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Related Concept Videos

Protein-protein Interfaces02:04

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 Interfaces02:04

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...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein Networks02:26

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,...
Conservation of Protein Domains Over Different Proteins02:26

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 form...

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Related Experiment Video

Updated: May 15, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Predicting PDZ domain mediated protein interactions from structure.

Shirley Hui1, Xiang Xing, Gary D Bader

  • 1The Donnelly Centre, University of Toronto, Toronto, ON, Canada.

BMC Bioinformatics
|January 23, 2013
PubMed
Summary
This summary is machine-generated.

We developed a structure-based predictor to identify protein-protein interactions (PPIs) mediated by PDZ domains. This new tool complements sequence-based methods, uncovering novel PDZ domain functions in human biology.

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Related Experiment Videos

Last Updated: May 15, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

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Published on: November 3, 2011

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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

Published on: July 14, 2015

Area of Science:

  • Structural biology
  • Computational biology
  • Bioinformatics

Background:

  • PDZ domains are crucial protein interaction modules recognizing linear motifs, mediating key biological processes.
  • Existing predictors rely on sequence data, potentially missing interactions influenced by structural features.

Purpose of the Study:

  • To develop and validate a novel computational predictor for PDZ domain-peptide interactions using structural information.
  • To explore the utility of structure-based prediction for identifying novel PDZ domain functions and interactions.

Main Methods:

  • Developed a support vector machine (SVM) model trained on PDZ domain structure and peptide sequence data.
  • Applied the structure-based predictor to scan the human proteome for PDZ domain ligands.
  • Validated predictions against known interactions and utilized functional enrichment analysis.

Main Results:

  • The structure-based predictor successfully identified known PDZ domain-peptide interactions and protein-protein interactions (PPIs).
  • It demonstrated complementarity to sequence-based predictors, discovering unique interactions and showing less dependence on sequence similarity.
  • Functional enrichment analysis revealed novel PDZ domain roles in xenobiotic metabolism, wound healing, and Wnt signaling.

Conclusions:

  • A novel structure-based predictor for PDZ domain-peptide interactions was successfully developed and validated.
  • This predictor expands the discovery of human PDZ-mediated PPIs beyond sequence-based approaches.
  • The study provides a functional map of human PDZ domain biology, predicting novel functions and interactions.