Related Experiment Video

Updated: Aug 31, 2025

Detection of Toxin Translocation into the Host Cytosol by Surface Plasmon Resonance
10:41

Detection of Toxin Translocation into the Host Cytosol by Surface Plasmon Resonance

Published on: January 3, 2012

13.4K

Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket

Masaru Goto1, Shoko Higashi2, Taro Ohba1

  • 1Department of Molecular Bioscience, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan.

Biochemical and Biophysical Research Communications
|August 23, 2022
PubMed

Insights

Researchers discovered novel pterin-7-carboxamide inhibitors that bind to both active site pockets of ricin toxin A-chain (RTA) in a unique 2-to-1 ratio, offering a new strategy for RTA inhibition.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Toxicology

Background:

  • Ricin toxin A-chain (RTA) is a potent ribosome-inactivating protein responsible for ricin's toxicity.
  • RTA's active site features two critical binding pockets targeted for inhibitor development.
  • Existing RTA inhibitors typically engage only one of these binding pockets.

Purpose of the Study:

  • To discover novel inhibitors that can simultaneously target both binding pockets in the RTA active site.
  • To investigate the binding mode of new inhibitor compounds with RTA.

Main Methods:

  • Synthesis and characterization of pterin-7-carboxamides with aromatic l-amino acid pendants.
  • Biochemical assays to assess RTA inhibition.
  • X-ray crystallography to determine the structure of inhibitor/RTA complexes.

Main Results:

  • Pterin-7-carboxamides demonstrated a unique 2-to-1 binding mode, occupying both primary and secondary active site pockets of RTA.
  • X-ray crystallography revealed that conformational changes in RTA residues Tyr80 and Asn122 are crucial for secondary pocket inhibitor entry.
  • This dual-pocket binding represents a novel mechanism for inhibiting RTA activity.

Conclusions:

  • Pterin-7-carboxamides offer a promising new class of RTA inhibitors with a unique dual-pocket binding mechanism.
  • Understanding the conformational changes in RTA is key to designing effective inhibitors targeting both active site pockets.
  • This study provides a foundation for developing potent therapeutic agents against RTA toxicity.

More Related Videos

A Simple Fluorescence-based Reporter Assay to Identify Cellular Components Required for Ricin Toxin A Chain RTA Trafficking in Yeast09:03

A Simple Fluorescence-based Reporter Assay to Identify Cellular Components Required for Ricin Toxin A Chain RTA Trafficking in Yeast

Published on: December 15, 2017

8.1K
Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors10:33

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

11.4K

Related Concept Videos

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...
4.3K
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
8.0K
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...
2.1K
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...
13.1K
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.5K
Factors Affecting Protein-Drug Binding: Drug-Related Factors01:18

Factors Affecting Protein-Drug Binding: Drug-Related Factors

Drug binding to proteins is a complex phenomenon influenced by various drug-related factors, each playing a significant role in the interaction between drugs and proteins within the body.
One crucial factor in drug-protein binding is the drug's lipophilicity or its affinity for fat. More lipophilic drugs tend to have higher binding extents. For example, highly lipophilic drugs like cloxacillin exhibit substantial protein binding, with as much as 95% of the drug binding to proteins. In...
180