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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

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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...
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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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Ligand-gated ion channels are transmembrane proteins with a channel for ions to pass through and a binding site for a ligand. The channel opens only when a ligand attaches to the binding site.
Three Subfamilies of Ligand-gated Ion Channels
Ligand-gated ion channels fall into three subfamilies. The 'Cys-loop' includes the nicotinic acetylcholine receptors, γ-aminobutyric acid (GABA), glycine, and 5-hydroxytryptamine receptors. The second one is the 'Pore-loop' channels that...
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The Equilibrium Binding Constant and Binding Strength02:18

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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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Recognizing and validating ligands with CheckMyBlob.

Dariusz Brzezinski1,2,3, Przemyslaw J Porebski1, Marcin Kowiel3

  • 1Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.

Nucleic Acids Research
|April 27, 2021
PubMed
Summary
This summary is machine-generated.

CheckMyBlob is a new web server that uses machine learning to identify potential drug ligands in protein structures. This tool helps researchers accurately interpret electron density maps, reducing bias in structure-guided drug design.

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Area of Science:

  • Structural biology
  • Computational chemistry
  • Drug discovery

Background:

  • Accurate ligand identification in protein crystal structures is crucial for structure-guided drug design.
  • Interpreting electron density maps can be challenging and prone to confirmation bias.

Purpose of the Study:

  • To present the CheckMyBlob web server, a novel platform for identifying and validating ligands in protein electron density maps.
  • To provide an automated solution to aid researchers in ligand identification and model validation.

Main Methods:

  • Utilized a machine learning algorithm (CheckMyBlob) trained on moiety data from the Protein Data Bank.
  • Developed a web server processing PDB/mmCIF and MTZ files.
  • Integrated interactive 3D visualizations and Coot plugin scripts for detailed analysis.

Main Results:

  • The CheckMyBlob web server successfully identifies ligands in unmodeled electron density fragments.
  • It provides a ranked list of the top 10 most probable ligands for each detected density blob.
  • The server validates ligands in existing structural models and generates analysis scripts.

Conclusions:

  • CheckMyBlob offers an automated, reliable method to assist in ligand identification and validation for structural biology.
  • The web server enhances the accuracy and efficiency of structure-guided drug design by mitigating interpretation bias.
  • The tool is publicly accessible, promoting reproducibility and broader application in the field.