Nanopore Discrimination of Protein-Small-Molecule Drug Complexes at Near-Atomic Resolution

Area of Science:

• Biophysics
• Molecular Biology
• Nanotechnology

Background:

• Biomolecular interactions are crucial for biological functions and drug responses.
• High-resolution nanopore sensing of protein-ligand interactions is a significant challenge.
• Existing methods struggle to detect subtle molecular interactions with high precision.

Purpose of the Study:

• To develop a nanopore sensing approach for high-resolution detection of biomolecular interactions.
• To demonstrate the capability of the YaxAB nanopore for sensing protein-peptide and protein-drug interactions.
• To investigate the dynamics of proteins within the nanopore for signal generation.

Main Methods:

• Utilized a YaxAB nanopore with LiCl-modulated electrostatic potential for sensing.
• Performed single-molecule electrical recordings and molecular dynamics simulations.
• Analyzed two-level current transitions generated by oscillating protein dynamics within the nanopore.

Main Results:

• The YaxAB nanopore successfully detected interactions of BRD4 protein with histone peptides and small-molecule drugs at the single-molecule level.
• Observed oscillating dynamics of BRD4 within the nanopore, leading to distinct current transitions.
• Achieved sensitive discrimination of BRD4-drug complexes with mass differences as low as 2.5 Da.

Conclusions:

• The YaxAB nanopore offers near-atomic, high-resolution sensing capabilities for biomolecular interactions.
• This technology holds promise for single-molecule drug discovery, proteomics, and diagnostics.
• The LiCl-modulated electrostatic potential is key to enabling sensitive detection of molecular complexes.