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

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:

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Protein Target Prediction and Validation of Small Molecule Compound
10:21

Protein Target Prediction and Validation of Small Molecule Compound

Published on: February 23, 2024

Correlation between protein function and ligand binding profiles.

Matthew D Shortridge1, Michael Bokemper, Jennifer C Copeland

  • 1Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States.

Journal of Proteome Research
|March 4, 2011
PubMed
Summary
This summary is machine-generated.

Proteins with similar functions bind the same small molecules. This discovery enables a new method for protein functional analysis using ligand binding profiles, aiding in the annotation of novel genes.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Last Updated: Jun 4, 2026

Protein Target Prediction and Validation of Small Molecule Compound
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Published on: February 23, 2024

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Biochemistry
  • Proteomics
  • Chemical Biology

Background:

  • Understanding protein function is crucial for biological research and drug discovery.
  • Current methods for functional annotation often rely on sequence, structure, or evolutionary data, which can be limiting for novel or uncharacterized proteins.

Purpose of the Study:

  • To develop a novel, rapid, and adaptable method for protein functional analysis based on small molecule binding profiles.
  • To demonstrate the utility of this method in distinguishing proteins of similar and different functions.

Main Methods:

  • Utilized a high-throughput Nuclear Magnetic Resonance (NMR) ligand affinity screen.
  • Employed a standardized, structurally diverse chemical library to measure ligand binding.
  • Applied the method to a set of 19 proteins with varying known functions.

Main Results:

  • Identified statistically significant similarities in ligand binding profiles exclusively between functionally identical albumins.
  • Observed significant ligand binding profile similarities among five functionally related amylases.
  • Demonstrated that the method is independent of protein sequence, structure, or evolutionary information.

Conclusions:

  • Protein functional similarity correlates with shared small molecule binding preferences.
  • The developed ligand binding profiling method offers a powerful, sequence- and structure-independent approach for protein functional analysis and annotation.
  • This technique has the potential to significantly enhance the functional characterization of novel genes and proteins.