Jan 072009
ResearchBlogging.orgAntibiotics such as chloramphenicol suppress infections by inhibiting bacteria from making proteins. They achieve this by binding to and blocking the peptidyl transferase center (PTC) of the ribosome, a large complex of RNA and protein that performs nearly polypeptide synthesis in living cells. Although PTC-binding antibiotics comprise several different families of compounds, mutations in the ribosome that confer resistance to one family often produce cross-resistance to other families. This is difficult to understand because the PTC itself is highly conserved and not very tolerant of mutations. In an upcoming paper (open access, read along) in the Proceedings of the National Academy of Sciences, a team of researchers from the Weizman Institute of Science analyze several crystal structures of the ribosome to understand how this cross-resistance arises.

Davidovich et al. mapped nucleotide mutations known to confer resistance to PTC antibiotics onto x-ray crystal structures of the large ribosomal subunit from D. radiodurans in complex with antibiotics. One interesting facet of the resistance mutations became immediately apparent: they were almost all clustered on one side of the antibiotic binding site.

You can see this pretty clearly in Figure 2 panels B&D. Although the antibiotics (large pink surface) are surrounded by nucleotides, most of those that are on the left side (thin tan sticks) do not confer resistance if mutated. Resistance-conferring mutations instead cluster around the “rear wall” of the PTC (to the right). The authors explain that in this region ribosomal functions primarily rely on the sugar-phosphate backbone of the rRNA. Because the backbone elements are the same for all ribonucleotide bases, mutations in this region are more likely to be tolerated without significant loss of function.

Another striking feature of resistance mutations is visible in Figure 2 and quantified in Figure 3A, namely that many of these mutated bases do not contact the antibiotics directly. In particular, mutation of G2032 appears to play a role in conferring resistance to several different antibiotics. Overall, however, it appears that numerous long-range interactions can interfere with antibiotic binding.

The lynchpin of these interactions seems to be U2504, a base that directly contacts the bound antibiotic in most cases. Mutations to U2504 itself do not appear to be well-tolerated, but many of the long-range mutations occur in the layer of bases surrounding it. The authors describe in detail several mechanisms by which the observed mutations might increase the flexibility of U2504, allowing it to adopt positions that could allow continued protein synthesis while reducing the binding of antibiotics. The commonality of interactions with U2504, and the importance of the structural context of the surrounding nucleotides, explains why many mutations can give rise to cross-resistance.

The practical upshot of these findings is that they may serve as a guide for the design of future antibiotics. Since the majority of the drug-resistance mutations lie on the rear wall of the PTC, the effectiveness of these antibiotics may be enhanced by improving their binding to other parts of the site. With further modeling it may also be possible to design antibiotics that can compensate for flexibility at U2504. These findings also remind us that dynamics and long-range interactions can be important to the function of any biomolecule with a folded three-dimensional structure, not just proteins.

C. Davidovich, A. Bashan, A. Yonath (2008). Structural basis for cross-resistance to ribosomal PTC antibiotics Proceedings of the National Academy of Sciences, 105 (52), 20665-20670 DOI: 10.1073/pnas.0810826105 OPEN ACCESS

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