Deciphering the Hieroglyphics of Functional Proteomics Using Small Molecule Probes

Abstract

Fluorescence-based total protein detection is generally acknowledged to provide superior capabilities relative to the classical staining methods. Simple measurement of differences in protein expression, however, does not directly measure changes in protein activity and often fails to detect key posttranslational modifications. A number of fluorescence-based strategies tailored to the analysis of protein posttranslational modifications, functional domains, and enzymatic activities have been introduced recently. The new fluorescent staining methods have spurred the rapid development of sophisticated imaging devices that provide the highest possible detection capabilities. A limitation of the newly devised functional proteomics stains is that the abundances of the target proteins are often quite low, and as a consequence, protein prefractionation has increasingly become an integral part of proteomics analysis. It is expected that fluorescence-based approaches, originally devised for gels, will ultimately be adapted to liquid chromatographymass spectrometry, protein microarrays, and cell-based assays. Additionally, the powerful capabilities of differential protein expression profiling will be engineered into future probes, allowing for multiplexed analysis of posttranslational modifications and enzyme activities. Integrating protein prefractionation and small molecule probe-based detection with multiwavelength imaging significantly expands the power of gel electrophoresis for the large-scale elucidation of the functional properties of proteins.