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Structural Explorations of NCp7-Nucleic Acid Complexes Give Keys to Decipher the Binding Process.

Romain Retureau1, Christophe Oguey2, Olivier Mauffret1

  • 1LBPA, UMR 8113, ENS Paris-Saclay-CNRS, 61 avenue du Président Wilson, 94235 Cachan cedex, France.

Journal of Molecular Biology
|March 17, 2019
PubMed
Summary

The HIV-1 nucleocapsid protein (NCp7) uses its zinc fingers (ZF1 and ZF2) to bind nucleic acids. ZF2 leads binding, while ZF1 stabilizes complexes, revealing a global binding scheme for NCp7-nucleic acid interactions.

Keywords:
NCp7Voronoi tesselationnucleo-capsid proteinprotein–nucleic acid binding processprotein–nucleic acid interactions

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Area of Science:

  • Structural biology
  • Biochemistry
  • Virology

Background:

  • The HIV-1 nucleocapsid protein (NCp7) is essential for viral replication, playing a key role in binding and annealing nucleic acids (NAs).
  • NCp7 possesses two zinc fingers, ZF1 and ZF2, which are critical for its NA binding and annealing functions.
  • Understanding the structural basis of NCp7-NA interactions is crucial for comprehending HIV-1 lifecycle and developing antiviral strategies.

Purpose of the Study:

  • To comprehensively analyze the structural properties of NCp7 in complex with DNA or RNA, and in its free state.
  • To elucidate the functional specialization of ZF1 and ZF2 in the context of NA binding.
  • To establish a global binding scheme for NCp7 to both DNA and RNA.

Main Methods:

  • Analysis of available experimental structural models of NCp7 bound to DNA or RNA, or free of ligand.
  • Characterization of the relative positioning of ZF1 and ZF2.
  • Measurement of amino acid accessibility.
  • Quantitative mapping of amino acid-nucleotide contacts using the VLDM tessellation method.

Main Results:

  • The VLDM approach revealed a strong correlation between NA binding and the conformational states of free NCp7.
  • ZF2 exhibits greater accessibility in free NCp7 and a consistent interface across different models, suggesting it initiates NA binding.
  • ZF1 stabilizes NCp7-NA complexes through diverse interface organizations.

Conclusions:

  • NCp7 employs a distinct functional specialization between ZF1 and ZF2 during nucleic acid binding.
  • ZF2 plays a leading role in initiating the binding process, while ZF1 contributes to complex stabilization.
  • This study provides a global binding scheme for NCp7 and insights into the stabilization mechanisms of protein-NA complexes.