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Open AccessArticle

Significant Differences in RNA Structure Destabilization by HIV-1 Gag∆p6 and NCp7 Proteins

1
Department of Physics, Northeastern University, Boston, MA 02115, USA
2
Department of Chemistry and Biochemistry, The Ohio State University, Center for Retroviral Research, and Center for RNA Biology, Columbus, OH 43210, USA
3
Department of Chemistry and Program in Biochemistry, Wellesley College, Wellesley, MA 02481, USA
*
Authors to whom correspondence should be addressed.
Viruses 2020, 12(5), 484; https://doi.org/10.3390/v12050484
Received: 10 March 2020 / Revised: 15 April 2020 / Accepted: 21 April 2020 / Published: 25 April 2020
(This article belongs to the Special Issue The 11th International Retroviral Nucleocapsid and Assembly Symposium)
Retroviral nucleocapsid (NC) proteins are nucleic acid chaperones that play distinct roles in the viral life cycle. During reverse transcription, HIV-1 NC facilitates the rearrangement of nucleic acid secondary structures, allowing the transactivation response (TAR) RNA hairpin to be transiently destabilized and annealed to a complementary RNA hairpin. In contrast, during viral assembly, NC, as a domain of the group-specific antigen (Gag) polyprotein, binds the genomic RNA and facilitates packaging into new virions. It is not clear how the same protein, alone or as part of Gag, performs such different RNA binding functions in the viral life cycle. By combining single-molecule optical tweezers measurements with a quantitative mfold-based model, we characterize the equilibrium stability and unfolding barrier for TAR RNA. Comparing measured results with a model of discrete protein binding allows us to localize affected binding sites, in addition to quantifying hairpin stability. We find that, while both NCp7 and Gag∆p6 destabilize the TAR hairpin, Gag∆p6 binding is localized to two sites in the stem, while NCp7 targets sites near the top loop. Unlike Gag∆p6, NCp7 destabilizes this loop, shifting the location of the reaction barrier toward the folded state and increasing the natural rate of hairpin opening by ~104. Thus, our results explain why Gag cleavage and NC release is an essential prerequisite for reverse transcription within the virion. View Full-Text
Keywords: HIV-1; TAR hairpin; Gag; nucleocapsid; optical tweezers; energy landscape; transition state; mfold HIV-1; TAR hairpin; Gag; nucleocapsid; optical tweezers; energy landscape; transition state; mfold
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MDPI and ACS Style

McCauley, M.J.; Rouzina, I.; Li, J.; Núñez, M.E.; Williams, M.C. Significant Differences in RNA Structure Destabilization by HIV-1 Gag∆p6 and NCp7 Proteins. Viruses 2020, 12, 484.

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