Identifying ligand-binding hot spots in proteins using brominated fragments

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.