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...

Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Protein Folding

Protein Folding

Protein Folding

Protein Folding

Protein Organization

Protein Organization

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....

Structural Protein Function

Structural Protein Function

You might also read

Related Articles

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

Sort by

Same author

Coarse-grained force fields via rotational entropy corrections to free-energy landscapes of diffusing molecules.

Physical review. E·2025

Same author

Generalized Einstein Relation for Markovian Friction Coefficients from Molecular Trajectories.

Physical review letters·2025

Same author

Chemical Potential of a Flexible Polymer Liquid in a Coarse-Grained Representation.

The journal of physical chemistry. B·2023

Same author

Weighted ensemble: Recent mathematical developments.

The Journal of chemical physics·2023

Same author

Identifying the leading dynamics of ubiquitin: A comparison between the tICA and the LE4PD slow fluctuations in amino acids' position.

The Journal of chemical physics·2022

Same author

Comparison between slow anisotropic LE4PD fluctuations and the principal component analysis modes of ubiquitin.

The Journal of chemical physics·2021

Search research articles

Related Experiment Video

Updated: Mar 28, 2026

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

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

Published on: July 16, 2017

Predicting protein dynamics from structural ensembles.

J Copperman¹, M G Guenza²

¹Department of Physics, University of Oregon, Eugene, Oregon 97403, USA.

The Journal of Chemical Physics

|January 3, 2016

Summary

This summary is machine-generated.

We developed a simulation-free method to predict protein dynamics using known protein structures. This approach accurately models protein motion, offering a faster alternative to traditional simulations.

More Related Videos

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Related Experiment Videos

Last Updated: Mar 28, 2026

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

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

Published on: July 16, 2017

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Area of Science:

Biophysics
Computational Biology
Structural Biology

Background:

Protein biological functions are dictated by their complex structure and dynamics.
Proteins in solution exist as an ensemble of metastable configurations, exhibiting dynamics across vast timescales.

Purpose of the Study:

To introduce a novel simulation-free coarse-grained approach for predicting protein dynamics.
To leverage known metastable folded states for accurate protein dynamics prediction.

Main Methods:

The Langevin Equation for Protein Dynamics (LE4PD) formalism was employed.
LE4PD utilizes protein backbone coordinates and organizes fluctuations via linear modes.
Experimental NMR conformers served as input structural ensembles.

Main Results:

LE4PD accurately predicts protein dynamics, achieving a correlation coefficient ρ = 0.93 with NMR backbone relaxation measurements across seven proteins.
Predicted dynamics using experimental NMR conformers align with molecular dynamics simulations.
The method bypasses computationally intensive simulations.

Conclusions:

LE4PD offers a computationally efficient and accurate method for predicting protein dynamics.
The approach validates the utility of experimental NMR data for dynamics prediction.
This method advances our understanding of protein structure-function relationships.