Proteome analysis. II. Protein subcellular redistribution: linking physiology to genomics via the proteome and separation technologies involved.

While annotated two-dimensional (2D) gel electrophoresis databases contain thousands of proteins, they do not represent the entire genome. High-molecular-mass proteins in particular are conspicuously absent from such databases. Filamin is prototypical of this class of proteins since it is a dimer with relative molecular mass (Mr) of 520000 containing at least 240 potential phosphorylation sites. Filamin is not readily separated by current 2D procedures, and is difficult to study with respect to cycles of phosphorylation-dephosphorylation. Novel technologies are needed to identify biochemical pathways impinging upon such targets. The success of immunofluorescence microscopy as a research tool can be attributed in part to the fact that proteins redistribute in response to a variety of physiological stimuli. Comparable quantitative methods are required in proteome analysis. Three components are necessary for development of an approach that is capable of screening for protein redistribution events: (1) subcellular fractionation, (2) protein labeling and (3) data acquisition. An integrated approach is presented that utilizes differential detergent fractionation combined with reversible, luminescent protein stains and analytical imaging for high-throughput analysis of signal transduction events leading to protein subcellular redistribution. The procedure has been successfully implemented to rapidly define key second messenger pathways leading to endothelial cell junctional permeability and to guide in the design of a new family of peptide-based anti-inflammatory drugs.