Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Protein-protein Interfaces

Protein-protein Interfaces

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...

Protein Networks

Protein Networks

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,...

You might also read

Related Articles

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

Sort by

Same author

DruGUI 2.0: Mapping Protein Druggability with Probe-Based Molecular Dynamics.

Bioinformatics (Oxford, England)·2026

Same author

Small Molecule Activators of Protein Phosphatase 2A Exert Global Stabilizing Effects on the Scaffold PR65.

JACS Au·2026

Same author

Challenging Ureteroscopy in Complex Anatomy: A Case Report.

Cureus·2026

Same author

D614G reshapes allosteric networks and opening mechanisms of SARS-CoV-2 spikes.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Generation of Pathway Signatures by Combining Normal Modes with Weighted Ensemble Simulations.

bioRxiv : the preprint server for biology·2026

Same author

Large-scale protein conformational transitions revealed by weighted ensemble simulations and EPR.

Chemical science·2026

Same journal

UPF3A and UPF3B shape the transcriptome cooperatively yet oppose cell function.

Journal of molecular biology·2026

Same journal

Antibody-secreting cells integrate efficient NMD with non‑canonical UPR signaling to maintain proteostasis and support massive immunoglobulin synthesis.

Journal of molecular biology·2026

Same journal

Small molecule stabilization of diverse amyloidogenic immunoglobulin light chains revealed by hydrogen-deuterium exchange mass spectrometry.

Journal of molecular biology·2026

Same journal

UPF1 at Work: Structural and Mechanistic Insights Into a Master Regulator of Nonsense-Mediated mRNA Decay.

Journal of molecular biology·2026

Same journal

Structural basis for the pro-amyloidogenic action and ligand binding of a novel W72R variant of human apolipoprotein A-I.

Journal of molecular biology·2026

Same journal

Cryo-EM Structure of the C. elegans Septin Tetramer Reveals a Revised Architecture and Conserved Positional Orthology.

Journal of molecular biology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 27, 2025

Evaluation of Protein–Protein Interactions using an On-Membrane Digestion Technique

Evaluation of Protein–Protein Interactions using an On-Membrane Digestion Technique

Published on: July 19, 2019

InSty: A ProDy Module for Evaluating Protein Interactions and Stability.

Karolina Mikulska-Ruminska¹, James M Krieger², Anupam Banerjee³

¹Institute of Physics, Faculty of Physics Astronomy and Informatics, Nicolaus Copernicus University in Torun PL87100 Torun, Poland.

Journal of Molecular Biology

|February 15, 2025

Summary

This summary is machine-generated.

A new module, InSty, enhances ProDy for analyzing protein interactions and dynamics. It quantifies intra- and intermolecular forces, aiding in understanding protein stability, function, and evolution.

Keywords:

PDB ProDy elastic network models molecular dynamics non-covalent interactions

More Related Videos

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Related Experiment Videos

Last Updated: May 27, 2025

Evaluation of Protein–Protein Interactions using an On-Membrane Digestion Technique

Evaluation of Protein–Protein Interactions using an On-Membrane Digestion Technique

Published on: July 19, 2019

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

Computational Biology
Structural Biology
Biophysics

Background:

Protein dynamics and interactions are crucial for biological function.
Existing tools may not fully capture the complexity of these interactions across ensembles.
Bridging protein structure and function requires advanced analytical methods.

Purpose of the Study:

Introduce InSty, a novel module for the ProDy application programming interface.
Identify and quantify intra- and intermolecular interactions influencing protein stability and dynamics.
Provide insights into the functional significance and evolutionary conservation of these interactions.

Main Methods:

Analysis of non-covalent interactions using conformational ensemble data (experimental and predicted).
Assessment of interaction time evolution and persistence during molecular dynamics simulations.
Evaluation of interaction conservation across homologous proteins.

Main Results:

InSty quantifies critical intra- and intermolecular interactions.
The module analyzes interaction dynamics, persistence, and conservation.
Outputs facilitate statistical evaluation, visualization, and automated ensemble analysis.

Conclusions:

InSty integrates seamlessly with ProDy, offering a versatile tool for computational biology.
The module aids in understanding protein stability, function, and allostery.
InSty supports mutagenesis studies and identifies key sites for functional interactions.