Electrospray Mass Spectrometry for the Direct Accurate Mass Measurement of Ligands in Complex With the Retinoid X Receptor α Ligand Binding Domain

Accurate mass measurements are often used in the structural determination of unknown compounds of low molecular mass (i.e., below ∼500 Da). Recently, it has been shown that accurate mass measurements also can be made on small denatured proteins (i.e., Mr, ∼17,000) to confirm their amino acid composition and identify the presence of isoforms. In the current report, we present nondenaturing electrospray (ES) mass spectrometry data on the direct accurate mass measurement of ligands in complex with the retinoid X receptor ligand binding domain (RXR LBD; Mr 31,370.92). Average mass errors were below 0.198 Da, 6.3 ppm (standard deviation [SD], 0.146; n = 10) for low-affinity fatty acid agonists analyzed in complex with the RXR LBD. Protein consumption was less than 15 pmol, with fatty acid ligands present at concentrations corresponding to their median effective concentration value (low micromolar, determined in transfection assays). Although determination of fatty acid mass was only sufficiently accurate to give nominal mass values, measurements were of sufficient accuracy to assign fatty acid chain length, degree of unsaturation, or cyclization. Using 17β-estradiol as a control, the ability to observe specific ligand binding is shown for both high- and low-affinity RXRα agonists. In addition, binding of a novel synthetic receptor agonist XCT0315908 to the RXRα LBD is reported. This compound showed a high degree of complex formation, and the receptor-ligand complex could be mass measured with an average mass error of −0.024 Da, 0.8 ppm (SD, 0.092; n = 9). Thus, specific binding of both nanomolar and micromolar affinity ligands to a nuclear receptor LBD can be directly observed using nondenaturing ES mass spectrometry and accurate mass measurements additionally can be made on intact complexes in the same experiment. This methodology also is applicable when ligands are present as components of mixtures.