Photoaffinity labeling combined with mass spectrometric approaches as a tool for structural proteomics

Abstract

Protein chemistry, such as crosslinking and photoaffinity labeling, in combination with modern mass spectrometric techniques, can provide information regarding protein–protein interactions beyond that normally obtained from protein identification and characterization studies. While protein crosslinking can make tertiary and quaternary protein structure information available, photoaffinity labeling can be used to obtain structural data about ligand–protein interaction sites, such as oligonucleotide–protein, drug–protein and protein–protein interaction. In this article, we describe mass spectrometry-based photoaffinity labeling methodologies currently used and discuss their current limitations. We also discuss their potential as a common approach to structural proteomics for providing 3D information regarding the binding region, which ultimately will be used for molecular modeling and structure-based drug design.

Keywords::

• mass spectrometry
• molecular modeling
• photoaffinity labeling
• photolabeling
• protein–drug interactions
• protein–peptide interactions
• stoichiometry
• structural proteomics
• structure-based drug design

Acknowledgements

This research was supported in part by the Intramural Research Program of the NIH, National Institute of Environmental Health Sciences, and Developmental Award #9P30 AI050410 from the University of North Carolina Center for AIDS Research (NC, USA).