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The RNA-binding protein KhpB binds dsRNA and retains binding activity at elevated temperatures.

Iara Macedo1, Larissa Menezes2, Mateus Dias-Oliveira3

  • 1Programa de Pós Graduação em Genética e Biologia Molecular. Avenida Gonçalves 9500 - Campus do Vale, Universidade Federal do Rio Grande do Sul, Brazil; Departamento de Biofísica, Avenida Gonçalves 9500 - Campus do Vale, Universidade Federal do Rio Grande do Sul, Brazil.

International Journal of Biological Macromolecules
|February 28, 2026
PubMed
Summary

This study reveals that the bacterial protein KhpB, containing RNA-binding domains, effectively binds double-stranded RNA (dsRNA) even at high temperatures. The R3H domain alone demonstrates significant dsRNA interaction, offering potential for biotechnological applications.

Keywords:
Nucleic acid binding proteinRNA interferenceRNAi

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • RNA-binding proteins regulate gene expression post-transcriptionally.
  • The roles of less-characterized domains like KH and R3H in dsRNA interaction require further investigation.

Purpose of the Study:

  • To characterize the dsRNA binding capabilities of engineered variants of the thermostable bacterial RNA-binding protein KhpB.
  • To elucidate the contributions of KH and R3H domains to dsRNA binding and stability.

Main Methods:

  • Engineered recombinant variants of KhpB (containing KH, R3H, or both domains).
  • In vitro electrophoretic mobility shift assays to assess dsRNA binding capacity.
  • In silico modeling, physicochemical analyses, and molecular dynamics simulations.

Main Results:

  • Engineered KhpB variants demonstrated stable dsRNA binding up to 95°C.
  • The R3H-only variant exhibited the strongest dsRNA interaction, suggesting it as a minimal functional module.
  • Molecular dynamics confirmed basic residues are crucial for maintaining the dsRNA:KhpB complex.

Conclusions:

  • Thermostable KhpB is a novel dsRNA-binding protein with potential biotechnological applications.
  • Insights into KH and R3H domain interactions with dsRNA expand understanding of modular RNA-binding architectures.