Quantifying Ligand-to-Protein Distances in Complex Environments Using Intermolecular ¹⁹F PRE NMR Spectroscopy

Area of Science:

• Biophysics
• Structural Biology
• Biochemistry

Background:

• Determining structural features of biomolecular complexes is key to understanding their function.
• Nuclear magnetic resonance (NMR) spectroscopy, particularly paramagnetic relaxation enhancement (PRE), offers methods to probe molecular structures.
• Fluorine's low natural abundance in biomolecules facilitates its use as a label in cellular environments.

Purpose of the Study:

• To investigate the structural dynamics of a protein-DNA complex under varying conditions using fluorine-based PRE.
• To determine intermolecular distances between Bacillus subtilis cold shock protein B (BsCspB) and a fluorine-labeled DNA ligand (dT4).

Main Methods:

• Utilized a single-cysteine mutant of BsCspB with a paramagnetic spin label.
• Complexed the labeled protein with a fluorine-labeled dT4 DNA ligand.
• Acquired intermolecular 19F-based PREs under in vitro, molecular crowding, and cell lysate conditions.

Main Results:

• Intermolecular distances between the spin-labeled BsCspB and the fluorine-labeled dT4 were measured.
• The determined distances showed no significant change across the three tested conditions.
• These findings align with previously observed conservation of binding affinities.

Conclusions:

• The structural integrity of the BsCspB-dT4 complex is maintained across different experimental environments.
• Fluorine-based PRE is a viable technique for probing biomolecular interactions in complex biological settings.
• The study highlights the robustness of protein-DNA interactions regardless of cellular context.