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The Proteasome Structure

The Proteasome Structure

The ubiquitin-proteasome pathway is a well-known mechanism utilized by eukaryotic cells to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, the protein that needs to be eliminated undergoes a process called ubiquitination, where a chain of ubiquitin molecules is attached to the 48th lysine residue of the target protein. This ubiquitin modification helps the proteasome distinguish between a target protein and a healthy protein.
The proteasome is an...

The Proteasome

The Proteasome

Eukaryotic cells can degrade proteins through several pathways. One of the most important among these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. This involves participation of a series of enzymes including— E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3 (ubiquitin...

The Proteasome

The Proteasome

Eukaryotic cells can degrade proteins through several pathways. One of the most important amongst these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. A series of enzymes carry out the ubiquitination of the target proteins - E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...

Radical Formation: Elimination

Radical Formation: Elimination

Another method of radical formation is the elimination process. It is the opposite of the addition route and is driven by the instability of the radical. For example, as depicted in Figure 1, dibenzoyl peroxide yields a pair of unstable radicals upon homolysis. Given its instability, this radical spontaneously undergoes elimination via a C–C bond cleavage to form a relatively more stable phenyl radical. The mechanism involves cleavage of the bond between the α and β positions with respect to...

Protein Denaturation

Protein Denaturation

The function of proteins depends on their native three-dimensional structure, which is dictated by the amino acid sequence of the specific protein. Folding of the polypeptide chain takes place under specific conditions that energetically favor the folded conformation. In contrast, protein denaturation occurs spontaneously under unfavorable conditions that disrupt the integrity of the folded conformation. Thus, the chemical and physical environment of a protein, such as significant changes in pH...

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Related Experiment Video

Updated: Jun 20, 2026

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

Protease dimer formation disrupted.

Jean Chmielewski¹

¹Department of Chemistry, Purdue University, West Lafayette, Indiana, USA. chml@purdue.edu

Nature Chemical Biology

|August 20, 2009

Summary

This summary is machine-generated.

Researchers identified a small-molecule inhibitor targeting the Kaposi's sarcoma-associated herpesvirus protease. This novel agent prevents the formation of the active enzyme dimer by trapping its individual components, offering a new therapeutic strategy.

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Chemical Inactivation of the E3 Ubiquitin Ligase Cereblon by Pomalidomide-based Homo-PROTACs

Chemical Inactivation of the E3 Ubiquitin Ligase Cereblon by Pomalidomide-based Homo-PROTACs

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X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

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Published on: May 13, 2020

Examining Proteasome Assembly with Recombinant Archaeal Proteasomes and Nondenaturing PAGE: The Case for a Combined Approach

Examining Proteasome Assembly with Recombinant Archaeal Proteasomes and Nondenaturing PAGE: The Case for a Combined Approach

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Chemical Inactivation of the E3 Ubiquitin Ligase Cereblon by Pomalidomide-based Homo-PROTACs

Chemical Inactivation of the E3 Ubiquitin Ligase Cereblon by Pomalidomide-based Homo-PROTACs

Published on: May 15, 2019

Area of Science:

Virology
Medicinal Chemistry
Structural Biology

Background:

Human Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic virus.
The viral protease is essential for KSHV replication and pathogenesis.
Targeting viral proteases is a validated strategy for antiviral drug development.

Discussion:

A novel small-molecule inhibitor has been identified that targets the KSHV protease.
The inhibitor operates via a "monomer trap" mechanism.
This mechanism prevents the formation of the active dimeric protease by binding to unfolded monomers.

Key Insights:

Discovery of a KSHV protease inhibitor with a unique "monomer trap" mechanism.
Demonstration of disruption of the enzymatically active protease dimer formation.
Potential for a new class of antiviral agents against KSHV.

Outlook:

Further preclinical and clinical studies are warranted to evaluate the therapeutic potential of this inhibitor.
The "monomer trap" strategy may be applicable to other dimeric viral proteases.
This research opens new avenues for KSHV-associated disease treatment.