Abstract
The analytical ultracentrifugation (AUC) is a classic biophysical instrument to analyze protein interactions in solutions. A recently introduced fluorescence detection system (FDS) improves the specificity and sensitivity of the AUC, and offers the potential to analyze the protein interactions in biological fluids. We explore challenges posed by the application of FDS-AUC to the study of protein interactions in E.coli whole cell extracts, using fluorescent proteins (EGFPs) as model system. At experimentally feasible concentrations of cell extracts, we find no discernable effects of hydrodynamic nonideality on the sedimentation of EGFPs. However, at high concentrations E.coli whole cell extracts produce significant signals from auto fluorescence with complicated quenching patterns. Goal of this work is to establish detection limits and develop procedures to improve specificity.
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