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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.
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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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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...
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Small-molecule binding-site discovery using silyl ether-enabled chemoproteomics.

Chau Ngo1,2, Sho Takechi3,4,5, Aditya Sivakumar1,2

  • 1Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.

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Summary

Chemoproteomics combined with photoaffinity labeling aids drug discovery. A new method, SEE-CITE, precisely identifies drug binding sites on proteins, revealing new therapeutic targets.

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Area of Science:

  • Chemical Biology
  • Proteomics
  • Drug Discovery

Background:

  • Mass spectrometry-based chemoproteomics and photoaffinity labeling are key for target discovery.
  • Photocrosslinked peptide-compound adducts present analytical challenges for quantitative binding site identification.

Purpose of the Study:

  • To develop a method for precise identification of drug binding sites.
  • To enable quantitative comparisons of compound engagement at specific protein sites.

Main Methods:

  • Introduction of the Silyl Ether Enables Chemoproteomic Interaction and Target Engagement (SEE-CITE) method.
  • Incorporation of a chemically cleavable photocrosslinking handle for precise labeling.
  • Extension of the MSFragger algorithm for high-confidence localization scoring.

Main Results:

  • SEE-CITE enables precise site-of-labeling identification.
  • The method allows head-to-head comparisons of binding site engagement by diverse compounds.
  • Application to kinase inhibitors delineated known sites and uncovered novel binding sites on RTN4 and COX5A.

Conclusions:

  • SEE-CITE addresses analytical challenges in chemoproteomics for drug discovery.
  • The method accurately identifies known and novel small-molecule binding sites.
  • SEE-CITE enhances target discovery and mode of action studies in chemical biology.