Mechanism of Coupled Folding and Binding in the siRNA-PAZ Complex

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• The PAZ domain is essential for gene silencing via the RNA-induced silencing complex (RISC).
• siRNA binding to the PAZ domain enhances its folding, but the underlying mechanism remains unclear.
• Understanding this binding-folding coupling is vital for elucidating gene silencing functions.

Purpose of the Study:

• To investigate the coupling mechanism between siRNA binding and PAZ domain folding.
• To elucidate how siRNA binding influences PAZ domain stability and dynamics.

Main Methods:

• Molecular dynamics (MD) simulations were performed on both apo-PAZ (unbound) and siRNA-bound PAZ.
• Room-temperature and high-temperature MD simulations were utilized.
• Kinetic analysis and transition probability calculations were employed to study unfolding pathways and transition states.

Main Results:

• siRNA binding increases the rigidity and stability of both PAZ and siRNA.
• Both bound and apo-PAZ exhibit two-state unfolding, but with distinct pathways (switched unfolding order of helical regions).
• The transition state of bound PAZ is more compact, with more native-like structures in helix III and β3-β7 sheets compared to apo-PAZ.

Conclusions:

• siRNA binding significantly alters PAZ domain folding dynamics and stability.
• The study provides mechanistic insights into how siRNA binding facilitates PAZ domain function in gene silencing.
• These findings contribute to a deeper understanding of the RNA-induced silencing complex mechanism.