Research Interests:

An increasing body of data suggests that most proteins that regulate intracellular processes are constructed in a modular fashion from a combination of interaction and catalytic domains. Interaction domains mediate the formation of multi-protein complexes that confine signaling proteins to appropriate subcellular locations and help determine the specificity of enzyme-substrate interactions. In addition, extracellular protein domains mediate interactions between adjacent cells and help control higher order processes such as the formation of nerve synapses in the brain. To date, biologists and biochemists have typically studied protein-protein interactions one at a time. While reductionism has provided a detailed understanding of individual components, it has been less successful in uncovering the complex function of biological systems. I am interested in identifying, characterizing, and perturbing whole families of domains as a first step in understanding how the cell exploits molecular recognition to regulate complex processes such as protein trafficking, intercellular communication, and apoptosis.

The approach my lab is taking consists of three steps. First, using high-throughput methods, we clone, express, and purify collections of proteins or protein domains involved in a biological system or process. As an example, we are studying the family of PDZ domain-containing proteins encoded in the mouse genome. PDZ domains are approximately 90 residue repeats found in a number of proteins associated with receptors, membrane channels, and signal transduction proteins. There are 266 predicted PDZ domains in over 100 different proteins in the mouse genome, many of which are expressed specifically in neural tissue. They are involved in spatial localization and clustering of functional complexes of proteins and in targeting signaling molecules to the plasma membrane. We are investigating the interactions mediated by these domains on a genome-wide level using protein microarrays [MacBeath G & Schreiber SL (2000) Science, 289, 1760]. As an aside, we continue to explore ways to improve our technology as we apply it to the study of biological systems.

Second, once we have identified specific protein-protein interactions in this in vitro format, we then seek to study the effects of perturbing such interactions in vivo. Our goal is to perform these studies using cell-permeable small molecules that modulate the function of specific proteins within the cell. Thus, my group is also developing high-throughput screening methods using protein microarrays to identify highly specific ligands. This we do in collaboration with the Broad Institute. By screening compounds using microarrays of protein rather than individual targets, we can not only increase the efficiency of the discovery process (by up to 2 orders of magnitude), but can assess each compound for its specificity.

Finally, as the third stage in our investigations, we seek to study the effects of perturbing protein function in vivo on a system-wide level. To do this, we are developing and applying antibody microarray technology to measure the abundance and modification states of multiple proteins simultaneously. As a model system, we are focusing on the ErbB signaling network. Our hope is that by using systems-level analyses, we will gain a better understanding of how cells use networks of interacting proteins to regulate biological processes.

Selected Publications:

Nielsen, U. B., Cardone, M. H., Sinskey, A. J., MacBeath, G., and Sorger, P. K. (2003). Profiling receptor tyrosine kinase activation by using Ab microarrays. Proc. Natl. Acad. Sci. USA 100: 9330-9335.

MacBeath G & Schreiber SL (2000). Printing proteins as microarrays for high-throughput function determination. Science 289: 1760-1763.

MacBeath G, Koehler AN, & Schreiber SL (1999). Printing small molecules as microarrays and detecting protein-ligand interactions en masse. J. Am. Chem. Soc. 121: 7967-7968.

MacBeath G (2002). Protein microarrays and proteomics. Nature Genetics 32 Suppl 2: 526-532.

MacBeath G (2001). Proteomics comes to the surface. Nature Biotechnology 19: 828-829.

MacBeath G (2001). Chemical genomics: what will it take and who gets to play? Genome Biology 2: 2005.1-2005.6.