My research group primarily uses capillary electrophoresis (CE) to analyze and characterize proteins. Capillary electrophoretic separations of protein "charge ladders" (otherwise pure proteins with intrinsic or induced charge heterogeneity) allow us to estimate the net charge and hydrodynamic radius of proteins in solution. We also study ligand binding to proteins using "affinity capillary electrophoresis" (ACE), which exploits the accompanying change in protein electrophoretic mobility. Combining charge ladders and ACE allows us to characterize overall conformational changes caused by ligand binding. And with laser-induced fluorescence (LIF) detection, we can study the conformational behavior of fluorescently labeled proteins under simulated intracellular conditions—especially in the presence of high concentrations of other macromolecules.
We also have an active collaboration with a group in the Department of Bioinformatics and Genomics. We are using a variant of ACE called "CEMSA" (capillary electrophoretic mobility shift assay) to detect binding of transcription factors (TFs) to synthetic, fluorescently labeled DNA probes. We use this technique to experimentally validate predicted TF binding site sequences. After screening by CEMSA, we can identify affinity-purified TFs using mass spectrometry.