Chemical Visualization of Human Pathogens : the Retroviral Capsids

Retroviruses are pathogens characterized by their ability to incorporate viral DNA into a host cell’s genome. Retroviruses like Rous Sarcoma Virus (RSV) infect cells during mitosis, when the chromatin is exposed to the cytoplasm. Conversely, the genus of lentiviruses, like the human immunodeficiency virus (HIV), have evolved to infect non-dividing cells [1]. Despite infecting cells at different stages of their life cycles, RSV and HIV share a similar late stage replication cycle that is highly dependent on the group actin polyprotein precursor (Gag), which contains the matrix (MA), capsid (CA) and nucleocapsid (NC) proteins. Both HIV’s CA and Gag are considered unexploited targets for pharmaceutical intervention. We describe the techniques that were used to build, simulate, analyze and visualize the structures of both Gag and CA, and we discuss scientific visualization needs that spurred development of an interactive GPU-accelerated ray tracing engine and the use of remote visualization technologies.

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