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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Ligand Binding Sites02:40

Ligand Binding Sites

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...
Ligand Binding Sites02:40

Ligand Binding Sites

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...
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...
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...

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Updated: Jun 1, 2026

An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions
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An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions

Published on: March 14, 2016

Helix-helix interfaces and ligand binding.

Natalya Kurochkina1, Tsering Choekyi

  • 1The School of Theoretical Modeling, Department of Biophysics, PO Box 15676, Chevy Chase, MD 20825, USA. info@schtm.org

Journal of Theoretical Biology
|May 31, 2011
PubMed
Summary

Specific amino acid patterns at core positions of helix-helix interfaces predict protein interhelical angles. This method accurately predicted angles in glutathione S-transferase, chloride channel, and annexin proteins.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Protein Science

Background:

  • Helix-helix interfaces are crucial for protein structure and function.
  • Specific amino acid residues at positions 'a' and 'd' (leucine zipper nomenclature) are known to be conserved in these interfaces.
  • These conserved residues are thought to influence the angle between parallel helices.

Purpose of the Study:

  • To investigate the role of specific amino acid combinations in characterizing parallel helix-helix interfaces.
  • To develop a predictive model for interhelical angles based on these amino acid patterns.
  • To explore the correlation between interhelical angles and ligand conformation in glutathione S-transferase.

Main Methods:

  • Analysis of amino acid sequences at core positions 'a' and 'd' in various protein families.
  • Application of identified amino acid patterns to predict interhelical angles.
  • Experimental validation of predicted angles in glutathione S-transferase, intracellular chloride channel, and annexin proteins.
  • Conformational analysis of glutathione S-transferase ligands.

Main Results:

  • Consistent amino acid combinations were identified at core positions 'a' and 'd' across homologous and nonhomologous proteins.
  • The developed method achieved high accuracy (58 out of 62 proteins) in predicting interhelical angles.
  • A significant correlation was observed between interhelical angles and the conformation of glutathione S-transferase ligands, including glutathione, s-hexylglutathione, glutathione sulfonic acid, and glutathione-s-dinitrobenzene.

Conclusions:

  • Amino acid patterns at helix-helix interfaces serve as reliable markers for predicting interhelical angles.
  • This predictive capability has implications for understanding protein structure and function.
  • The findings suggest a link between protein structure, ligand binding, and the conformational states of ligands in glutathione S-transferase.