Integrative modeling of the HIV-1 ribonucleoprotein complex

A coarse-grain computational method integrates biophysical and structural data to generate models of HIV-1 genomic RNA, nucleocapsid and integrase condensed into a mature ribonucleoprotein complex. Several hypotheses for the initial structure of the genomic RNA and oligomeric state of integrase are tested. In these models, integrase interaction captures features of the relative distribution of gRNA in the immature virion and increases the size of the RNP globule, and exclusion of nucleocapsid from regions with RNA secondary structure drives an asymmetric placement of the dimerized 5'UTR at the surface of the RNP globule. Author summary The genome of HIV-1 is composed of two strands of RNA that are packaged in the mature virion as a condensed ribonucleoprotein complex with nucleocapsid, integrase, and other proteins. We have generated models of the HIV-1 ribonucleoprotein that integrate experimental results from multiple structural and biophysical experiments, exploring several hypotheses about the state of the RNA before condensation, and the role of crosslinking by integrase. The models suggest that the 5'UTR, which shows extensive secondary structure, has a propensity to be placed on the surface of the condensed globule, due to reduced binding of nucleocapsid to double-stranded regions within the 5'UTR. This unexpected localization of the 5'UTR may have consequences for the subsequent structural transitions that occur during the process of reverse transcription.