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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...
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

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 pathway,...

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Related Experiment Video

Updated: Jun 6, 2026

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

Measuring Differences in Protein Allosteric Graphs Constructed via Molecular Dynamics Simulations.

Jiale Shi1, Zhongyi Wan1, Renjie Zhu1

  • 1Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.

Journal of Chemical Theory and Computation
|June 4, 2026
PubMed
Summary
This summary is machine-generated.

We developed a new method to quantitatively compare protein allostery networks. This approach reveals how mutations impact protein communication, aiding protein engineering and function studies.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation
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Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation

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Related Experiment Videos

Last Updated: Jun 6, 2026

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

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

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

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Protein allostery is crucial for biological processes, involving long-range communication.
  • Three-dimensional Shortest Path Map (3D SPM) graphs represent protein dynamics and allosteric pathways.
  • Quantitative comparison of 3D SPM graphs has been limited.

Purpose of the Study:

  • To develop a quantitative algorithm for comparing 3D SPM graphs.
  • To assess the sensitivity of allosteric networks to computational parameters.
  • To distinguish mutations affecting allosteric communication.

Main Methods:

  • Utilized Earth Mover's Distance (EMD) and normalized graph Laplacian for quantitative comparison.
  • Evaluated spatial distributions and network connectivity of 3D SPM graphs.
  • Decomposed EMD to identify key residues and edges influencing communication shifts.

Main Results:

  • Established a quantitative method to measure distances between 3D SPM graphs.
  • Demonstrated sensitivity of allosteric networks to force fields and parameters.
  • Successfully differentiated mutations based on their impact on allosteric communication networks.
  • Identified specific residues and network edges critical for communication changes.

Conclusions:

  • The developed algorithm provides quantitative insights into protein allostery.
  • Enables precise analysis of mutation effects on protein communication pathways.
  • Facilitates high-throughput analysis for protein function, evolution, and engineering.