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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...
Ligand Binding and Linkage00:49

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 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...

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Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules
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Allosteric coupling and conformational fluctuations in proteins.

H Ongun Onaran1, Tommaso Costa

  • 1Ankara University Faculty of Medicine, Department of Pharmacology and Clinical Pharmacology, Molecular Biology and Technology Development Unit, Ankara, Turkey. onaran@medicine.ankara.edu.tr

Current Protein & Peptide Science
|April 10, 2009
PubMed
Summary

Ligand binding perturbs protein fluctuations, inevitably causing allosteric coupling. A COREX-based strategy links structural changes to allosteric free energy, aiding prediction of ligand-regulated protein function.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Proteins exhibit conformational fluctuations and multiple energy minima at physiological temperatures.
  • Allosteric coupling describes how ligand binding at one site affects binding at another site on the same protein.

Purpose of the Study:

  • To quantitatively relate ligand-induced perturbations of protein conformational fluctuations to allosteric coupling.
  • To propose a computational strategy for predicting allosteric regulation of protein function.

Main Methods:

  • Modeling protein conformational fluctuations as probability distributions of substates.
  • Utilizing the COREX algorithm to bridge protein ensemble energetics and structural coordinates.
  • Developing a COREX-based approach to link structural perturbations with allosteric free energy changes.

Main Results:

  • Allosteric coupling is an inevitable consequence of ligand-induced alterations in protein conformational substate distributions.
  • The COREX algorithm can connect substate energetics to structural data.
  • A novel strategy is proposed to link structural changes to allosteric free energy.

Conclusions:

  • Ligand binding fundamentally influences protein dynamics, leading to allosteric effects.
  • The proposed COREX-based strategy offers a framework for predicting allosteric regulation.
  • This approach has broad utility in understanding and predicting how ligands modulate protein function.