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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...

Protein-Protein Interfaces

Protein-Protein Interfaces

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Protein Networks

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Intrinsically Disordered Proteins

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...

Intrinsically Disordered Proteins

Intrinsically Disordered Proteins

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Related Experiment Video

Updated: Feb 28, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Dynamic control of IDP interaction network via diverse binding pathways.

Jae-Yeol Kim¹, Hoi Sung Chung²

¹Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.

Nature Communications

|February 26, 2026

Summary

This summary is machine-generated.

Intrinsically disordered proteins (IDPs) interact with multiple partners. This study reveals two binding pathways for p53

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Area of Science:

Biochemistry and Molecular Biology
Protein-protein interactions
Intrinsically disordered proteins (IDPs)

Background:

Intrinsically disordered proteins (IDPs) exhibit binding promiscuity, interacting with multiple partners simultaneously.
Quantitative characterization of multi-component interactions involving IDPs is complex.
The transactivation domain (TAD) of p53 is a key regulatory region involved in protein interactions.

Purpose of the Study:

To characterize the binding pathways of the p53 transactivation domain (TAD) with its binding partners Taz2 and Mdm2.
To investigate the mechanisms of multi-component interactions involving IDPs.
To understand how heterogeneous binding networks contribute to cellular responses.

Main Methods:

Utilized three-color single-molecule Förster resonance energy transfer (smFRET) spectroscopy.
Employed high time-resolution FRET with photon-by-photon analysis.
Conducted kinetic analysis of protein-protein interactions.

Main Results:

Identified two distinct binding pathways: a competitive pathway and an allosteric pathway involving a ternary complex.
Demonstrated that the allosteric pathway facilitates faster exchange of binding partners with opposing functions.
Revealed that heterogeneous three-component interaction pathways are linked to diverse two-component binding transition paths.

Conclusions:

A heterogeneous allosteric binding network enables rapid responses to environmental changes.
The study provides quantitative insights into the complex binding dynamics of IDPs.
Understanding these mechanisms is crucial for deciphering cellular signaling and regulation.