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
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

12.7K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
12.7K
Protein Organization01:24

Protein Organization

6.1K
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....
6.1K

You might also read

Related Articles

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

Sort by
Same author

From Intermolecular Poses to Thermodynamics Using Subdivided Spheres.

The journal of physical chemistry. B·2026
Same author

The colder, the better? Sustainability in frozen storage of a monoclonal antibody drug substance.

International journal of pharmaceutics: X·2026
Same author

Dissolved oxygen effects on human growth hormone stability during freeze-thaw and metal-catalyzed oxidation.

Journal of pharmaceutical sciences·2026
Same author

New insights into the intrinsic tryptophan fluorescence emission spectra of IgG antibodies and the impact of protein unfolding and aggregation.

European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V·2026
Same author

Emerging technologies and scientific advances in lyophilization of pharmaceuticals: insights from the 2025 freeze-drying of pharmaceuticals & biologicals conference.

European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V·2026
Same author

Elucidating the Mechanism of Protein Particle Formation under Mechanical Stress at Different Compressible Interfaces by Molecular Dynamics and Experiments.

Molecular pharmaceutics·2026

Related Experiment Video

Updated: May 22, 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

Enhancing Martini 3 for protein self-interaction simulations.

Jonas Binder1, Matja Zalar2, Martin Huelsmeyer3

  • 1Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universität München 81377 Munich, Germany.

European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences
|March 12, 2025
PubMed
Summary

Reparameterizing the Martini 3 force field improves coarse-grained molecular dynamics (CG-MD) simulations of protein interactions. This refinement leads to accurate predictions of protein self-interaction, crucial for drug development.

Keywords:
B(22)Coarse-grained molecular dynamicsDiffusion coefficientMartini 3 force fieldNMRProtein-protein interactionsReparameterization

More Related Videos

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability
09:49

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

10.5K
Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

308

Related Experiment Videos

Last Updated: May 22, 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
Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability
09:49

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

10.5K
Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

308

Area of Science:

  • Biophysics
  • Computational Chemistry
  • Protein Dynamics

Background:

  • Coarse-grained molecular dynamics (CG-MD) simulations are essential for studying protein-protein interactions.
  • Existing force fields, including Martini 3, often overestimate protein interaction strengths, limiting simulation accuracy.
  • Accurate modeling of protein self-interaction is vital for understanding protein behavior and stability.

Purpose of the Study:

  • To evaluate the performance of the Martini 3 force field in predicting the self-interaction of lysozyme and subtilisin using Metadynamics.
  • To reparameterize the Martini 3 force field to improve the accuracy of protein self-interaction predictions.
  • To enable more reliable CG-MD simulations for applications in protein stability, aggregation, and drug development.

Main Methods:

  • Coarse-grained molecular dynamics (CG-MD) simulations.
  • Metadynamics enhanced sampling technique.
  • Reparameterization of Martini 3 force field bead interactions.
  • Comparison with experimental data for second virial and diffusion coefficients.

Main Results:

  • The original Martini 3 force field overestimates protein self-interaction strength.
  • Reparameterization of bead interactions in Martini 3 significantly improved agreement with experimental data.
  • The refined force field accurately predicts the second virial coefficient and diffusion coefficient for lysozyme and subtilisin.

Conclusions:

  • The refined Martini 3 force field provides a more accurate representation of protein self-interaction in CG-MD simulations.
  • This improved accuracy has significant implications for predicting protein stability, aggregation, and solubility.
  • The refined force field can aid in the development of protein-based therapeutics and understanding protein behavior.