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Related Concept Videos

Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Allosteric Regulation01:08

Allosteric Regulation

Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
Allosteric Regulation01:08

Allosteric Regulation

Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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Related Experiment Video

Updated: Jun 4, 2026

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

Modeling allosteric signal propagation using protein structure networks.

Keunwan Park1, Dongsup Kim

  • 1Department of Bio and Brain Engineering, KAIST, S Korea.

BMC Bioinformatics
|February 24, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a new method using protein structure networks and Markov random walks to map allosteric signaling pathways. High expected visiting time (EVT) values identify key residues crucial for protein communication.

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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Related Experiment Videos

Last Updated: Jun 4, 2026

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

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
07:57

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Allosteric communication is vital for protein regulation, but identifying affected remote sites and transmission pathways remains challenging.
  • Understanding how perturbations propagate through protein structures is key to deciphering allosteric mechanisms.

Purpose of the Study:

  • To develop a novel computational method for estimating signal propagation and effects in proteins.
  • To identify key residues involved in allosteric signaling pathways.

Main Methods:

  • Constructed protein structure networks.
  • Modeled signal transmission using a Markov random walk.
  • Estimated global perturbation effects via Expected Visiting Time (EVT).

Main Results:

  • Developed a method to estimate signal propagation and identify residues with high EVT values.
  • Validated the model using experimental data on two protein structures.
  • Found that protein binding interface hot spots exhibit high EVT values, indicating their role in signal mediation.

Conclusions:

  • The EVT method effectively identifies critical residues in allosteric signaling.
  • High EVT residues are important for mediating signal communication between protein domains.
  • This approach enhances understanding of protein allosteric regulation and function.