Protein–ligand binding detected using ultrafiltration Raman difference spectroscopy

Abstract A new ultra-filtration-Raman-difference (UFRD) method facilitates the tag-free screening and quantitation of protein–ligand binding constants. The method relies on drop-coating-deposition-Raman (DCDR) combined with ultrafiltration and difference spectroscopy. Ultrafiltration is used to remove free (unbound) ligands from pre-equilibrated protein/ligand solutions. Difference DCDR spectroscopy is used to detect binding-induced vibrational spectral changes obtained from proteins with and without a bound ligand. The capabilities of the UFRD method are demonstrated using the binding of 2,4-dinitrophenol (DNP) to transthyretin (TTR), as well as preliminary measurements in several other systems. The UFRD results clearly reveal DNP spectral features induced by binding to TTR and confirm that only a 1:1 complex is formed even under 10-fold excess DNP conditions. The UFRD method is shown to be most useful when applied to strongly Raman active ligands (such as aromatic compounds). Weakly Raman-active ligands (such as sugars) are typically not compatible with UFRD detection (unless they produce a sufficiently large binding-induced change in protein secondary structure). Theoretical predictions suggest that UFRD may be used to screen binding events with a dissociation constant cut-off of the order of 10 μM, and perhaps also to quantify dissociation constants in the 100 nM to 100 μM range.