The interactions between proteins and other biomolecules is essential to proper biological function. However, protein misfolding and the introduction of exogenous species into the body can result in the presence of unnatural interactions, such as the formation of amyloid plaques.¹ By understanding the location and nature of these protein-protein interaction interfaces, development of targeted inhibitors of undesired interactions should be possible.

While several methods currently exist for the study of protein-protein interfaces, such as x-ray crystallography and hydrogen-deuterium exchange, these methods are costly and low-throughput. In addition, these methods will subject proteins to non-physiological conditions, which can give misleading conclusions about protein structure and interfaces. This project proposes the usage of fast-acting, covalent tags to label the protein surface. These tags, when used in tandem with traditional mass spectrometry, will give information about the protein’s tertiary structure, as well as the interface between two proteins.

Fluorescamine, a fluorogenic dye that binds specifically to lysine (Lys) and arginine (Arg), has been demonstrated (via fluorescence) to only target solvent-accessible amino acid residues.² As the binding interface between two proteins is shielded from solvent interactions, a combination of fluorescamine labeling and mass spectrometry will be able to determine the location of this interface on each protein, via comparison of the degree and location of tagging of the individual protein versus the protein-protein complex (figure above). This method can also be used to assess protein conformational changes upon binding events, as well as look at protein misfolding.

1. Gonzalez, M. W.; Kann, M. G., Chapter 4: Protein Interactions and Disease. Plos Computational Biology 2012, 8 (12).

2. Ashby, J.; Duan, Y. K.; Ligans, E.; Tamsi, M.; Zhong, W. W., High-Throughput Profiling of Nanoparticle-Protein Interactions by Fluorescamine Labeling. Analytical Chemistry 2015, 87 (4), 2213-2219.