Targeted Releasable Affinity Probe (TRAP) for In Vivo Photocrosslinking

• Published in: Chembiochem : a European journal of chemical biology 2009-06, Vol.10 (9), p.1507-1518
• Main Authors: Yan, Ping, Wang, Ting, Newton, Gregory J, Knyushko, Tatyana V, Xiong, Yijia, Bigelow, Diana J, Squier, Thomas C, Mayer, M. Uljana
• Format: Article
• Language: English
• Subjects: Affinity Labels - chemical synthesis; Affinity Labels - chemistry; Amino Acid Sequence; Animals; arsenic; Binding Sites; bioorganic chemistry; Calmodulin - chemistry; Calmodulin - metabolism; Cell Line, Tumor; Cross-Linking Reagents - chemical synthesis; Cross-Linking Reagents - chemistry; DNA-Directed RNA Polymerases - chemistry; DNA-Directed RNA Polymerases - metabolism; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Fluorescent Dyes - chemical synthesis; Fluorescent Dyes - chemistry; fluorescent probes; mass spectrometry; Mice; Molecular Sequence Data; Myosin-Light-Chain Kinase - chemistry; Myosin-Light-Chain Kinase - metabolism; Peptidylprolyl Isomerase - chemistry; Peptidylprolyl Isomerase - metabolism; photoaffinity labeling; Protein Binding; Protein Interaction Domains and Motifs; Proteins - chemistry; Proteins - metabolism
• ISSN: 1439-4227; 1439-7633
• DOI: 10.1002/cbic.200900029

A protein TRAP: The in vivo photocrosslinking of TRAP after its intracellular targeting to a binding sequence on the bait protein stabilizes protein interactions. Because the crosslinker is releasable, simple mass spectrometry can be used to identify the protein binding sites after purification.Protein crosslinking, especially coupled to mass-spectrometric identification, is increasingly used to determine protein binding partners and protein-protein interfaces for isolated protein complexes. The modification of crosslinkers to permit their targeted use in living cells is of considerable importance for studying protein-interaction networks, which are commonly modulated through weak interactions that are formed transiently to permit rapid cellular response to environmental changes. We have therefore synthesized a targeted and releasable affinity probe (TRAP) consisting of a biarsenical fluorescein linked to benzophenone that binds to a tetracysteine sequence in a protein engineered for specific labeling. Here, the utility of TRAP for capturing protein binding partners upon photoactivation of the benzophenone moiety has been demonstrated in living bacteria and mammalian cells. In addition, ligand exchange of the arsenic-sulfur bonds between TRAP and the tetracysteine sequence to added dithiols results in fluorophore transfer to the crosslinked binding partner. In isolated protein complexes, this release from the original binding site permits the identification of the proximal binding interface through mass spectrometric fragmentation and computational sequence identification.