Determining a molecular pathway for formation of a T=3 capsid using mass spectrometry

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Viruses remain major human, animal and plant pathogens. The most successful current anti-viral therapies rely on traditional vaccination, a technique first identified in the West over a century ago, and unfortunately not simply applicable to many viruses. More modern treatments are directed at inhibiting specialised enzymes within viruses with small molecular weight compounds, anti-viral drugs, such as those used to treat AIDS. Unfortunately, such enzymes usually share many features with host molecules and as a result most anti-viral drugs show unwanted side-effects. In fact viruses offer a unique molecular target that has so far not been exploited therapeutically, namely their assembly pathways. Simple viruses that contain only a nucleic acid enclosed in a protein shell form those shells as symmetrical aggregates from very few different types of subunits. The overall particle has a spherical cross-section and looks somewhat like a soccer ball. Similar structures form within more complex membrane-containing viruses as well. Despite a wealth of information about viral structures it has not yet been possible to map out experimentally an assembly pathway from protein subunit to shell in any virus. In part this is because it has traditionally been technically difficult to study this aspect of viral life-cycles. One key feature of assembly intermediates is their different molecular masses. In our model virus, a bacteriophage that normally infects a laboratory bacterium, but whose architecture mimics that of viruses that infect humans, we have recently discovered how to slow the assembly process in a test tube and measure the masses of all the intermediates formed in the pathwayto the final spherical shell using a modern mass spectrometer. This assay now allows us to take the most detailed look at the assembly pathway, examine how both the phage coat protein and RNA contribute to the assembly process, and hopefully identify generic principles that could reveal novel anti-viral drug targets.