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Exploring the Conformational Landscape of the Neh4 and Neh5 Domains of Nrf2 Using Two Different Force Fields and

Megan Chang1, Carter J Wilson1,2, Nadun Chanaka Karunatilleke1

  • 1Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada.

Journal of Chemical Theory and Computation
|April 16, 2021
PubMed

Insights

Nuclear factor erythroid 2-related factor 2 (Nrf2) pathway activation aids cancer cell survival. Understanding Nrf2

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • The Nrf2-ARE pathway protects cells from oxidative stress but can be hijacked by cancer cells, reducing treatment efficacy.
  • Nrf2 interacts with CREB binding protein (CBP) via its Neh4 and Neh5 domains, a crucial interaction for its function.
  • Disrupting the Nrf2-CBP interaction is a potential therapeutic strategy against cancer, but the disordered nature of Neh4 and Neh5 hinders structure-based drug design.

Purpose of the Study:

  • To elucidate the free-state structures and conformational landscapes of the Nrf2 Neh4 and Neh5 domains.
  • To investigate the differences in structural properties between Neh4 and Neh5.
  • To compare the performance of two molecular dynamics force fields (Amber99SB*-ILDNP and CHARMM36m) in simulating these disordered domains and validate against experimental data.

Main Methods:

  • Performed 48 μs of unbiased molecular dynamics (MD) simulations using Amber99SB*-ILDNP and CHARMM36m force fields.
  • Conducted circular dichroism (CD) spectropolarimetry experiments to obtain experimental structural data.
  • Analyzed simulation trajectories to determine the conformational ensembles of Neh4 and Neh5.

Main Results:

  • Neh5 was found to be significantly more disordered than Neh4.
  • Neh4 exhibited some α-helical propensity in its central region, suggesting distinct binding mechanisms.
  • The CHARMM36m force field demonstrated better agreement with experimental CD data compared to Amber99SB*-ILDNP, particularly for the Neh5 domain.

Conclusions:

  • Neh4 and Neh5 possess different conformational properties, implying distinct interaction mechanisms with CBP.
  • Molecular dynamics simulations, when validated by experimental data, can provide insights into the structures of intrinsically disordered proteins.
  • The CHARMM36m force field is more suitable for simulating the Nrf2 Neh4 and Neh5 domains in their free state.

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