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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.6K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
2.6K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

3.8K
3.8K
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
Protein and Protein Structures02:15

Protein and Protein Structures

10.6K
10.6K
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
Multicompartment Models: Overview01:14

Multicompartment Models: Overview

182
Multicompartment models are mathematical constructs that depict how drugs are distributed and eliminated within the body. They segment the body into several compartments, symbolizing various physiological or anatomical areas connected through drug transfer processes such as absorption, metabolism, distribution, and elimination.
These models offer a more comprehensive representation of drug behavior in the body than one-compartment models. They accommodate the complexity of drug distribution,...
182

You might also read

Related Articles

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

Sort by
Same author

Introduction to Markov State Modeling of Conformational Dynamics.

Journal of chemical theory and computation·2026
Same author

Learning data-efficient coarse-grained molecular dynamics from forces and noise.

Nature communications·2026
Same author

Extending the range of graph neural networks with global encodings.

Nature communications·2026
Same author

Peering inside the black box by learning the relevance of many-body functions in neural network potentials.

Nature communications·2025
Same author

Machine learning-accelerated path integral molecular dynamics simulations of reactive organic electrolytes.

The Journal of chemical physics·2025
Same author

Operator forces for coarse-grained molecular dynamics.

The Journal of chemical physics·2025

Related Experiment Video

Updated: Jul 21, 2025

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.2K

Multibody Terms in Protein Coarse-Grained Models: A Top-Down Perspective.

Iryna Zaporozhets1,2,3, Cecilia Clementi1,2,3

  • 1Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States.

The Journal of Physical Chemistry. B
|July 27, 2023
PubMed
Summary

Many-body terms in coarse-grained models are essential for accurately simulating protein stability changes caused by mutations, especially when considering solvent effects. These advanced models improve computational biology research.

More Related Videos

T-wave Ion Mobility-mass Spectrometry: Basic Experimental Procedures for Protein Complex Analysis
16:40

T-wave Ion Mobility-mass Spectrometry: Basic Experimental Procedures for Protein Complex Analysis

Published on: July 31, 2010

24.7K
Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

2.1K

Related Experiment Videos

Last Updated: Jul 21, 2025

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.2K
T-wave Ion Mobility-mass Spectrometry: Basic Experimental Procedures for Protein Complex Analysis
16:40

T-wave Ion Mobility-mass Spectrometry: Basic Experimental Procedures for Protein Complex Analysis

Published on: July 31, 2010

24.7K
Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

2.1K

Area of Science:

  • Computational Biology
  • Protein Dynamics
  • Biomolecular Modeling

Background:

  • Coarse-grained models enable simulations of biomolecular processes at longer time and length scales than atomistic methods.
  • Traditional models often use pairwise potentials, but reducing degrees of freedom suggests many-body interactions are crucial.

Purpose of the Study:

  • To investigate the necessity of many-body terms in coarse-grained models for protein stability.
  • To parametrize models using experimental data from protein mutants.

Main Methods:

  • Utilized experimental data on mutant protein stability for model parametrization.
  • Developed and compared coarse-grained models with and without many-body interaction terms.

Main Results:

  • Coarse-grained models incorporating many-body terms quantitatively reproduced the effects of point mutations on protein stability.
  • Many-body terms were found to implicitly account for solvent effects.

Conclusions:

  • Many-body interactions are critical for accurate coarse-grained protein modeling.
  • These findings advance the development of more predictive computational tools for biomolecular research.