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Spare Receptors

Spare Receptors

Some receptors remain unoccupied even when an agonist produces a maximal response. Such empty ones are called spare receptors. In presence of spare receptors the maximum effect of an agonist drug is achieved with fewer than 100% of the receptors being occupied. To determine the presence of spare receptors, scientists often compare the concentration of the drug needed to produce 50% of the maximum effect (EC50) with the concentration of the drug needed to occupy 50% of the receptors (Kd). If the...

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 the...

Conserved Binding Sites

Conserved Binding Sites

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 analyses the...

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

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:

Protein-protein Interfaces

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...

Drug-Receptor Bonds

Drug-Receptor Bonds

Drug-receptor bonds are formed through various chemical forces when drugs interact with target cells. Covalent bonds, strong and irreversible, are exemplified by DNA-alkylating anticancer agents that inhibit cell division. However, such irreversible drug binding lacks selectivity and can modify the DNA of the surrounding healthy cells. Covalent binding often contributes to tissue toxicity, as seen with chloroform and paracetamol metabolites binding to the liver, causing hepatotoxicity.
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Related Experiment Video

Updated: Jun 21, 2026

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Published on: December 6, 2017

High affinity extremes in combinatorial libraries and repertoires.

Mark M Tanaka¹, Scott A Sisson, Garry C King

¹Evolution & Ecology Research Centre, University of New South Wales, Kensington NSW 2052, Australia. m.tanaka@unsw.edu.au

Journal of Theoretical Biology

|August 12, 2009

Summary

This summary is machine-generated.

The maximum antibody affinity in large molecular libraries increases with library size. This study models affinity properties, showing logarithmic growth with library size, aiding future molecular design.

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Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

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Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

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Extracellular Protein Microarray Technology for High Throughput Detection of Low Affinity Receptor-Ligand Interactions

Extracellular Protein Microarray Technology for High Throughput Detection of Low Affinity Receptor-Ligand Interactions

Published on: January 7, 2019

Area of Science:

Biotechnology
Immunology
Computational Biology

Background:

The immune system generates diverse antibodies for antigen binding.
Combinatorial biotechnology screens large compound libraries for high-affinity molecules.
Understanding extreme affinities is crucial for optimizing library design.

Purpose of the Study:

To investigate how maximum molecular affinity scales with library size.
To model the properties of extreme affinities in large molecular libraries.
To provide insights for designing more effective combinatorial libraries.

Main Methods:

Developed two models for extreme affinity properties: lognormal distribution and target sequence matching.
Applied extreme value theory to analyze affinity distributions.
Modeled nucleic acids (DNA/RNA) and proteins like antibodies.

Main Results:

The logarithm of the mean highest affinity grows linearly with the square root of the log of library size.
An absolute maximum affinity is approached linearly with root log library size.
This upper limit is reached abruptly as library size increases.

Conclusions:

The scaling relationship between library size and maximum affinity provides a predictive framework.
Library design can be informed by understanding how maximum affinity plateaus with increasing size.
These findings are applicable to antibody engineering and drug discovery.