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 Dynamics in Living Cells

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

You might also read

Related Articles

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

Sort by

Same author

Effects of dietary spirulina (Arthrospores platensis) on the growth performance and meat quality of broiler chickens.

Poultry science·2026

Same author

Synergistic effects of two bacteriophages with distinct infection patterns and broad host specificity against multidrug-resistant Salmonella Typhimurium and their potential applications in the poultry industry.

Poultry science·2026

Same author

Uncertainty quantification in stochastic simulations of nitrogen-carbon gas-surface interactions.

The Journal of chemical physics·2026

Same author

Dietary Artemisia annua leaf powder modulates intestinal response and cecal microbiota of broiler chickens during peak Eimeria infection.

Poultry science·2026

Same author

Appetite gene expression and gut microbiota in broiler chickens with varying body weights: a new perspective on flock uniformity.

Poultry science·2026

Same author

Effects of Aspergillus sp. supplementation with or without xylanase on growth performance, nutrient digestibility, and the gastrointestinal microbiome of broilers.

Poultry science·2026

Same journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026

Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026

Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026

Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026

Same journal

Achieving protease substrate-specific inhibition by mAb dual functional selections.

Protein science : a publication of the Protein Society·2026

Same journal

How important are quantum mechanical effects in controlling biological functions: Enzymes, electron transfer and bird navigation.

Protein science : a publication of the Protein Society·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 26, 2025

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

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

Published on: April 26, 2024

An accelerated molecular dynamics study for investigating protein pathways using the bond-boost hyperdynamics method.

Soon Woo Park¹, Moon-Ki Choi², Byung Ho Lee³

¹School of Mechanical Engineering, Sungkyunkwan University, Suwon, Republic of Korea.

Protein Science : a Publication of the Protein Society

|February 25, 2025

Summary

This summary is machine-generated.

This study introduces a modified bond-boost method (BBM) for accelerated molecular dynamics (aMD) simulations. The new approach enhances protein conformational sampling and pathway analysis, overcoming computational limitations.

Keywords:

accelerated molecular dynamics adenylate kinase bond‐boost method molecular dynamics simulation ribose binding protein

More Related Videos

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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

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

Related Experiment Videos

Last Updated: May 26, 2025

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

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

Published on: April 26, 2024

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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

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

Area of Science:

Computational Biology
Biophysics
Molecular Modeling

Background:

Molecular dynamics (MD) simulations are crucial for studying protein dynamics and thermodynamics.
High computational costs limit the exploration of protein conformational space in conventional MD.
Accelerated MD (aMD) methods aim to overcome these limitations by enhancing sampling efficiency.

Purpose of the Study:

To develop a novel accelerated molecular dynamics (aMD) method based on the bond-boost method (BBM) for efficient protein conformational transition analysis.
To improve upon existing aMD techniques by utilizing dihedral angles and hydrogen bonds for bias potential construction.
To provide an efficient algorithm compatible with LAMMPS for broader applicability.

Main Methods:

A modified bond-boost method (BBM) was developed, employing dihedral angles and hydrogen bonds to construct bias potentials.
The enhanced method was implemented within an efficient algorithm compatible with the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS).
Validation was performed by comparing conventional and accelerated MD simulations of ribose binding protein and adenylate kinase conformational changes.

Main Results:

The modified BBM successfully accelerated the exploration of protein conformational space, revealing transition pathways.
Free energy landscapes calculated via umbrella sampling confirmed the identified states as free energy minima.
The aMD simulations accurately predicted transition pathways consistent with the free energy landscape.

Conclusions:

The developed BBM-based aMD method significantly enhances the efficiency of protein conformational sampling and pathway investigation.
This approach provides a reliable tool for studying protein dynamics and thermodynamics, overcoming computational barriers.
The method is expected to be valuable for a wide range of protein simulation studies.