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Related Concept Videos

The Proteasome01:13

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 Proteasome02:18

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...
The Proteasome Structure01:17

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...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
Regulated Protein Degradation02:58

Regulated Protein Degradation

It is vital to regulate the activity of enzymatic as well as non-enzymatic proteins inside the cell. This can be achieved either through creating a balance between their rate of synthesis and degradation or regulating the intrinsic activity of the protein. Both these regulation mechanisms play an essential role in the normal functioning of cells.
Protein degradation plays two important roles in the cells. It helps to protect cells from misfolded or damaged proteins before they lead to a...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

Updated: Jun 18, 2026

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry
11:54

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

Proteome-wide Ubiquitinome Profiling Reveals Substrate-specific Dynamics Within the USP7 Network.

Joyce Wolf van der Meer1, Jan A van der Knaap1, Ayestha Sijm1

  • 1Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.

Molecular & Cellular Proteomics : MCP
|June 16, 2026
PubMed
Summary

Ubiquitin-specific protease 7 (USP7) impacts tumor suppression and neurodevelopment by deubiquitylating proteins. This study reveals USP7

Keywords:
Hao-Fountain syndromeUSP7deubiquitylasesproteomicsubiquitylation

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Profiling Ubiquitin and Ubiquitin-like Dependent Post-translational Modifications and Identification of Significant Alterations
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Profiling Ubiquitin and Ubiquitin-like Dependent Post-translational Modifications and Identification of Significant Alterations

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Evaluation of Substrate Ubiquitylation by E3 Ubiquitin-ligase in Mammalian Cell Lysates
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Evaluation of Substrate Ubiquitylation by E3 Ubiquitin-ligase in Mammalian Cell Lysates

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Related Experiment Videos

Last Updated: Jun 18, 2026

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry
11:54

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

Profiling Ubiquitin and Ubiquitin-like Dependent Post-translational Modifications and Identification of Significant Alterations
10:26

Profiling Ubiquitin and Ubiquitin-like Dependent Post-translational Modifications and Identification of Significant Alterations

Published on: November 7, 2019

Evaluation of Substrate Ubiquitylation by E3 Ubiquitin-ligase in Mammalian Cell Lysates
09:47

Evaluation of Substrate Ubiquitylation by E3 Ubiquitin-ligase in Mammalian Cell Lysates

Published on: May 10, 2022

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Proteomics

Background:

  • USP7 is a deubiquitylating enzyme crucial for tumor suppression, neurodevelopment, chromatin regulation, and DNA damage response.
  • The precise mechanisms by which USP7 regulates these diverse cellular pathways remain incompletely understood.

Purpose of the Study:

  • To comprehensively profile the proteome-wide effects of USP7 on substrate deubiquitylation and protein abundance.
  • To elucidate the role of USP7 domains in substrate selection and understand the substrate-specific nature of its deubiquitylation activity.

Main Methods:

  • Utilized data-independent acquisition and label-free quantitation mass spectrometry (DIA-LFQ-MS) to profile the proteome.
  • Employed immunopurification to identify endogenous USP7-associated proteins.
  • Mapped proteome-wide changes in ubiquitination dynamics using K-ε-GG peptide enrichment after USP7 inhibition.

Main Results:

  • Identified a consensus set of high-confidence USP7 protein targets by integrating new and existing interactome data.
  • Revealed that USP7's ubiquitin-like domains, in addition to its TRAF domain, are critical for substrate recognition.
  • Demonstrated that USP7-mediated deubiquitylation has variable and substrate-specific effects on target protein stability.
  • Established that USP7's activity profile is substrate-dependent, not an intrinsic enzymatic property.

Conclusions:

  • USP7's deubiquitylation activity is highly variable and substrate-specific, influencing diverse pathways including neurodevelopment and tumor suppression.
  • Provides a proteome-wide map of USP7 target sites and insights into its regulatory mechanisms.
  • Highlights the connection between USP7, neurodevelopmental syndromes, and tumor suppression pathways.