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Cooperative Allosteric Transitions

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 Transitions

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Allosteric Regulation

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...

Ligand Binding and Linkage

Ligand Binding and Linkage

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...

Ligand Binding and Linkage

Ligand Binding and Linkage

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Related Experiment Video

Updated: Jan 7, 2026

Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation

Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation

Published on: October 4, 2024

Loop Modulates Long-Range Allosteric Communications in a Knotted Protein.

Sanjib Thakuria¹, Sandip Paul¹

¹Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India.

The Journal of Physical Chemistry. B

|December 26, 2025

Summary

This summary is machine-generated.

Protein knots, like the trefoil knot in AOTCase, can regulate communication pathways. Mutating a key residue disrupted these allosteric networks, revealing knots

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Light-mediated Reversible Modulation of the Mitogen-activated Protein Kinase Pathway during Cell Differentiation and Xenopus Embryonic Development

Light-mediated Reversible Modulation of the Mitogen-activated Protein Kinase Pathway during Cell Differentiation and Xenopus Embryonic Development

Published on: June 15, 2017

Area of Science:

Biochemistry and Molecular Biology
Structural Biology
Computational Biology

Background:

Protein knots are topological structures with unclear biological roles, potentially influencing stability, catalysis, or dynamics.
N-acetyl-l-ornithine transcarbamoylase (AOTCase) contains a trefoil knot, with a specific loop and residue (N183) implicated in allosteric regulation.

Purpose of the Study:

To investigate the role of the trefoil knot in AOTCase, particularly the knotted loop and residue N183, in mediating long-range allosteric communication to the active site.
To understand how mutations affect the allosteric network and protein dynamics.

Main Methods:

Classical molecular dynamics simulations.
Network-based correlation analysis.
Mutagenesis studies (N183A).
Free energy surface calculations.
Principal component analysis.
Contact-based analysis.

Main Results:

The ligand-bound state exhibits redundant communication routes through the knotted loop, which are absent in the apo state.
Mutation N183A disrupted the allosteric network, shortening pathways and shifting communication hubs away from the knotted loop.
Mutated proteins showed increased conformational restrictions and a tightened knotted loop and thread gap.

Conclusions:

The knotted loop in AOTCase not only provides structural shielding but also actively modulates allosteric networks.
Residue N183 serves as a tunable node controlling these allosteric pathways.
This study elucidates the functional significance of protein knots in biological regulation.