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 Networks02:26

Protein Networks

3.9K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
3.9K
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.5K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.5K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

10.8K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.8K
Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

13.1K
Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
13.1K
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

5.7K
Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
5.7K
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K

You might also read

Related Articles

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

Sort by
Same author

Direct synthesis of amorphous metal-organic frameworks from nanoclusters.

Nature communications·2026
Same author

Trapping a Metastable Node in an Amorphous Metal-Organic Framework.

Angewandte Chemie (International ed. in English)·2026
Same author

Collective Intermolecular Motions of Water in Sodium Montmorillonite.

The journal of physical chemistry. B·2026
Same author

Nonporous hydrophobic organic crystals for carbon dioxide capture via chain-melting phase transition.

Nature communications·2026
Same author

Bimodal Mechanical Response of Membrane Necks: Implications for the Nuclear Envelope.

ACS nano·2025
Same author

TS2CG as a Membrane Builder.

Journal of chemical theory and computation·2025

Related Experiment Video

Updated: Jun 11, 2025

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
05:56

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

1.3K

Physics-Based Protein Networks Might Recover Effectful Mutations─a Case Study on Cathepsin G.

Fabian Schuhmann1, Heloisa N Bordallo2, Weria Pezeshkian1

  • 1Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark.

The Journal of Physical Chemistry. B
|October 2, 2024
PubMed
Summary

Analyzing protein dynamics with a novel physics-based network reveals key interactions, outperforming distance-based methods for identifying functional sites in enzymes like cathepsin G.

More Related Videos

The Importance of Correct Protein Concentration for Kinetics and Affinity Determination in Structure-function Analysis
19:16

The Importance of Correct Protein Concentration for Kinetics and Affinity Determination in Structure-function Analysis

Published on: March 17, 2010

20.6K
Using Caenorhabditis elegans to Screen for Tissue-Specific Chaperone Interactions
06:55

Using Caenorhabditis elegans to Screen for Tissue-Specific Chaperone Interactions

Published on: June 7, 2020

2.9K

Related Experiment Videos

Last Updated: Jun 11, 2025

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
05:56

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

1.3K
The Importance of Correct Protein Concentration for Kinetics and Affinity Determination in Structure-function Analysis
19:16

The Importance of Correct Protein Concentration for Kinetics and Affinity Determination in Structure-function Analysis

Published on: March 17, 2010

20.6K
Using Caenorhabditis elegans to Screen for Tissue-Specific Chaperone Interactions
06:55

Using Caenorhabditis elegans to Screen for Tissue-Specific Chaperone Interactions

Published on: June 7, 2020

2.9K

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Molecular dynamics simulations are crucial for studying protein structure and dynamics, but often fail to capture relevant timescales.
  • Analyzing simulation data is essential for identifying functionally important regions like mutation sites or allosteric hotspots.
  • Existing analysis methods may not fully capture the complex dynamics influencing protein function.

Purpose of the Study:

  • To introduce and validate a physics-based protein network for analyzing molecular dynamics simulation data.
  • To assess the network's ability to identify functionally relevant regions in serine proteases.
  • To compare the efficacy of the physics-based network against traditional distance-based methods.

Main Methods:

  • Development of a physics-based network model representing residue interactions within proteins.
  • Application of the network analysis to molecular dynamics simulations of cathepsin G and neutrophil elastase.
  • Comparative analysis of network outputs with distance-based network approaches.

Main Results:

  • The physics-based network successfully identified the catalytic triad in both cathepsin G and neutrophil elastase.
  • The network effectively distinguished functional differences between highly similar enzymes, including a mutant cathepsin G.
  • Physics-based network analysis demonstrated superior performance in capturing protein structural behavior compared to distance-based networks.

Conclusions:

  • Physics-based protein networks offer a powerful approach for analyzing complex protein dynamics from simulation data.
  • This method enhances the identification of critical functional sites and differences between related proteins.
  • The developed network provides a more accurate representation of protein structural behavior than distance-based methods.