Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein Folding01:25

Protein Folding

8.1K
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...
8.1K
Protein Denaturation01:28

Protein Denaturation

4.3K
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...
4.3K
The Proteasome Structure01:17

The Proteasome Structure

808
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...
808
Protein Organization01:24

Protein Organization

6.6K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
6.6K
The Proteasome02:18

The Proteasome

8.8K
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...
8.8K
Structural Protein Function01:56

Structural Protein Function

2.8K
2.8K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

APOBEC3A is the predominant global editor of cytosines in human mRNAs and in single-strand RNA viruses.

bioRxiv : the preprint server for biology·2026
Same author

MPXV RNA-seq data provide evidence for protection of viral transcripts from APOBEC3 editing.

Journal of virology·2026
Same author

Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria.

Nature microbiology·2025
Same author

Analysis of the abundance and diversity of RNA secondary structure elements in RNA viruses using the RNAsselem Python package.

Scientific reports·2024
Same author

Genome-wide bioinformatics analysis of human protease capacity for proteolytic cleavage of the SARS-CoV-2 spike glycoprotein.

Microbiology spectrum·2024
Same author

Glycidamide-induced hypermutation in yeast single-stranded DNA reveals a ubiquitous clock-like mutational motif in humans.

Nucleic acids research·2023

Related Experiment Video

Updated: Jul 23, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

131

Predicting Structural Susceptibility of Proteins to Proteolytic Processing.

Evgenii V Matveev1,2,3, Vyacheslav V Safronov4, Gennady V Ponomarev1,2

  • 1Skolkovo Institute of Science and Technology, Moscow 121205, Russia.

International Journal of Molecular Sciences
|July 14, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces a novel method for predicting protein susceptibility to proteolysis using 3D structural features. This approach enhances the accuracy of identifying proteolytic sites, outperforming existing bioinformatics tools.

Keywords:
protease substratesproteasesregulatory proteolysissubstrate identification

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.7K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

1.9K

Related Experiment Videos

Last Updated: Jul 23, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

131
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.7K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

1.9K

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Structural Biology

Background:

  • Proteolytic processing is crucial, yet few prediction methods use substrate 3D structure.
  • No current methods predict structural susceptibility to proteolysis.

Purpose of the Study:

  • Develop a method to predict protein regions' structural susceptibility to proteolysis.
  • Enhance prediction of proteolytic sites by incorporating structural features.

Main Methods:

  • Utilized CutDB data of experimentally verified proteolytic events.
  • Employed structural features: solvent accessibility, secondary structure, temperature factor, loop protrusion length, and terminus flexibility.
  • Optimized machine learning model via curated training sets and negative sample balancing.

Main Results:

  • Developed a novel method for predicting structural susceptibility to proteolysis.
  • Combined method with protease specificity models outperforms existing bioinformatics tools for proteolytic site prediction.
  • Demonstrated the potential for predicting other post-translational modifications.

Conclusions:

  • Structural features are vital for accurate proteolysis prediction.
  • The developed method offers a significant advancement in predicting proteolytic events.
  • This approach has broader implications for predicting other post-translational modifications.