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Related Concept Videos

Conserved Binding Sites01:49

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...
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...

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Related Experiment Video

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Covalent Fragment Screening Using the Quantitative Irreversible Tethering Assay
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Identifying ligand-binding hot spots in proteins using brominated fragments.

Morten K Grøftehauge1, Martin Ø Therkelsen, Rolf Taaning

  • 1Department of Chemistry, Durham University, South Road, Durham DH1 3LE, England. m.k.groftehauge@dur.ac.uk

Acta Crystallographica. Section F, Structural Biology and Crystallization Communications
|August 31, 2013
PubMed
Summary

Researchers identified a small molecule binding to the tRNA CCA-end pocket of Thermus thermophilus EF-Tu using fragment screening. This finding enhances understanding of drug binding and biological function in structural contexts.

Keywords:
EF-Tubrominated fragmentsligand binding

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Area of Science:

  • Structural biology
  • Biochemistry
  • Drug discovery

Background:

  • High-quality crystals of Thermus thermophilus EF-Tu in the GTP-bound conformation were obtained.
  • Fragment screening is a common method for identifying small molecules that bind to proteins.

Purpose of the Study:

  • To identify small molecules that bind to the tRNA CCA-end binding pocket of Thermus thermophilus EF-Tu.
  • To explore the utility of fragment screening in understanding protein-ligand interactions and drug binding.

Main Methods:

  • Crystallography was used to obtain high-resolution structures of Thermus thermophilus EF-Tu.
  • Eighteen small organic molecules, all brominated, were screened for binding.
  • Anomalous difference maps were used for confident identification of bound molecules.

Main Results:

  • A small molecule was identified binding to the functionally important tRNA CCA-end binding pocket of EF-Tu.
  • The antibiotic GE2270 A, known to interact with this pocket, was confirmed as a potential binder.
  • Bromide ions were locatable in low-resolution data without full structure refinement.

Conclusions:

  • Fragment screening is a valuable approach for structural biology and drug discovery.
  • Collecting fragment screening data alongside primary structural data can enhance knowledge of biological function and drug binding.
  • This method provides experimental structural context for understanding ligand interactions.