Abstract
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.
Highlights
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
The models suggest that the 5’ untranslated region (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
Summary
Electron microscopy of mature HIV-1 shows a condensed ribonucleoprotein (RNP) complex [1] packaged within the cone-shaped capsid, which is thought to include genomic RNA, nucleocapsid, integrase, transfer RNA, reverse transcriptase, and other components [2]. It is formed through a complex, multistep process where genomic RNA (gRNA) associates with a lattice of Gag polyproteins at the cell surface, which buds from the surface to form an immature virion, followed by proteolytic cleavage of Gag into capsid, nucleocapsid, integrase and other viral proteins, and condensation and encapsidation of the mature RNP within the capsid
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