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Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein.
Mari L DeMarco1, Darwin O V Alonso, Valerie Daggett
1Biomolecular Structure and Design Program, University of Washington, Seattle 98195-7610, USA.
Journal of Molecular Biology
|August 27, 2004
Summary
Molecular dynamics simulations reveal the engrailed homeodomain (En-HD) protein unfolds through distinct states, driven by salt-bridges and helical interactions. These findings clarify protein folding pathways and stability.
Area of Science:
- Protein dynamics and biophysics
- Computational structural biology
- Molecular modeling
Background:
- Ultra-fast folding proteins are ideal for molecular dynamics simulations.
- The engrailed homeodomain (En-HD) protein folds via the diffusion-collision model.
Purpose of the Study:
- To characterize the unfolding pathway of En-HD using extensive molecular dynamics simulations.
- To identify conformational states and the role of specific interactions in protein folding/unfolding.
Main Methods:
- Seven simulations of En-HD and 12 simulations of its helical fragments were performed.
- Over 1.1 microseconds of simulation time in water were analyzed.
- Thermal denaturation experiments were used to assess helix stability.
Main Results:
- Identified key states: native-like transition state, U-shaped helical intermediate, and unfolded state with dynamic helices.
- Demonstrated the crucial role of long-range tertiary contacts, particularly salt-bridges, in stabilizing helix II (HII).
- Fragment simulations showed HII as the least stable helix and revealed the unraveling of helix III (HIII) as the initial unfolding event.
Conclusions:
- Salt-bridges are critical for stabilizing HII before hydrophobic core formation during En-HD folding.
- Contact-assisted helix formation, involving salt-bridges and fluctuating tertiary contacts, aids HII formation.
- The instability of HIII is the primary driver for En-HD unfolding, consistent with experimental data.