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Significant Differences in RNA Structure Destabilization by HIV-1 GagDp6 and NCp7 Proteins.

Micah J McCauley1, Ioulia Rouzina2, Jasmine Li3

  • 1Department of Physics, Northeastern University, Boston, MA 02115, USA.

Viruses
|April 30, 2020
PubMed
Summary

HIV-1 nucleocapsid (NC) protein and GagDp6 both destabilize the TAR RNA hairpin. However, NCp7 targets the loop, increasing hairpin opening rates by 10,000-fold, essential for reverse transcription.

Keywords:
GagHIV-1TAR hairpinenergy landscapemfoldnucleocapsidoptical tweezerstransition state

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Area of Science:

  • Molecular Biology
  • Virology
  • Biophysics

Background:

  • Retroviral nucleocapsid (NC) proteins are crucial nucleic acid chaperones with distinct roles in viral replication.
  • During reverse transcription, HIV-1 NC destabilizes RNA structures like the TAR hairpin.
  • During viral assembly, NC, as part of the Gag polyprotein, binds genomic RNA for packaging.

Purpose of the Study:

  • To elucidate the distinct RNA binding mechanisms of NCp7 and GagDp6 on the HIV-1 TAR RNA hairpin.
  • To understand how these proteins modulate TAR hairpin stability and dynamics.
  • To explain the necessity of Gag cleavage and NC release for viral processes.

Main Methods:

  • Single-molecule optical tweezers to measure TAR RNA hairpin stability and unfolding barriers.
  • Quantitative mfold-based modeling to analyze protein binding sites and hairpin stability.
  • Comparison of binding characteristics between NCp7 and GagDp6.

Main Results:

  • Both NCp7 and GagDp6 destabilize the TAR hairpin.
  • GagDp6 binds to two sites within the TAR hairpin stem.
  • NCp7 binds near the top loop, destabilizing it and increasing the hairpin opening rate by approximately 10^4-fold.

Conclusions:

  • NCp7's distinct binding and destabilization of the TAR hairpin loop are critical for facilitating reverse transcription.
  • Gag cleavage and subsequent NC release are essential prerequisites for initiating reverse transcription within the virion.
  • The differential binding modes explain the distinct functions of NC in viral assembly and replication.