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Updated: Jun 25, 2025

Investigating the Function of Coronin A in the Early Starvation Response of Dictyostelium discoideum by Aggregation Assays
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Stability and dynamics of extradenticle modulates its function.

Aakanksha Singh1, Bidisha Acharya1, Beas Mukherjee1

  • 1School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India.

Current Research in Structural Biology
|May 24, 2024
PubMed
Summary
This summary is machine-generated.

Mutating glycine to alanine in Extradenticle (EXD) protein enhances its DNA-binding affinity and stability. This mutation improves EXD

Keywords:
Hydrogen exchangeMD simulationNMR spectroscopyProtein-DNA interactionTranscription factor

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Developmental Biology

Background:

  • Extradenticle (EXD) is a crucial HOX transcription factor partner in Drosophila development.
  • EXD enhances HOX protein DNA-binding affinity and specificity.
  • EXD's DNA-binding homeodomain exhibits weaker affinity compared to HOX homeodomains.

Purpose of the Study:

  • To investigate the role of glycine at position 290 (G290) in the EXD DNA-binding helix.
  • To determine how mutating G290 to alanine affects EXD's stability and DNA-binding affinity.
  • To understand the structural and dynamic changes associated with the G290A mutation.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy to study protein stability and dynamics.
  • Molecular Dynamics (MD) simulations to analyze protein behavior at an atomic level.
  • Molecular Mechanics with Generalized Born and Surface Area Solvation (MMGBSA) for binding energy analysis.

Main Results:

  • The G290A mutation increased the stability of the EXD DNA-binding helix and the entire homeodomain (ΔΔG = -2.6 kcal/mol).
  • NMR and MD simulations revealed quenched dynamic motions in the G290A mutant compared to wild-type EXD.
  • The mutant protein exhibited a three-fold increase in DNA-binding affinity, with enhanced interactions at the DNA-binding interface and N-terminal arm.

Conclusions:

  • The G290A mutation significantly enhances EXD's protein stability and DNA-binding affinity.
  • Interplay between the DNA-binding helix and the N-terminal arm, mediated by DNA, influences binding.
  • Evolutionary preference for glycine at position 290 suggests a trade-off, possibly related to EXD's role in DNA sequence discrimination as a HOX co-factor.