MULTISCALE MODELS FOR PACKAGING VIRAL RNAS

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The crystal structure of pariacoto virus (PaV) reveals about 35% of the RNA genome. This RNA forms a dodecahedral cage just under the capsid (Tang et al., 2001). In last year¿s progress report, we reported development a model for the phosphate positions of the remaining 65% of the RNA. The double-helical regions of the dodecahedral cage in our model are essentially identical to those in the crystal structure. The three-way junctions are disordered in the crystal structure, suggesting structural heterogeneity at the threefold crystallographic axes. Our model includes a mixture of three-way junctions, two-way junctions with a stem-loop on the third arm, and four-way junctions. The latter occur when three double helices meet at the threefold axis and the RNA drops down into the interior of the virus from that axis, forming the fourth arm of the junction.