Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides.

Academic Article


  • Interactions between RNA molecules and proteins are critical to many cellular processes and are implicated in various diseases. The RNA-peptide complexes are good model systems to probe the recognition mechanism of RNA by proteins. In this work, we report studies on the binding-unbinding process of a helical peptide from a viral RNA element using nonequilibrium molecular dynamics simulations. We explored the existence of various dissociation pathways with distinct free-energy profiles that reveal metastable states and distinct barriers to peptide dissociation. We also report the free-energy differences for each of the four pathways to be 96.47 ± 12.63, 96.1 ± 10.95, 91.83 ± 9.81, and 92 ± 11.32 kcal/mol. Based on the free-energy analysis, we further propose the preferred pathway and the mechanism of peptide dissociation. The preferred pathway is characterized by the formation of sequential hydrogen-bonding and salt-bridging interactions between several key arginine amino acids and the viral RNA nucleotides. Specifically, we identified one arginine amino acid (R8) of the peptide to play a significant role in the recognition mechanism of the peptide by the viral RNA molecule.
  • Authors

  • Levintov, Lev
  • Vashisth, Harish
  • Status

    Publication Date

  • November 16, 2021
  • Published In


  • Arginine
  • Hydrogen Bonding
  • Molecular Dynamics Simulation
  • Peptides
  • Protein Binding
  • RNA, Viral
  • Digital Object Identifier (doi)

    Start Page

  • 5060
  • End Page

  • 5073
  • Volume

  • 120
  • Issue

  • 22