Related Experiment Video

Updated: Jul 13, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Structural and functional analysis of the ligand specificity of the HtrA2/Omi PDZ domain

Yingnan Zhang1, Brent A Appleton, Ping Wu

  • 1Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA.

Protein Science : a Publication of the Protein Society
|July 28, 2007
PubMed

Insights

The HtrA2/Omi PDZ domain recognizes unstructured, hydrophobic polypeptides, crucial for mitochondrial protein quality control. This promiscuous binding explains its role in handling misfolded proteins within mitochondria.

Area of Science:

  • Mitochondrial biology
  • Protease function
  • Protein-protein interactions

Background:

  • HtrA2/Omi is a mitochondrial serine protease vital for protein quality control and apoptosis.
  • Its PDZ domain inhibits protease activity and may mediate substrate recognition.
  • Understanding PDZ domain specificity is key to HtrA2/Omi's cellular functions.

Purpose of the Study:

  • To characterize the structural and functional specificity of the human HtrA2/Omi PDZ domain.
  • To elucidate the molecular basis of PDZ domain-ligand interactions.
  • To determine the role of the PDZ domain in substrate recognition for HtrA2/Omi.

Main Methods:

  • Peptide library screening and affinity assays to define binding specificity.
  • X-ray crystallography to visualize PDZ domain-ligand complexes.
  • Alanine-scanning mutagenesis to probe the peptide-binding groove.

Main Results:

  • The HtrA2/Omi PDZ domain binds extended, hydrophobic polypeptide stretches (C-terminal and internal).
  • High-affinity binding involves interactions with multiple hydrophobic side chains.
  • The PDZ domain exhibits promiscuous recognition of unstructured hydrophobic sequences.

Conclusions:

  • HtrA2/Omi PDZ domain specificity is consistent with recognizing diverse misfolded proteins in mitochondria.
  • The promiscuous binding suggests a role in general protein quality control rather than specific substrate targeting in apoptosis.
  • Further studies are needed to fully exclude a role in apoptosis-related substrate targeting.

More Related Videos

Transmembrane Domain Oligomerization Propensity determined by ToxR Assay06:45

Transmembrane Domain Oligomerization Propensity determined by ToxR Assay

Published on: May 26, 2011

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...
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...
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...
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...
The Two-State Receptor Model01:29

The Two-State Receptor Model

The two-state receptor model explains a drug's interaction with receptors, such as G protein-coupled receptors and ligand-gated ion channels, to induce or inhibit a biological response. When no natural ligands are present, a receptor exists in an equilibrium of inactive (Ri) and active (Ra) conformations. The inactive form does not produce a response, while the active form generates a basal effect known as constitutive activity.
The binding affinity of a drug determines its interaction with one...
Ligand-Gated Ion Channel Receptor: Gating Mechanism01:30

Ligand-Gated Ion Channel Receptor: Gating Mechanism

Ligand-gated ion channels are transmembrane proteins that play a vital role in intercellular communication and functions of the nervous system. They allow the influx of ions across the membrane once the neurotransmitter binds, allowing the subsequent transmission of electrical excitation across the neurons. Other ligand-gated ion channels, like the γ-aminobutyric acid (GABA) receptor, permit anions like chloride into the cells on the binding of the GABA molecule. Their entry into the cell...