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The Josephin Domain (JD), crucial for Ataxin 3 protein function, exists in flexible open and closed states. Our study reveals the closed-like conformation is most probable for JD in aqueous solutions.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biophysics

Background:

  • The Josephin Domain (JD) of Ataxin 3 (At3) protein is implicated in spinocerebellar ataxia 3.
  • JD's thermodynamic stability is linked to Ataxin 3 fibrillogenesis and aggregation risk.
  • Previous NMR studies suggest JD exists in multiple conformations, particularly in its hairpin region, with dynamic equilibrium between open and closed states.

Purpose of the Study:

  • To investigate the conformational landscape of the Josephin Domain (JD).
  • To determine the most likely conformational state of JD in solution.
  • To characterize the free energy landscape of JD conformational transitions.

Main Methods:

  • Classical molecular dynamics (MD) simulations.
  • Metadynamics simulations utilizing essential coordinates as collective variables.
  • In silico analysis of JD conformational arrangements.

Main Results:

  • A detailed representation of the free energy landscape for JD conformational transitions was generated.
  • The study identified distinct pathways between JD open-like and closed-like structures.
  • Computational findings strongly indicate that the closed-like conformation is the most stable and likely state for JD in water.

Conclusions:

  • The Josephin Domain (JD) exhibits a conformational flexibility with a preference for a closed-like state in aqueous environments.
  • Understanding JD conformational dynamics is vital for elucidating the mechanisms of Ataxin 3 aggregation and related neurodegenerative diseases.
  • This study provides key insights into the structural behavior of JD, contributing to the broader understanding of protein folding and misfolding.