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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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...
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,...
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...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

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Related Experiment Video

Updated: Jun 16, 2026

In Vitro Analysis of PDZ-dependent CFTR Macromolecular Signaling Complexes
10:05

In Vitro Analysis of PDZ-dependent CFTR Macromolecular Signaling Complexes

Published on: August 13, 2012

Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms.

Jonathan M Elkins1, Carina Gileadi, Leela Shrestha

  • 1Structural Genomics Consortium, Oxford University, Oxford, OX3 7DQ, United Kingdom.

Protein Science : a Publication of the Protein Society
|February 2, 2010
PubMed
Summary

This study reveals how PDZ domains bind protein targets, showing that noncanonical binding modes, where residues outside the main groove interact, may represent key intermediate steps in the binding process.

Related Experiment Videos

Last Updated: Jun 16, 2026

In Vitro Analysis of PDZ-dependent CFTR Macromolecular Signaling Complexes
10:05

In Vitro Analysis of PDZ-dependent CFTR Macromolecular Signaling Complexes

Published on: August 13, 2012

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • PDZ domains are crucial protein interaction modules.
  • They typically recognize C-terminal motifs of target proteins, primarily at the P0 and P-2 positions.
  • Understanding PDZ domain binding is vital for deciphering cellular signaling pathways.

Purpose of the Study:

  • To elucidate the structural basis of PDZ domain-target interactions.
  • To investigate both canonical and noncanonical binding modes.
  • To explore the role of remote residues in PDZ domain selectivity.

Main Methods:

  • X-ray crystallography of seven human PDZ domains, including five PDLIM family members.
  • Analysis of protein-protein interaction interfaces.
  • Comparison of distinct binding modes within the same crystal structure.

Main Results:

  • Structures revealed canonical and noncanonical binding modes for GRASP PDZ domain.
  • PDLIM2, PDLIM5, and PDLIM7 PDZ domains showed binding primarily through the P0 residue.
  • Noncanonical binding, involving interactions outside the main groove, was observed, suggesting kinetic intermediates.

Conclusions:

  • PDZ domain binding is more diverse than previously thought, with noncanonical modes offering insights into binding dynamics.
  • Residues outside the canonical binding groove significantly influence PDZ domain selectivity.
  • Observed noncanonical binding may represent a general kinetic intermediate state in PDZ domain-ligand recognition.