protein-fragment complementation assays (PCAs) increased specificity, offering a promising therapeutic development strategy.

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Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Area of Science:

Protein engineering
Biochemistry
Drug discovery

Background:

Developing therapeutic peptides with high interaction stability is crucial.
Native protein complexes often lack the stability required for therapeutic applications.

Purpose of the Study:

To generate novel interfering peptides (iPEPs) with enhanced stability against therapeutically relevant proteins.
To improve the specificity of peptide selection using advanced screening techniques.

Main Methods:

Utilized semi-rational design in conjunction with protein-fragment complementation assays (PCAs) and phage-display screening.
Enhanced PCA selection to incorporate competitive and negative design principles.
Analyzed the folding pathways of designed peptide pairs.

Main Results:

Generated a range of iPEPs exhibiting significantly higher interaction stability compared to native complexes.
Improved PCA selection led to enhanced specificity of the selected peptides.
Folding pathway analysis indicated early hydrophobic collapse and helix formation, followed by electrostatic interactions.

Conclusions:

Semi-rational design combined with improved PCAs and phage display is effective for creating highly stable and specific interfering peptides.
The developed iPEPs show potential for therapeutic applications targeting various proteins.
Understanding folding pathways provides insights into the design of stable protein-protein interactions.