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

Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

2.4K
2.4K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

5.0K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
5.0K
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

5.9K
Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
5.9K
Amplifying Signals via Second Messengers01:15

Amplifying Signals via Second Messengers

7.3K
Many receptor binding ligands are hydrophilic; they do not cross the cell membrane but bind to cell-surface receptors. Thus, their message must be relayed by second messengers present in the cell cytoplasm. There are several second messenger pathways, each with its own way of relaying information. For example, the G protein-coupled receptors can activate both phosphoinositol and cyclic AMP (cAMP) second messenger pathways. The phosphoinositol pathway is active when the receptor induces...
7.3K
Types of Signaling Molecules01:32

Types of Signaling Molecules

11.0K
In multicellular organisms, many molecules transmit signals between cells to pass information. These signals vary in complexity and include small peptides, nucleotides, steroids, fatty acid derivatives, and dissolved gases such as nitric oxide. Some signaling molecules diffuse through the plasma membrane to act locally between neighboring cells or travel long distances. Others remain attached to the cell surface, transmitting information to other cells only when they make contact. In some...
11.0K
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

6.6K
Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
6.6K

You might also read

Related Articles

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

Sort by
Same author

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026
Same author

Rapid and interpretable protein contact map prediction using a pattern-matching strategy.

Physical biology·2026
Same author

The Gaussian network model as a framework for allosteric analysis: dynamic distance, edge centrality, and entropy sensitivity in KRAS.

Physical biology·2026
Same author

Author Correction: Computational design of synthetic receptors with programmable signalling activity for enhanced cancer T cell therapy.

Nature biomedical engineering·2025
Same author

Extending the Gaussian network model: integrating local, allosteric, and structural factors for improved residue-residue correlation analysis.

Physical biology·2025
Same author

Computational design of synthetic receptors with programmable signalling activity for enhanced cancer T cell therapy.

Nature biomedical engineering·2025
Same journal

Metastable excited states of iodide-alkyl halide cluster anions: Insights from photodetachment spectroscopy and non-Hermitian quantum chemistry.

The Journal of chemical physics·2026
Same journal

Pressure-induced thermal expansion anomalies in dhcp iron hydride associated with magnetoelastic coupling.

The Journal of chemical physics·2026
Same journal

Seniority eigenstate configuration interaction.

The Journal of chemical physics·2026
Same journal

A data-driven modeling study on the accurate identification of Doppler-free saturated absorption spectra in diatomic tellurium (130Te2).

The Journal of chemical physics·2026
Same journal

Anharmonic phonons via quantum thermal bath simulations.

The Journal of chemical physics·2026
Same journal

Quantum simulation of alignment dependent differential cross sections in co-propagating molecular beams at cold collision energies.

The Journal of chemical physics·2026
See all related articles

Related Experiment Video

Updated: Sep 23, 2025

Bio-layer Interferometry for Measuring Kinetics of Protein-protein Interactions and Allosteric Ligand Effects
13:57

Bio-layer Interferometry for Measuring Kinetics of Protein-protein Interactions and Allosteric Ligand Effects

Published on: February 18, 2014

29.6K

Information flow and allosteric communication in proteins.

Aysima Hacisuleyman1, Burak Erman2

  • 1Institute of Bioengineering, Swiss Federal Institute of Technology (EPFL), 1015 Lausanne, Switzerland.

The Journal of Chemical Physics
|May 14, 2022
PubMed
Summary
This summary is machine-generated.

A new molecular theory quantifies nonlinear information transfer between protein residues. This approach reveals communication pathways and transfer rates crucial for understanding protein allostery.

More Related Videos

Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation
08:00

Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation

Published on: October 4, 2024

715
Enzymatic Modification and Flow Cytometry Assessment of Yeast Surface Displayed Proteins
10:54

Enzymatic Modification and Flow Cytometry Assessment of Yeast Surface Displayed Proteins

Published on: May 30, 2025

403

Related Experiment Videos

Last Updated: Sep 23, 2025

Bio-layer Interferometry for Measuring Kinetics of Protein-protein Interactions and Allosteric Ligand Effects
13:57

Bio-layer Interferometry for Measuring Kinetics of Protein-protein Interactions and Allosteric Ligand Effects

Published on: February 18, 2014

29.6K
Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation
08:00

Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation

Published on: October 4, 2024

715
Enzymatic Modification and Flow Cytometry Assessment of Yeast Surface Displayed Proteins
10:54

Enzymatic Modification and Flow Cytometry Assessment of Yeast Surface Displayed Proteins

Published on: May 30, 2025

403

Area of Science:

  • Biophysics
  • Computational Biology
  • Biochemistry

Background:

  • Mutual information quantifies maximum information transfer between protein residues but not the actual amount or rate.
  • Understanding allosteric activity in proteins requires knowledge of information transfer dynamics between residue pairs.

Purpose of the Study:

  • Develop a molecular theory for nonlinear information transfer between protein residue pairs.
  • Quantify the amount and speed of information transfer relevant to protein allostery.

Main Methods:

  • Developed a molecular theory based on transfer entropy and Schreiber's work.
  • Utilized tensor Hermite polynomials to model joint distribution functions of residue fluctuations.
  • Solved the Langevin equation and employed molecular dynamics trajectories to analyze information transfer.
  • Applied the theory to study allosteric communication in human NAD-dependent isocitrate dehydrogenase.

Main Results:

  • Identified collective information transfer paths and key residues in human NAD-dependent isocitrate dehydrogenase.
  • Estimated time-resolved information transfer, amplitudes, and rates (1-20 megabits per second).
  • Calculated peak information transfer values (∼0.01-0.04 bits) comparable to mutual information.
  • Found third-order nonlinear contributions to be significantly smaller than harmonic terms.

Conclusions:

  • The developed molecular theory accurately estimates information transfer dynamics between protein residues.
  • Harmonic analysis provides a good approximation for information transfer in proteins.
  • The findings offer insights into the mechanisms of allosteric communication in proteins.