Computational tools for the design of cell-based sensors

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John Dileo, Matthew Peterson, EIleen Chang, David Walburger

MITRE, United States

Cells have an inherent sense-and-respond capability that makes novel synthetic cells a promising area for the design of sensor systems. The design of such systems consists of a number of subsystems, including potentially novel sensing mechanisms – for example proteins adapted to recognize a novel ligand, signal transduction mechanisms, and reporter constructs. Additionally, for sensors expected to be released into the environment, a “kill-switch” mechanism may have to be designed to prevent proliferation of the synthetic species. We are utilizing Clotho (http://www.clothocad.org), an open source platform for the design of synthetic biological systems, to build tools in support of this work. Clotho provides a rich data model designed specifically for synthetic biology, as well as an extensible infrastructure for the design of applications and tools to support research in the field. In addition to storing the data produced by our analyses, we are building Clotho modules for the visualization and analysis of parts and data. We have designed a module for viewing protein structures created and scored using our protein design pipeline (PDP) and importing the results as parts into Clotho. Additionally, we are designing tools for running jobs locally and remotely using Clotho’s actor computation model, as well as the Akka (http://akka.io) framework. Our work has largely focused on structure-based methods for design. This includes the design of novel ligand-binding proteins and riboswitches. This poster describes the methods we have used, as well as the tools we are building within Clotho with the goal of producing and end-to-end workflow for the design of cell-based sensor systems.