DEAD-box-protein-assisted RNA structure conversion towards and against thermodynamic equilibrium values

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• RNA molecules undergo dynamic structural conversions crucial for biological processes.
• Protein assistance and ATP hydrolysis are frequently involved in these RNA structure conversions.
• The precise mechanisms of protein-mediated RNA structure conversion and the role of ATP remain incompletely understood.

Purpose of the Study:

• To investigate the in vitro mechanisms by which the DEAD-box ATPase Ded1 facilitates RNA structure conversions.
• To elucidate the distinct roles of ATP hydrolysis in protein-assisted RNA structural dynamics.

Main Methods:

• In vitro biochemical assays using a model RNA system.
• Kinetic analysis of RNA structure conversion pathways.
• Characterization of protein-RNA intermediates.

Main Results:

• Ded1 facilitates RNA structure conversions through two distinct pathways.
• One pathway is ATP-dependent, involving complete RNA strand disassembly and enabling conversion against thermodynamic equilibrium.
• The second pathway is ATP-independent, proceeding through Ded1-stabilized multipartite intermediates.

Conclusions:

• Ded1 employs diverse mechanisms to assist RNA structure conversions.
• ATP hydrolysis by Ded1 drives RNA structure conversion via a kinetically controlled pathway.
• The findings provide a mechanistic framework for understanding protein-assisted RNA dynamics and the role of ATP.