Cells are the greatest known molecular engineers, having built extraordinary catalysts, nanomachines, and information processing systems that greatly surpass our capabilities and know-how. How has evolution produced such amazingly complex systems, and how can we catch up? The extensive diversity of related forms in biology suggests that there are natural regulatory points within these systems that can be targeted by simple mutational processes to diversify function. I approach complex molecular systems with an aim to identify these natural control points, understand them in terms of molecular mechanism, and exploit them to build new systems with altered function.

I am currently using this approach to understand how mechanical behaviors are specified and programmed in ciliates, a diverse group of single-celled protozoans that perform an array of dazzling mechanical responses such as jumping, twisting, reorientation and hunting. Remarkably, this wide-range of behaviors arises from organizing various common ciliary and contractile activities together and coordinating their actuation through signaling, and I am charting the design principles that govern the systems biology and biodynamics of these behaviors. In parallel, I am using reconstitution approaches to construct new materials, devices, and networks inspired by these organisms.



Previous Research

My graduate work focused on how cells are able to make sense of the complex sea of ever-changing molecules in their environment. The molecular mechanisms by which these external cues are processed are well understood for many individual signaling pathways. However, fundamental questions for cell biology remain about how the collection of all such pathways within a cell—the signaling network—correctly responds to the many inputs it receives. My dissertation work focused not only on determining the detailed biochemical mechanisms that resolve the complexities and ambiguities of individual cell signaling networks, but also on how these networks can change or grow to accommodate new pathways during evolution. To this end, I reconstituted intact signaling systems in vitro to probe their behavior under different environmental conditions or network compositions, as well as to rigorously compare evolutionarily related systems.

ezgif-1-321b7f0a14Using this approach, I studied two different ambiguous network structures from model systems: overlapping signaling pathways arising from duplication/divergence events, derived from fungal ERK kinase signaling; and central signaling nodes that respond to multiple inputs and fan out to many possible outputs, derived from Ras GTPase signaling. In the former case, allosteric dependencies on pathway-specific scaffold proteins were found to distinguish evolutionarily related molecules from one another and to facilitate the use of homologous molecules in distinct signaling pathways. These allosteric dependencies appear to have evolved by exploitation of pre-existing differences in the conformational landscapes of otherwise-equivalent redundant signaling molecules.

knobsIn the latter case, I explored the behavior and dynamics of Ras•effector signaling assemblies in a systems-level, multi-turnover in vitro setting for the first time. This revealed that Ras systems can transmit both sustained and transient signals and that the concentration and identity of signaling components in the network strongly impacts the timing, duration, shape and amplitude of the output. Moreover, the extent to which oncogenic mutations in Ras distorted outputs was highly dependent on this underlying network configuration.

While in the Lim Lab, I also applied my expertise and understanding of the molecular mechanisms of cell signaling to a T-cell engineering project in which we developed a new method for generation and screening of combinatorial libraries of Chimeric Antigen Receptors. To complete this project, I helped found CellDesignLabs, an immunotherapy startup company. There, as a founding scientist, I led an effort to “port” a variety of proof-of-principle synthetic immune signaling receptors into a clinically relevant context. This involved the development and optimization of new heterodimerization systems built from fully humanized components that operate with FDA-approved drugs. By incorporating these components into synthetic immune receptors and exploiting multivalency of the components, we were able to use small molecules to tune the functional output of these receptors and the signaling synapses they assemble, thus increasing their clinical safety. In a partnership with Kite Pharma, this technology is on track for its first clinical tests to treat acute myeloid leukemia in 2018.