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Related Concept Videos

Protein Digestion01:02

Protein Digestion

Protein digestion begins in the stomach, where the highly acidic environment can easily disrupt protein structure by exposing the peptide bonds of polypeptide chains. After polypeptide chains are broken into individual amino acids by a series of digestive enzymes, the amino acids are transported to the liver via the bloodstream to produce energy.
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 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...
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...
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...
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

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Related Experiment Video

Updated: May 31, 2026

The Determination of Protease Specificity in Mouse Tissue Extracts by MALDI-TOF Mass Spectrometry: Manipulating PH to Cause Specificity Changes
09:47

The Determination of Protease Specificity in Mouse Tissue Extracts by MALDI-TOF Mass Spectrometry: Manipulating PH to Cause Specificity Changes

Published on: May 25, 2018

Structural determinants of limited proteolysis.

Marat D Kazanov1, Yoshinobu Igarashi, Alexey M Eroshkin

  • 1Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA.

Journal of Proteome Research
|June 21, 2011
PubMed
Summary

Understanding limited proteolysis is key for drug discovery. This study reveals that protein structure, particularly exposure and flexibility, significantly predicts cleavage sites, outperforming sequence-based methods.

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Using Caenorhabditis elegans as a Model System to Study Protein Homeostasis in a Multicellular Organism
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Published on: December 18, 2013

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Last Updated: May 31, 2026

The Determination of Protease Specificity in Mouse Tissue Extracts by MALDI-TOF Mass Spectrometry: Manipulating PH to Cause Specificity Changes
09:47

The Determination of Protease Specificity in Mouse Tissue Extracts by MALDI-TOF Mass Spectrometry: Manipulating PH to Cause Specificity Changes

Published on: May 25, 2018

Using Caenorhabditis elegans as a Model System to Study Protein Homeostasis in a Multicellular Organism
12:38

Using Caenorhabditis elegans as a Model System to Study Protein Homeostasis in a Multicellular Organism

Published on: December 18, 2013

Area of Science:

  • Biochemistry
  • Structural Biology
  • Proteomics

Background:

  • Limited or regulatory proteolysis is crucial for biological processes like blood coagulation, cell proliferation, and apoptosis.
  • Identifying cleavage sites is essential for understanding these pathways and developing therapeutics.

Purpose of the Study:

  • To assess the statistical significance and predictive power of structural descriptors for identifying proteolytic cleavage sites.
  • To establish a foundation for automated prediction of protein segments susceptible to proteolytic processing.

Main Methods:

  • Analysis of >200 proteolytic events from the CutDB database for mammalian regulatory proteases and their substrates.
  • Evaluation of individual and combined structural features (exposure, flexibility, local interactions) and sequence-based descriptors.
  • Comparison of predictive performance using experimentally determined structures versus homology-based models.

Main Results:

  • Protein structural features, ranked as exposure > flexibility > local interactions, are significant predictors of cleavage sites.
  • Loops and helices show the highest frequency of proteolytic cleavage, with some β-strands also exhibiting appreciable cleavage.
  • Sequence-based descriptors have limited predictive capability, while homology models perform comparably to experimentally determined structures.

Conclusions:

  • Structural context, especially solvent exposure and flexibility, is more predictive of proteolytic cleavage than amino acid sequence alone.
  • This study provides a framework for accurately predicting protein segments vulnerable to proteolysis and other post-translational modifications.