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Related Concept Videos

Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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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...
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The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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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...
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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Pull-down of Calmodulin-binding Proteins
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Single Binding Pockets Versus Allosteric Binding.

Kun Song1, Jian Zhang2

  • 1Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.

Methods in Molecular Biology (Clifton, N.J.)
|October 19, 2018
PubMed
Summary
This summary is machine-generated.

This chapter explores allosteric sites, distinct from orthosteric sites, as regulatory targets on proteins. Allosteric modulators offer a promising drug design strategy by modulating protein function.

Keywords:
Allosteric siteAllosteryComputational methodsDrug designOrthosteric site

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Area of Science:

  • Biochemistry
  • Pharmacology
  • Structural Biology

Background:

  • Orthosteric sites are primary binding pockets for endogenous ligands, crucial for biological function.
  • Malfunctioning active sites are implicated in various diseases, including metabolic and neurological disorders.
  • Competitive inhibitors targeting orthosteric sites can block receptor function.

Purpose of the Study:

  • To introduce allosteric sites as distinct regulatory regions on protein surfaces.
  • To explain the mechanism of allosteric modulation via allosteric ligands.
  • To present tools and protocols for allosteric site analysis and drug design.

Main Methods:

  • Analysis of allosteric site characteristics and interactions.
  • Design strategies for allosteric ligands.
  • Computational and experimental techniques for studying allosteric regulation.

Main Results:

  • Allosteric sites offer a distinct regulatory mechanism compared to orthosteric sites.
  • Allosteric modulators can potentiate or inhibit protein function, providing therapeutic advantages.
  • Identification and characterization of allosteric sites are key for novel drug discovery.

Conclusions:

  • Allosteric regulation presents a promising avenue for developing targeted therapies.
  • Understanding allosteric mechanisms is crucial for advancing drug design.
  • This chapter provides a framework for exploring and exploiting allosteric sites.