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Protein Networks

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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.
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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...

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...

Protein Dynamics in Living Cells

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Conservation of Protein Domains Over Different Proteins

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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 form...

Conservation of Protein Domains

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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.
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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

Energetic pathway sampling in a protein interaction domain.

Greta Hultqvist¹, S Raza Haq, Avinash S Punekar

¹Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden.

Structure (London, England : 1993)

|July 2, 2013

Summary

This summary is machine-generated.

Energetic crosstalk shapes protein-ligand interactions. This study reveals how subtle structural changes in postsynaptic density 95/discs large/zonula occludens 1 (PDZ) proteins rewire allosteric pathways, influencing binding specificity.

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Last Updated: May 10, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Published on: March 3, 2015

Mapping Dysfunctional Protein-Protein Interactions in Disease

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Area of Science:

Biochemistry
Structural Biology
Molecular Biophysics

Background:

Protein-ligand interactions are crucial for biological processes.
Allosteric regulation within protein domains influences binding affinity and specificity.
The molecular mechanisms of intradomain allostery remain incompletely understood.

Purpose of the Study:

To investigate the molecular details of intradomain allosteric pathways in postsynaptic density 95/discs large/zonula occludens 1 (PDZ) proteins.
To understand how structural perturbations affect energetic signaling and ligand specificity.
To explore the diversity of allosteric pathways within the PDZ protein family.

Main Methods:

Experimental detection of interaction pathways using wild-type and circularly permuted PDZ proteins.
Computational prediction of allosteric pathways.
Analysis of PDZ-peptide ligand interactions.

Main Results:

Circularly permuted PDZ proteins exhibited altered tertiary structures and rewired allosteric pathways.
Subtle structural changes significantly reshaped energetic signaling.
Distinct interaction pathways were identified for different peptide ligands within the PDZ family.
Multiple energetic pathways are sampled within a single PDZ domain, activated by specific ligands.

Conclusions:

Intradomain allostery in PDZ proteins is mediated by distinct energetic pathways.
Structural variations can lead to significant rewiring of allosteric signaling.
Understanding these pathways is key to deciphering protein-ligand interaction specificity.