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Related Concept Videos

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...
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...
Dose-Response Relationship: Selectivity and Specificity01:25

Dose-Response Relationship: Selectivity and Specificity

Drugs exert their therapeutic effects by interacting with receptors, enzymes, or ion channels that are present throughout the human body. The strength and duration of the interaction between a drug and its target receptor are characterized by the selectivity and specificity of the drug. Selectivity refers to a drug's strong preference for its intended target over other targets. For instance, isoprenaline, a non-selective β-adrenergic agonist, interacts with both β1- and β2-adrenergic receptors...
Drug-Receptor Interactions01:29

Drug-Receptor Interactions

Drug-receptor interaction describes the binding of receptors by drugs, but not all drug-receptor interactions result in activation and tissue response. For instance, the binding of agonists activates the receptor to generate a cellular reaction, while antagonists bind to receptors without causing their activation.
Several parameters, such as the drug's affinity for its receptor and its efficacy, which is its ability to activate the receptor, determine the drug's effect on the tissue.

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Related Experiment Video

Updated: Jun 17, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Competitively selected protein ligands pay their increase in specificity by a decrease in affinity.

Silke Hoffmann1, Susanne Aileen Funke, Katja Wiesehan

  • 1ISB-3, Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany.

Molecular Biosystems
|December 22, 2009
PubMed
Summary

Ligands with higher specificity for LckSH3 domains show reduced affinity but improved binding in competitive conditions. This specificity trade-off is beneficial in realistic cellular environments.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions
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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Protein-ligand interactions are crucial for cellular functions.
  • Protein specificity is determined by relative ligand affinities.
  • Optimizing ligands for specificity versus affinity is key.

Purpose of the Study:

  • Investigate ligands optimized for specificity over affinity.
  • Identify specific ligands for the LckSH3 domain.
  • Evaluate the impact of specificity on binding behavior.

Main Methods:

  • Modified phage display screening for ligand identification.
  • Surface plasmon resonance (SPR) for binding analysis.
  • Mathematical modeling of competitive binding.

Main Results:

  • Specific ligands for LckSH3 were identified.
  • Increased specificity led to reduced affinity for LckSH3 and other SH3 domains.
  • SPR experiments showed enhanced binding of specific ligands under competitive conditions.

Conclusions:

  • Enhanced specificity can be achieved at the cost of reduced affinity.
  • Increased specificity is advantageous under realistic, competitive binding conditions.
  • This study provides insights into ligand design for biological applications.