title: A chemical proteomic probe for detecting dehydrogenases: catechol rhodanine.
abstract: Inherent complexity of the proteome often demands that it be studied as manageable subsets, termed subproteomes. A subproteome can be defined in a number of ways, although a pragmatic approach is to define it based on common features in an active site that lead to binding of a common small molecule ligand (e.g., a cofactor or a cross-reactive drug lead). The subproteome, so defined, can be purified using that common ligand tethered to a resin, with affinity chromatography. Affinity purification of a subproteome is described in the next chapter. That subproteome can then be analyzed using a common ligand probe, such as a fluorescent common ligand that can be used to stain members of the subproteome in a native gel. Here, we describe such a fluorescent probe, based on a catechol rhodanine acetic acid (CRAA) ligand that binds to dehydrogenases. The CRAA ligand is fluorescent and binds to dehydrogenases at pH > 7, and hence can be used effectively to stain dehydrogenases in native gels to identify what subset of proteins in a mixture are dehydrogenases. Furthermore, if one is designing inhibitors to target one or more of these dehydrogenases, the CRAA staining can be performed in a competitive assay format, with or without inhibitor, to assess the selectivity of the inhibitor for the targeted dehydrogenase. Finally, the CRAA probe is a privileged scaffold for dehydrogenases, and hence can easily be modified to increase affinity for a given dehydrogenase.
authors: Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI, USA.
authors: Xia
authors: X
authors: Ge
authors: Daniel S
authors: DS
authors: Sem
mesh_terms: D001667:Binding, Competitive; D002396:Catechols / Q000378:metabolism*; D004591:Electrophoresis, Polyacrylamide Gel; D005453:Fluorescence; D015335:Molecular Probes / Q000378:metabolism*; D010088:Oxidoreductases / Q000378:metabolism*; D020543:Proteome / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012236:Rhodanine / Q000031:analogs & derivatives* / Q000378:metabolism*; D013194:Staining and Labeling
chemical_list: D002396:Catechols; D015335:Molecular Probes; D020543:Proteome; D012236:Rhodanine; D010088:Oxidoreductases