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Mapping allosteric pathway in NIa-Pro using computational approach.

Rashmi Panigrahi1, Senthilkumar Kailasam2

  • 1Department of Biochemistry University of Alberta Edmonton T6G 2H7 Canada.

Quantitative Biology (Beijing, China)
|February 12, 2026
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Summary
This summary is machine-generated.

Computer simulations reveal the allosteric communication pathway in nuclear inclusion protein-a protease (NIa-Pro). This study maps how viral protein genome linked (VPg) binding influences NIa-Pro activity by altering residue interactions.

Keywords:
NIa‐ProVPgallosteryresidue interaction networksimulation

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Computer simulations complement in vitro experiments for understanding allosteric regulation.
  • Molecular dynamics (MD) simulations trace communication pathways between catalytic and allosteric sites in proteins.
  • This study focuses on the nuclear inclusion protein-a protease (NIa-Pro) and its viral protein genome linked (VPg) binding region.

Purpose of the Study:

  • To identify the allosteric communication pathway between the VPg binding region and the catalytic active site of NIa-Pro.
  • To delineate the residue interaction network governing NIa-Pro allosteric regulation by VPg.
  • To understand the molecular mechanisms modulating NIa-Pro activity.

Main Methods:

  • Utilized molecular dynamics (MD) simulations.
  • Performed in silico analyses to map the allosteric pathway.
  • Conducted simulation studies involving point mutations (His142Ala, His167Ala) in the VPg interaction interface.

Main Results:

  • Delineated the residue interaction network critical for VPg-mediated allosteric regulation of NIa-Pro.
  • Demonstrated that mutations in the VPg interaction interface disrupt networks and alter catalytic residue orientation.
  • Observed that His142Ala and His167Ala mutations impact residue interaction networks and catalytic site geometry without significantly changing overall protease structure.

Conclusions:

  • The study successfully delineated the allosteric pathway in NIa-Pro.
  • Provides molecular-level insights into NIa-Pro activity modulation by VPg, even without its complex structure.
  • In silico analysis explains molecular concepts and dynamics underlying previous experimental findings.