X ray crystallography of ribosomes:

• Antibiotic interaction with the small and large subunit
• Ribosome recycling factor interaction with the large subunit
• The Ribosome modulation factor (RMF) binds the active center of the large subunit
• The trigger factor chaperone binds at the tunnel exit site of the large subunit unit
  
  

Two general approaches are being taken to crystallize ribosome functional complexes:

(1) The first approach involves formation of the functional complex by optimisation of the conditions for binding of the factor to the ribosome and then determining conditions under which this functional complex crystallizes, either with or without purification of the unbound ligands. The advantage of this approach is that the complexes are also suitable for study by cryo-EM, as was seen for the T. thermophilus 30S-Era complex .

(2) The second approach utilizes the ability of our group to produce crystals of both the small and large ribosomal subunit, that diffract to between 3.0-3.5 Å. These native crystals can thus be soaked in solutions containing antibiotics or translational factors (or domains of these factors) that are: (i) small enough to diffuse through the solvent space present in the crystal lattice (see Figure) and (ii) known to bind to the ribosome in a position distinct from the crystal contact sites. This technique has been successfully applied to investigate the binding position of multiple antibiotic binding sites on the ribosome as well as more recently for domains of translation factors.

In the past three years, we have determined the structure of the D. radiodurans large 50S ribosomal subunit in complex with the streptogramin A + B antibiotics, quinopristin and dalfopristin, the ketolide telithromycin, as well as the pleuromutilin tiamulin – projects that were conducted in collaboration with Prof. Ada Yonath .

These studies provide insight into how such small molecules can inhibit such a large machine like the ribosome and also pave the way for development of improved ribosome inhibitors.