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

Entropy within the Cell01:22

Entropy within the Cell

12.5K
A living cell's primary tasks of obtaining, transforming, and using energy to do work may seem simple. However, the second law of thermodynamics explains why these tasks are harder than they appear. None of the energy transfers in the universe are completely efficient. In every energy transfer, some amount of energy is lost in a form that is unusable. In most cases, this form is heat energy. Thermodynamically, heat energy is defined as the energy transferred from one system to another that...
12.5K
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

2.5K
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...
2.5K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

13.8K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
13.8K
Entropy and Solvation02:05

Entropy and Solvation

8.0K
The process of surrounding a solute with solvent is called solvation. It involves evenly distributing the solute within the solvent. The rule of thumb for determining a solvent for a given compound is that like dissolves like. A good solvent has molecular characteristics similar to those of the compound to be dissolved. For example, polar solutions dissolve polar solutes, and apolar solvents dissolve apolar solutes. A polar solvent is a solvent that has a high dielectric constant (ϵ...
8.0K
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

19.0K
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
19.0K
Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

5.3K
Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
5.3K

You might also read

Related Articles

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

Sort by
Same author

Evergene: an interactive webtool for large-scale gene-centric analysis of primary tumours.

Bioinformatics advances·2024
Same author

Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules.

Journal of chemical information and modeling·2024
Same author

Energy-entropy multiscale cell correlation method to predict toluene-water log <i>P</i> in the SAMPL9 challenge.

Physical chemistry chemical physics : PCCP·2023
Same author

pyCHARMM: Embedding CHARMM Functionality in a Python Framework.

Journal of chemical theory and computation·2023
Same author

Local CpG density affects the trajectory and variance of age-associated DNA methylation changes.

Genome biology·2022
Same author

Free Gangliosides Can Alter Amyloid-β Aggregation.

The journal of physical chemistry letters·2022
Same journal

tmGNN-XAI: An Explainable Graph Neural Network Tool for Predicting Electronic Properties of Transition Metal Complexes from SMILES.

Journal of chemical information and modeling·2026
Same journal

QSAR in the Browser: An Interactive Cheminformatics Web Application.

Journal of chemical information and modeling·2026
Same journal

FoldDoF: Utilizing the Primary Degrees of Freedom of Protein Backbone for Geometric Modeling and Generation.

Journal of chemical information and modeling·2026
Same journal

Derisking Affinity Optimization for Macrocycles and Cyclic Peptides: High-Precision Free Energy Simulations across Five Diverse Targets.

Journal of chemical information and modeling·2026
Same journal

An End-User Audit of Reproducibility, Data Leakage, and Overfitting of the Top-Ranked ADMET Prediction Models in TDC Leaderboards.

Journal of chemical information and modeling·2026
Same journal

PFASGroups: An Open-Source Framework for Automated Identification, Structural Classification, and Prioritization of Per- and Polyfluoroalkyl Substances.

Journal of chemical information and modeling·2026
See all related articles

Related Experiment Video

Updated: Dec 8, 2025

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

2.4K

Entropy of Proteins Using Multiscale Cell Correlation.

Arghya Chakravorty1, Jonathan Higham2, Richard H Henchman3,4

  • 1Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.

Journal of Chemical Information and Modeling
|September 21, 2020
PubMed
Summary
This summary is machine-generated.

A new Multiscale Cell Correlation (MCC) method efficiently calculates protein entropy from molecular dynamics simulations. This approach offers faster convergence and detailed insights into entropy contributions at various scales.

More Related Videos

Detection of Protein Aggregation using Fluorescence Correlation Spectroscopy
14:04

Detection of Protein Aggregation using Fluorescence Correlation Spectroscopy

Published on: April 25, 2021

5.9K
Dual-Color Fluorescence Cross-Correlation Spectroscopy to Study Protein-Protein Interaction and Protein Dynamics in Live Cells
14:12

Dual-Color Fluorescence Cross-Correlation Spectroscopy to Study Protein-Protein Interaction and Protein Dynamics in Live Cells

Published on: December 11, 2021

5.8K

Related Experiment Videos

Last Updated: Dec 8, 2025

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

2.4K
Detection of Protein Aggregation using Fluorescence Correlation Spectroscopy
14:04

Detection of Protein Aggregation using Fluorescence Correlation Spectroscopy

Published on: April 25, 2021

5.9K
Dual-Color Fluorescence Cross-Correlation Spectroscopy to Study Protein-Protein Interaction and Protein Dynamics in Live Cells
14:12

Dual-Color Fluorescence Cross-Correlation Spectroscopy to Study Protein-Protein Interaction and Protein Dynamics in Live Cells

Published on: December 11, 2021

5.8K

Area of Science:

  • Computational Biology
  • Biophysics
  • Protein Dynamics

Background:

  • Calculating protein entropy is crucial for understanding molecular behavior.
  • Existing methods like normal-mode and quasiharmonic analysis have limitations in speed and detail.

Purpose of the Study:

  • Introduce a novel multiscale method for protein entropy calculation.
  • Improve efficiency and provide deeper insights into entropy contributions.

Main Methods:

  • Developed the Multiscale Cell Correlation (MCC) method.
  • Decomposed proteins into hierarchical rigid-body units (molecule, residue, united atom).
  • Evaluated vibrational and topographical entropy using forces, torques, and dihedrals, considering inter-unit correlations.

Main Results:

  • MCC results closely align with normal-mode analysis.
  • Achieved faster convergence compared to quasiharmonic analysis.
  • Provided detailed entropy decomposition by length scale, amino acid type, and solvent exposure.

Conclusions:

  • MCC is an efficient and accurate method for protein entropy calculation.
  • Offers valuable insights into how amino acid properties influence entropy.
  • The method reveals nuanced relationships between solvent exposure, amino acid polarity, and conformational/vibrational entropy.