Induced fit or conformational selection for RNA/U1A folding.

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• The U1 snRNA hairpin II binds the U1A protein with high affinity.
• NMR data indicate RNA loop region transitions from unstructured to folded upon U1A binding.
• The mechanism of RNA folding coupled with protein binding remains poorly understood.

Purpose of the Study:

• To investigate the mechanism of RNA folding coupled with protein binding.
• To elucidate the folding kinetics and free energy landscape of U1 snRNA and U1A protein interaction.
• To identify key bases and interactions governing the folding process.

Main Methods:

• Explicit-solvent molecular dynamics (MD) simulations at room and high temperatures.
• Kinetic analysis and free energy landscape analysis of simulation data.
• Prediction of Phi-values and analysis of mutant effects (Arg52Gln).

Main Results:

• Bound RNA conformation is more stable upon U1A binding.
• Both bound and apo-RNA unfold via a two-state process.
• Bound RNA folding occurs sequentially: RNA contraction, U1A binding, and tertiary folding.
• Bases A8, C10, A11, and G16 are identified as key for bound RNA folding.
• Mutant Arg52Gln reduces electrostatic interactions and hydrogen bonds between RNA and U1A.

Conclusions:

• MD simulations provide insights into the coupled folding and binding mechanism of U1 snRNA and U1A protein.
• The study identifies key structural elements and interactions critical for the binding process.
• The employed simulation methodology can be applied to other biomolecular binding and folding studies.