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Base pair dynamics, electrostatics, and thermodynamics at the LTR-III quadruplex:duplex junction.

Haley M Michel1, Justin A Lemkul2

  • 1Department of Biochemistry, Virginia Tech, Blacksburg, Virginia.

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|April 5, 2024
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Human immunodeficiency virus 1 G-quadruplexes (GQs) regulate viral gene expression. Molecular dynamics simulations reveal dynamic base pairing within the LTR-III quadruplex:duplex junction (QDJ), a potential drug target.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Dynamics

Background:

  • G-quadruplexes (GQs) are crucial regulatory elements in genomes across various life forms.
  • Human immunodeficiency virus 1 (HIV-1) utilizes two GQs in its promoter region to modulate viral gene expression.
  • The LTR-III GQ in HIV-1 features a unique quadruplex:duplex junction (QDJ), a potential site for therapeutic intervention.

Purpose of the Study:

  • To investigate the dynamic behavior of the quadruplex:duplex junction (QDJ) in the LTR-III G-quadruplex of HIV-1.
  • To elucidate the electrostatics and thermodynamics governing the QDJ structure and stability.
  • To explore the potential of the QDJ as a selective drug targeting site.

Main Methods:

  • Conventional and enhanced-sampling molecular dynamics (MD) simulations were employed.
  • The Drude-2017 force field was utilized for accurate simulation of molecular interactions.
  • Analysis focused on base pairing dynamics, electrostatic interactions, and energy barriers within the QDJ.

Main Results:

  • Simulations demonstrated unbiased and reversible formation of additional base pairs (Ade4:Thy14 and Gua3:Thy14) within the QDJ.
  • Both base pairs exhibited favorable electrostatic interactions.
  • Geometric constraints within the junction appeared to favor the Ade4:Thy14 base pair, with small energy barriers allowing transitions between states.

Conclusions:

  • The LTR-III QDJ exhibits dynamic base pairing behavior influenced by electrostatic and geometric factors.
  • These findings provide critical insights into the structural dynamics and thermodynamics of the HIV-1 LTR-III QDJ.
  • The study supports the hypothesis of the QDJ as a druggable target for antiviral therapies.