Multi-scale simulations of MUT-16 scaffold protein phase separation and client recognition

Area of Science:

• Biophysics
• Molecular Biology
• Cellular Organization

Background:

• Protein phase separation drives cellular organization and function.
• Understanding condensate specificity and client recruitment is crucial.
• Mutator foci in C. elegans are essential for RNA silencing.

Purpose of the Study:

• Investigate MUT-16 protein phase separation.
• Determine MUT-16's role in recruiting MUT-8 client protein.
• Elucidate the molecular mechanisms of MUT-8 recruitment to MUT-16 condensates.

Main Methods:

• Multi-scale molecular simulations (coarse-grained CALVADOS2, Martini3; atomistic).
• In vitro phase separation propensity assays.
• In vitro co-expression pull-down experiments.

Main Results:

• Coarse-grained models predicted MUT-16 phase separation propensities, confirmed experimentally.
• Simulations identified key residues and interactions driving phase separation.
• Atomistic simulations revealed cation-π and hydrogen bonding interactions between MUT-16 (Arg) and MUT-8 (Tyr) are critical for recruitment.

Conclusions:

• MUT-16 phase separation and MUT-8 recruitment are essential for Mutator foci assembly.
• Specific Arg-Tyr interactions in MUT-16 M8BR are vital for high-affinity MUT-8 binding.
• Findings advance understanding of RNA silencing mechanisms in C. elegans.