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RNA recognition by an isolated alpha helix

R Tan1, L Chen, J A Buettner

  • 1Department of Biochemistry and Biophysics, University of California, San Francisco 94143.

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A peptide from HIV Rev protein specifically binds RNA, forming an alpha helix crucial for high-affinity binding. This interaction is vital for HIV gene regulation and offers insights into peptide-RNA recognition mechanisms.

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Area of Science:

  • Molecular Biology
  • Virology
  • Biochemistry

Background:

  • The HIV Rev protein is essential for viral gene expression.
  • Rev interacts with the Rev response element (RRE) RNA to facilitate nuclear export of viral transcripts.

Purpose of the Study:

  • To investigate the structural basis of peptide-RNA binding.
  • To determine the role of alpha-helical conformation in Rev-RRE interaction.
  • To identify key amino acid residues involved in specific RNA recognition.

Main Methods:

  • Synthesis and modification of a 17-amino acid peptide from the HIV Rev protein's arginine-rich region.
  • Alpha-helical content determination in solution.
  • RNA binding assays using IIB RNA (a primary binding site within RRE).
  • Analysis of mutant peptides to assess the importance of specific amino acid side chains.
  • In vivo studies using Tat-Rev peptide hybrids and HIV LTR transactivation.

Main Results:

  • The peptide forms an alpha helix in solution upon N- and C-terminal modification, enhancing binding affinity to IIB RNA.
  • Binding affinity correlates with alpha-helical content, while non-specific binding is unaffected.
  • Specific amino acid residues (Thr, Asn, 4 Arg) were identified as critical for sequence-specific recognition.
  • In vivo studies confirmed the peptide adopts an alpha-helical conformation during HIV gene regulation.

Conclusions:

  • The arginine-rich peptide from HIV Rev protein adopts a functionally relevant alpha-helical structure upon binding to RRE RNA.
  • Specific amino acid side chains are crucial for the sequence-specific recognition of RNA.
  • Interactions with the RNA backbone likely stabilize the alpha helix within the major groove of RNA, facilitating HIV replication.