Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling.

Area of Science:

• Biochemistry and Molecular Biology
• Structural Biology
• Computational Biology

Background:

• Chaperones are essential for maintaining proteostasis by preventing protein aggregation and facilitating proper protein folding.
• The precise mechanisms by which chaperones influence substrate conformational dynamics remain incompletely understood.

Purpose of the Study:

• To elucidate the dynamic interactions between the chaperone Spy and its substrate immunity protein 7 (Im7) at a residue level.
• To develop and validate a computational approach integrating NMR data with simulations for studying flexible biomolecular complexes.

Main Methods:

• Utilized site-specific Nuclear Magnetic Resonance (NMR) data to construct system-specific force fields for individual binding partners.
• Employed coarse-grained molecular simulations to model the chaperone-substrate complex dynamics.
• Validated simulation results against experimental biophysical measurements.

Main Results:

• Simulations accurately reproduced experimental binding data for the Spy-Im7 complex.
• Upon binding, Im7 folding is accompanied by reduced conformational exchange, while Spy's flexible regions enhance interactions with various substrate conformations.
• Spy facilitates the release of Im7 in a well-folded state, balancing substrate dynamics.

Conclusions:

• The integrated NMR and simulation approach provides a detailed, residue-level understanding of dynamic chaperone-substrate interactions.
• This strategy offers a generalizable platform for investigating other flexible biomolecular systems.
• The findings enhance our comprehension of chaperone-mediated protein folding pathways.