The Witte group is interested in the role of non-template encoded biomolecules during biological processes. Cells can change the activity, function and location of a protein by posttranslationally modifying the protein with carbohydrates, phosphate groups, lipids and sulfate groups. Similarly, enzymes modifying the sulfation pattern of sulfated glycosaminoglycans alter signaling, growth and metastasis. Finally, enzymes involved in the synthesis and degradation of phospholipids are for example involved in immune response and oxidative stress. These non-template encoded modifications are difficult to study using traditionally biochemical techniques. The Witte group focuses on the development of new Chemical Biology tools to study the role of these modifications and will apply these tools to study the role of these modifications in for example chemokine signaling.

Activity-based probes (ABPs) for activity-based protein profiling

To study enzymes that are involved in the synthesis and degradation of non-template encoded biomolecules, the Witte group develops activity-based probes (ABPs) based on the mechanism of these enzymes. ABPs generally consist of three fragments: a reactive group, a linker and a label. The reactive group is often based on the mechanism of the enzyme and selectively reacts with the enzyme or class of enzymes of interest. The linker can be used to introduce the selectivity. The third part of the probe, the label, can be used for direct read out or for purification and further analysis. In a typically profiling experiment, the complex proteome is incubated with the probe. If the label is a fluorophore, the labeled proteins can be directly visualized by fluorescence scan. Proteins can be purified using the label to identify the protein by MS.

Development of protein labeling techniques.

Many posttranslational modifications are heterogeneous in nature and this complicates determining the role of the modification. A method to selectively and homogeneously introduce a posttranslational modification can be helpful to establish the role of the specific modification. The Witte group applies a transpeptidation reaction catalyzed by the bacterial enzyme sortase A to selectively introduce posttranslational modifications. Sortase A is involved in the synthesis of the bacterial cell wall, but due to its high substrate tolerance has become a useful protein labeling tool. The enzyme recognizes a peptide sequence, LPXTGG, and cleaves this sequence after the threonine residue forming a thioester. Nucleophiles having an N-terminal oligoglycine sequence react with the thioester, thereby releasing the enzyme and forming a new peptide bond. Using this strategy, protein-protein fusion can be prepared, proteins can be decorated with a variety of labels and unnaturally fused proteins can be prepared.