Development of a highly sensitive three-dimensional gel electrophoresis method for characterization of monoclonal protein heterogeneity

Band-collision gel electrophoresis

Electrophoretic mobility shift assays are widely used in gel electrophoresis to study binding interactions between different molecular species loaded into the same well. However, shift assays can access only a subset of reaction possibilities that could be otherwise seen if separate bands of reagent species might instead be collisionally reacted. Here, we adapt gel electrophoresis by fabricating two or more wells in the same lane, loading these wells with different reagent species, and applying an electric field, thereby producing collisional reactions between propagating pulse-like bands of these species, which we image optically. For certain pairs of anionic and cationic dyes, propagating bands pass through each other unperturbed; yet, for other pairs, we observe complexing and precipitation reactions, indicating strong attractive interactions. We generalize this band-collision gel electrophoresis (BCGE) approach to other reaction types, including acid-base, ligand exchange, and redox, as well as to colloidal species in passivated large-pore gels.

Electrophoretic mobility shift assays are widely used in gel electrophoresis to study binding interactions between different molecular species, but these assays access only a subset of reaction possibilities. Here, the authors develop a band-collision gel electrophoresis (BCGE) approach that demonstrates a much wider variety of reaction types.

Decoding 2-D Maps by Autocovariance Function

This chapter describes a mathematical approach based on the study of the 2-D autocovariance function (2-D ACVF) useful for decoding the complex signals resulting from the separation of protein mixtures. The method allows to obtain fundamental analytical information hidden in 2-D PAGE maps by spot overlapping, such as the number of proteins present in the sample and the mean standard deviation of the spots, describing the separation performance. In addition, it is possible to identify ordered patterns potentially present in spot positions, which can be related to the chemical composition of the protein mixture, such as post-translational modifications.The procedure was validated on computer-simulated maps and successfully applied to reference maps obtained from literature sources.