Dr Vasudevan Ramesh - research

Inhibition of protein synthesis by RNA-binding antibiotics

Project: NMR structure determination of peptidyl transferase inhibitor antibiotics and their interactions with conserved secondary structural RNA motifs of 23S ribosomal RNAs.

As RNA molecules play fundamental role in prokaryotic translation and viral replication functions, they are recognized as potential target sites for therapeutic intervention by small molecules such as antibiotics. We have successfully designed and chemically synthesised two 35mer ribosomal RNA motifs of Hh and E. coli 23S rRNAs and demonstrated by NMR spectroscopic measurements that they adopt a stable, well folded A-RNA conformation in solution. The results of the NMR studies also provide direct experimental evidence for the specific binding of amicetin antibiotic to the RNA motifs and this is supported by the unconstrained molecular modelling of the amicetin-RNA complex.

The model of amicetin-RNA complex highlights several key interactions between the two molecular components which may be functionally significant and a section of the model is shown in the Figure below. The model of the complex also shows a folded conformation for the amicetin antibiotic. This folding appears strained, but its stability is gained from a network of intra-molecular hydrogen bonds contacts and stacking interaction and may be structurally critical for RNA binding. The above results lay a strong foundation for further NMR studies to determine the 3D structure of the 35mer RNA motifs complexed to amicetin and the amicetin-resistant mutants. In a wider perspective, the proposed NMR studies will provide a deeper and critical insight into the molecular basis of antibiotic action and antibiotic resistance.

IRES elements of Picornaviruses - Structure of conserved RNA motifs

Project: Application of NMR spectroscopy and computational methods to determine the structure and interactions of the IRES RNA element of EMCV picornavirus RNA.

The picornaviruses are a family of small icosahedral animal viruses that contain single-stranded RNA genomes (~ 8K bases). A salient feature of these viral RNAs is that initiation of protein synthesis has been shown to take place by a novel mechanism known as internal ribosomal entry sites (IRES). Within the IRES RNA elements, at the end of one predicted domain, is a hammerhead motif that contains a GNRA tetraloop (residues 547-550, Figure below). The importance of this tetra loop is demonstrated by the complete loss of IR