Conformational selection or induced fit for Brinker and DNA recognition.

Area of Science:

• Molecular Biology
• Biophysics
• Structural Biology

Background:

• Brinker is a key target protein in the Drosophila Decapentaplegic (Dpp) morphogen signaling pathway.
• Brinker exhibits widespread expression and DNA-binding capabilities.
• NMR data indicate apo-Brinker is intrinsically unstructured, folding upon DNA interaction, but the binding-folding mechanism remains unclear.

Purpose of the Study:

• To elucidate the coupled binding and folding mechanism of Brinker using molecular dynamics (MD) simulations.
• To investigate the structural and dynamic changes of Brinker upon DNA binding.

Main Methods:

• Performed room-temperature and high-temperature MD simulations for both DNA-bound and apo-Brinker.
• Analyzed unfolding kinetics, transition state ensembles (TSEs) using Φ-values, and root-mean-square deviation (RMSD) differences.
• Applied Kolmogorov-Smirnov (KS) test for mechanism analysis.

Main Results:

• MD simulations suggest Brinker gains rigidity and stability upon DNA binding.
• Kinetic analysis indicates a two-state unfolding process for both forms.
• Φ-value analysis predicts more native-like TSEs for DNA-bound Brinker.
• RMSD and KS tests support an induced-fit mechanism for Brinker folding upon DNA binding.

Conclusions:

• Brinker folding upon DNA binding likely follows an induced-fit mechanism.
• MD simulations provide a powerful approach for studying biomolecular folding and ligand-binding interactions.
• Findings offer insights into the regulation of the Dpp signaling pathway.