Microsecond molecular dynamics simulations of intrinsically disordered proteins involved in the oxidative stress...

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Intrinsically disordered proteins (IDPs) like Prothymosin alpha (ProTα) and the Neh2 domain of Nuclear factor erythroid 2-related factor 2 (Nrf2) are vital in cellular protein-protein interaction networks.
• Their interaction with Kelch-like ECH-associated protein 1 (Keap1) is critical for regulating the cellular response to oxidative stress, a pathway implicated in diseases like cancer and neurodegeneration.

Purpose of the Study:

• To elucidate the molecular mechanisms by which the intrinsically disordered proteins ProTα and Neh2 bind to Keap1.
• To investigate the structure and dynamics of free-state ProTα and Neh2 and the thermodynamics of their binding to Keap1.

Main Methods:

• Extensive atomistic molecular dynamics (MD) simulations (0.5-1.0 microseconds).
• Isothermal titration calorimetry experiments.

Main Results:

• Both ProTα and Neh2 exhibit a propensity to form bound-state-like β-turn structures in their free states, though to varying degrees.
• Residues outside the canonical Keap1-binding motifs appear to stabilize these pre-binding structures for both proteins.
• The binding of ProTα and Neh2 to Keap1 is proposed to occur synergistically through preformed structural elements (PSEs) and coupled folding-binding, with a strong preference for PSEs, especially in Neh2.

Conclusions:

• The study reveals that intrinsically disordered proteins ProTα and Neh2 utilize preformed structural elements for binding to Keap1, influencing the oxidative stress response pathway.
• These findings offer valuable insights for developing therapeutics aimed at enhancing cellular oxidative stress defense mechanisms.