Small molecules as versatile tools for activity-based protein profiling experiments

Genome sequencing projects have provided a wealth of information on gene identities in prokaryotic and eukaryotic organisms. Currently, a total of 720 genome sequences are completed and a large number is still in progress (http://www.ncbi.nlm.nih.gov). The daunting challenge for proteomic research now is to assign the molecular, cellular, and (patho)physiological functions for the full complement of proteins encoded by the genome.¹ Since significant fractions of sequenced genomes encode uncharacterized enzymes, the analysis of genome sequences alone will not be sufficient to achieve this task especially if one considers that a single gene can in principle code for several proteins as a result of posttranscriptional and posttranslational processing. New technologies have been developed to characterize gene transcription on the mRNA level and on the protein expression level of cells including RNA microarrays and two-dimensional sodium dodecyl sulfate (SDS) gel electrophoresis, respectively. However, these established technologies focus on the abundance of RNA or proteins not taking into account that the cell uses in many cases additional posttranslational processing steps to generate the active protein that participates in its dedicated physiological or pathological cellular function (Figure 1).² The necessity of additional tools for the determination of activity and function can be illustrated by the example of the protease enzyme family: Many proteases are key players of crucial cellular processes requiring a tight regulation of their activity in order to keep the balance between needed proteolytic power and uncontrolled proteolytic degradation.³ Under physiological conditions, the cell has developed a sophisticated system that regulates protease....