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 Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

4.6K
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...
4.6K
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

2.3K
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...
2.3K
Overview of Protein Sorting and Transport01:45

Overview of Protein Sorting and Transport

11.9K
Eukaryotic cells have different membrane-bound organelles with distinct protein requirements. The process by which proteins are targeted to a specific organelle is called protein sorting.
Protein sorting can be of two types: signal-based sorting and vesicle-based trafficking. In signal-based sorting, specific amino acid sequences called sorting signals target proteins to the proper location inside the cell either via gated transport or by protein translocation.  In gated transport, folded...
11.9K
ER Retrieval Pathway01:45

ER Retrieval Pathway

3.9K
In the secretory pathway, vesicles transport proteins from one cellular compartment to another in forward transport to deliver the protein to its correct location. Occasionally, misfolded proteins and incorrect proteins escape their original compartments, and a retrieval pathway is used to return the escaped proteins to their original compartment.
The ER uses many checkpoints to prevent the entry of incorrectly folded or a resident protein as cargo onto a transport vesicle. These mechanisms...
3.9K
Diffusion01:12

Diffusion

198.5K
Diffusion is the passive movement of substances down their concentration gradients—requiring no expenditure of cellular energy. Substances, such as molecules or ions, diffuse from an area of high concentration to an area of low concentration in the cytosol or across membranes. Eventually, the concentration will even out, with the substance moving randomly but causing no net change in concentration. Such a state is called dynamic equilibrium, which is essential for maintaining overall...
198.5K
Amyloid Fibrils03:03

Amyloid Fibrils

9.8K
Amyloid fibrils are aggregates of misfolded proteins.  Under most circumstances, misfolded proteins are either refolded by chaperone proteins or degraded by the proteasome. However, in the case of a mutation or a disease, these proteins can accumulate to form large clusters and often further assemble to form elongated fibers, called fibrils. 
Amyloid deposits were observed as early as 1639 in the liver and the spleen.   In 1854, Rudolph Virchow performed iodine staining,...
9.8K

You might also read

Related Articles

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

Sort by
Same author

Rotational memory function of SPC/E water.

The Journal of chemical physics·2026
Same author

Dynamics of low-temperature water are driven by electrostatics.

The Journal of chemical physics·2026
Same author

Protein Electron Transfer in Solution, Protein Powders, and Electrode Confinement.

ACS omega·2026
Same author

Photosynthetic Reaction Center: A Nonergodic, Dynamically Anisotropic, and Nonlinear Charge-Transport Engine.

The journal of physical chemistry letters·2025
Same author

Aqueous Ion Mobility over a Broad Concentration Range.

Physical review letters·2025
Same author

Correction to "Remarkable Insensitivity of Protein Diffusion to Protein Charge".

The journal of physical chemistry letters·2025
Same journal

Revisiting crossed-correlated baths in open quantum systems simulated by HEOM or T-TEDOPA.

The Journal of chemical physics·2026
Same journal

Vesicle size and membrane composition control monomer transfer pathways in multicomponent lipid vesicles.

The Journal of chemical physics·2026
Same journal

Polaron-mediated exciton dynamics of P(NDI2OD-T2) unveiled by transient absorption spectroscopy under electrochemical conditions.

The Journal of chemical physics·2026
Same journal

Green-Kubo relation in a mesoscale odd fluid model.

The Journal of chemical physics·2026
Same journal

Nitrogenation of microscopic MoS2 surfaces by oxidation scanning probe lithography.

The Journal of chemical physics·2026
Same journal

Molecular structure, binding, and disorder in TDBC-Ag plexcitonic assemblies.

The Journal of chemical physics·2026
See all related articles

Related Experiment Video

Updated: Sep 9, 2025

Image Processing Protocol for the Analysis of the Diffusion and Cluster Size of Membrane Receptors by Fluorescence Microscopy
12:15

Image Processing Protocol for the Analysis of the Diffusion and Cluster Size of Membrane Receptors by Fluorescence Microscopy

Published on: April 9, 2019

8.8K

Memory function for protein diffusion.

Setare Mostajabi Sarhangi1, Dmitry V Matyushov2

  • 1Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, USA.

The Journal of Chemical Physics
|September 2, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces a new "force route" to calculate diffusion constants in simulations, offering a more accurate method than standard displacement or velocity approaches. This new method shows less dependence on system size, improving protein diffusion analysis.

More Related Videos

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions
14:43

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

Published on: August 27, 2014

11.7K
Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules
10:20

Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules

Published on: September 5, 2019

8.3K

Related Experiment Videos

Last Updated: Sep 9, 2025

Image Processing Protocol for the Analysis of the Diffusion and Cluster Size of Membrane Receptors by Fluorescence Microscopy
12:15

Image Processing Protocol for the Analysis of the Diffusion and Cluster Size of Membrane Receptors by Fluorescence Microscopy

Published on: April 9, 2019

8.8K
Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions
14:43

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

Published on: August 27, 2014

11.7K
Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules
10:20

Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules

Published on: September 5, 2019

8.3K

Area of Science:

  • Computational physics
  • Biophysics
  • Physical chemistry

Background:

  • Standard diffusion constant calculations rely on mean-squared displacement or velocity autocorrelation functions.
  • These methods do not account for the physical nature of the random forces involved.
  • The force route, utilizing the Kirkwood equation, addresses this limitation for diffusive particles.

Purpose of the Study:

  • To formulate and validate the force route for calculating diffusion constants in molecular dynamics (MD) simulations.
  • To compare the accuracy and system-size dependence of the force route against traditional methods.
  • To investigate protein diffusion using MD simulations of green fluorescent protein and plastocyanin mutants.

Main Methods:

  • Molecular dynamics (MD) simulations of six charge mutants of green fluorescent protein and plastocyanin.
  • Calculation of memory functions to determine memory time.
  • Application of the Kirkwood equation using the force route and comparison with velocity/displacement routes.
  • Analysis of system-size effects on diffusion constant calculations.

Main Results:

  • The force route, using memory time, provides a more accurate calculation of the diffusion constant compared to standard methods.
  • The Kirkwood equation, when applied via the force route, overestimates protein diffusion constants by approximately a factor of four.
  • Diffusion constants calculated via velocity/displacement routes exhibit strong system-size dependence, with standard corrections showing significant flaws for protein diffusion.
  • Diffusion constants derived from the force route demonstrate minimal system-size dependence, yielding corrected values largely independent of system size.

Conclusions:

  • The force route offers a more robust and accurate method for calculating diffusion constants, particularly for proteins, by accounting for the physical nature of forces.
  • Traditional methods for calculating diffusion constants and correcting for finite-size effects are inadequate for protein diffusion.
  • The force route's reduced system-size dependence makes it a superior approach for accurate diffusion analysis in complex biological systems.