Dr. Arbely’s lab develops and uses genetic code expansion technology that facilitates the site-specific incorporation of noncanonical amino acids into proteins expressed in live cells. Conventional protein engineering is limited to the 20 common amino acids, whereas expansion of the genetic code to include noncanonical residues can genetically confer differences such as post-translational modifications (PTMs) and the addition of photosensitive groups or biorthogonal chemical handles. In doing so, the lab essentially performs protein engineering with a larger vocabulary, thereby providing new approaches for biochemical and biophysical studies of proteins in vitro, as well as in living systems. The technology also provides the biotechnology industry with the unprecedented ability to modify old as well as new therapeutic proteins, and thus confer new functionality and value.
The lab is working to achieve two main things. One is the study of the human acetylome – the entire complement of acetylated proteins, and the other is site-specific labeling for fluorescence imaging (bio-orthogonal labeling).
The scientific community realized that lysine acetylation is an important post-translational modification (PTM) with thousands of potential acetylation sites on different proteins in the cell. However, there are still not enough tools for studying the effect of acetylation on protein structure and function, or its regulation. We are interested in the effect of acetylation on the catalytic activity of different enzymes, transcription factors, and metabolic proteins. Since acetylated proteins can also be attractive drug targets, this is also important information when it comes to epigenetic drugs. These molecules control the level of acetylation by blocking the catalytic activity of histone deacetylases, which are enzymes that remove the acetylation from the protein. Therefore, the research group develops methodologies for identifying specific deacetylases and their interaction with their substrates both in vivo and in vitro. These methods are useful both as basic research tools (they can be used for studying the entire human acetylome) and also in drug development (the lab’s deacetylation assay can be used for the screening of more potent and specific deacetylase inhibitors).
The lab’s work on site-specific fluorescent labeling is a collaboration with Dr. Natalie Elia who specializes in cellular dynamics and 3-dimensional macromolecular architecture. Current fluorescent labeling techniques tend to use large protein molecules such as GFP, which have their limitations (mainly large size and poor photophysical parameters). Small fluorescent organic dyes attached via bio-orthoganal labeling have several advantages: they’re more stable, require less UV light to excite and therefore may cause less damage to the cell, can be measured for a longer time, and due to their small size, have minimal effect on the structure and function of the labeled protein. The researchers develop new methodologies and optimize current methods to allow robust site-specific labeling of proteins in live mammalian cells for fluorescent imaging, both as a research tool in academia and as a powerful labeling technique for the biotechnology industry.