Projects in our laboratory seek answers to these and related questions. Members of the latter category pose particular challenges, both for the technology of multiprotein expression and for the biochemical strategies required to trap a defined state of a dynamic assembly. Our recently determined structure of the entry protein from reovirus suggests that a major conformational rearrangement in the protein may unmask surfaces that help it transiently disrupt a patch of cell membrane to allow the viral core to penetrate. The structures of the viral core and of the dsRNA-dependent RNA polymerase contained within it show how the organization of the virus particle coordinates and guides each of the steps in viral RNA synthesis. The domain is inserted into a larger polypeptide chain, which like the reovirus entry protein probably undergoes a major rearrangement after receptor binding.
Enveloped viruses enter cells by fusion of viral and cellular membranes.
Inhibitors of these rearrangements will help us dissect their mechanism and may also provide starting points for drug discovery. The flaviviruses, such as yellow fever virus, dengue virus, and West Nile virus, have an apparently quite different fusion machinery, and we are using a combination of x-ray crystallography and electron microscopy to work out its mechanism of action. Some of the fundamental mechanistic steps, such as a conformational change that brings viral and cellular membranes into close apposition, are probably shared with the fusion pathway deduced for HIV-1, influenza virus, and their relatives, but the structures that mediate these steps are unrelated. The switching mechanisms that underlie transcriptional regulation in eukaryotes embody relatively complex logical circuits. A longer-range goal is to fathom how a single, very large, multidomain protein like CBP interacts specifically with assemblies embodying very different logical decisions on different promoters and enhancers.