Interactions of Retroviral Proteins with Nucleic Acids

Division Of Basic Sciences - Nci

Investigators

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Abstract

We have studied the interactions between HIV-1 Gag proteins and nucleic acids for many years. These interactions are crucial in virus replication, as protein-RNA interactions contribute to assembly of the immature particle; moreover, the protein must select the genomic RNA for encapsidation out of a vast excess of cellular mRNAs, which can also be encapsidated (Muriaux et al., PNAS 2001; Rulli et al., J.Virol. 2007). How the correct RNA is selected is still not clear. Gag binds viral RNA and control RNAs with very similar affinities at physiological salt concentrations (Webb et al.. RNA 2013; Comas-Garcia et al., eLife 2017). We have suggested that perhaps assembly is initiated or nucleated more rapidly or more efficiently on viral RNA than on other RNAs (Rein, Trends in Microbiology, 2019). We have recently measured the rate at which Gag protein binds to RNA containing the "packaging signal" (Y), using the newly developed SwitchSense instrument. We find that Gag binds Y significantly more rapidly than it binds control RNAs.. To our knowledge, this is the first investigation of the kinetics of Gag binding to biologically relevant RNAs. The interaction of Gag with an RNA is, of course, determined in large part by the 3-dimensional structure of the RNA. RNA structures have been very difficult to determine. This is partly because RNA molecules are quite flexible and individual molecules may assume different conformations even within a single solution. Most techniques of structure determination rely on averaging the results from many molecules, but this will not give an accurate picture if the solution is a mixture of different conformations. We have participated in the work of Yun-Xing Wang's group using atomic force microscopy to obtain conformational information about individual molecules.