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Related Concept Videos

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...
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.
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...
The Unfolded Protein Response01:37

The Unfolded Protein Response

The ER is the hub of protein synthesis in a cell. It has robust systems to quality control protein folding and also for degradation of terminally misfolded proteins. Under normal conditions, a small proportion of misfolded proteins that cannot be salvaged need to be transported to the cytoplasm by the ER-associated degradation or ERAD pathways. However, if the ERAD cannot handle the misfolded proteins, the cell activates the unfolded protein response or UPR to adjust the protein folding...

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Related Experiment Video

Updated: Jun 23, 2026

In Vitro Analysis of E3 Ubiquitin Ligase Function
06:06

In Vitro Analysis of E3 Ubiquitin Ligase Function

Published on: May 14, 2021

Periodic forces trigger a complex mechanical response in ubiquitin.

Piotr Szymczak1, Harald Janovjak

  • 1Institute of Theoretical Physics, Warsaw University, Poland.

Journal of Molecular Biology
|May 12, 2009
PubMed
Summary

Periodic mechanical forces significantly alter protein structure and unfolding pathways, even with broadly distributed frequencies. This study reveals ubiquitin

Area of Science:

  • Biophysics
  • Molecular Biology
  • Mechanobiology

Background:

  • Mechanical forces are crucial for physiological processes.
  • Understanding protein responses to dynamic mechanical forces is limited.
  • Ubiquitin is a vital eukaryotic protein.

Purpose of the Study:

  • Investigate how ubiquitin unfolds under periodic mechanical forces.
  • Analyze the frequency- and amplitude-dependent effects of these forces.
  • Develop models to predict protein responses to repetitive mechanical stimuli.

Main Methods:

  • Coarse-grained molecular dynamics simulations.
  • Unfolding single and multimeric ubiquitin proteins.
  • Developing a kinetic energy landscape model.

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Ubiquitin Chain Analysis by Parallel Reaction Monitoring
08:33

Ubiquitin Chain Analysis by Parallel Reaction Monitoring

Published on: June 17, 2020

In Vitro Ubiquitination and Deubiquitination Assays of Nucleosomal Histones
11:36

In Vitro Ubiquitination and Deubiquitination Assays of Nucleosomal Histones

Published on: July 25, 2019

Related Experiment Videos

Last Updated: Jun 23, 2026

In Vitro Analysis of E3 Ubiquitin Ligase Function
06:06

In Vitro Analysis of E3 Ubiquitin Ligase Function

Published on: May 14, 2021

Ubiquitin Chain Analysis by Parallel Reaction Monitoring
08:33

Ubiquitin Chain Analysis by Parallel Reaction Monitoring

Published on: June 17, 2020

In Vitro Ubiquitination and Deubiquitination Assays of Nucleosomal Histones
11:36

In Vitro Ubiquitination and Deubiquitination Assays of Nucleosomal Histones

Published on: July 25, 2019

Main Results:

  • Periodic forces weaken ubiquitin and alter unfolding pathways.
  • Complex dynamic responses include secondary structure refolding.
  • Protein response is frequency- and amplitude-dependent.
  • Ubiquitin shows remarkable insensitivity to periodic forces when linked for degradation.

Conclusions:

  • Periodic forces significantly impact protein mechanics.
  • Repetitive mechanical forces have predictable effects on protein stability.
  • Insights into ubiquitin's mechanical role in protein degradation.
  • Framework for modeling dynamic protein stability under repetitive forces.