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Publications of Eduardo D. Sontag jointly with S.D. Khare
Articles in journal or book chapters
and E.D. Sontag.
Mathematical models of protease-based enzymatic biosensors.
Note: Submitted. Preprint here: https://www.biorxiv.org/content/10.1101/525279v1.Keyword(s): synthetic biology,
An important goal of synthetic biology is to build biosensors and circuits with well-defined input-output relationships that operate at speeds found in natural biological systems. However, for molecular computation, most commonly used genetic circuit elements typically involve several steps from input detection to output signal production: transcription, translation, and post-translational modifications. These multiple steps together require up to several hours to respond to a single stimulus, and this limits the overall speed and complexity of genetic circuits. To address this gap, molecular frameworks that rely exclusively on post-translational steps to realize reaction networks that can process inputs at a timescale of seconds to minutes have been proposed. Here, we build mathematical models of fast biosensors capable of producing Boolean logic functionality. We employ protease-based chemical and light-induced switches, investigate their operation, and provide selection guidelines for their use as on-off switches. We then use these switches as elementary blocks, developing models for biosensors that can perform OR and XOR Boolean logic computation while using reaction conditions as tuning parameters. We use sensitivity analysis to determine the time-dependent sensitivity of the output to proteolytic and protein-protein binding reaction parameters. These fast protease-based biosensors can be used to implement complex molecular circuits with a capability of processing multiple inputs controllably and algorithmically. Our framework for evaluating and optimizing circuit performance can be applied to other molecular logic circuits.
and S.D. Khare.
Computation-guided design of a stimulus-responsive multi-enzyme supramolecular assembly.
This paper reports on the construction of a phosphorylation- and optically-responsive supramolecular complex of metabolic pathway enzymes for the biodegradation of an environmental pollutant. Fusing of enzymes led to an increase in pathway efficiency, and illustrates the possibility of spatio-temporal control over formation and functioning of a wide variety of synthetic biotransformations.
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