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Related Experiment Video

Updated: Apr 15, 2026

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
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ASBench: benchmarking sets for allosteric discovery.

Wenkang Huang1, Guanqiao Wang1, Qiancheng Shen1

  • 1Department of Pathophysiology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.

Bioinformatics (Oxford, England)
|March 27, 2015
PubMed
Summary
This summary is machine-generated.

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Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
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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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Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
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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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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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Researchers developed benchmark datasets of experimentally determined allosteric sites. This data aids in creating computational tools for predicting allosteric sites and advancing allosteric drug design.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Pharmacology

Background:

  • Allosteric regulation fine-tunes protein function, making allosteric sites attractive drug targets.
  • Discovering allosteric sites is challenging, driving the need for robust computational methods.
  • High-quality, accessible data is crucial for developing and validating these computational tools.

Purpose of the Study:

  • To establish standardized benchmarking datasets of experimentally validated allosteric sites.
  • To facilitate the development of computational methods for predicting allosteric sites.
  • To support the discovery of novel allosteric ligand-protein interactions for drug design.

Main Methods:

  • Curated a 'Core set' of 235 unique allosteric sites.
  • Developed a 'Core-Diversity set' comprising 147 structurally diverse allosteric sites.

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  • Ensured all sites were experimentally determined.

    • Main Results:

    • Established two comprehensive benchmarking datasets for allosteric sites.
    • Provided a foundation for evaluating computational prediction methods.
    • Highlighted the importance of diverse structural data for robust benchmarking.

    Conclusions:

    • The presented benchmarking sets are essential resources for computational allosteric site prediction.
    • These datasets will accelerate the development of novel allosteric drugs.
    • Facilitates a deeper understanding of allosteric ligand-protein interactions.