Analysis and Design of Nonlinear Processing and Emergent Behavior in Biocatalytic Networks
Abstract
This program uses the fatty acid pathway of Escherichia coli as a model system with which to examine the design rules and logic structures that enable multi-enzyme systems to perform complex, nonlinear operations. In the field of systems and synthetic biology, it departs from contemporary investigations of transcriptional regulation and genetic circuits by undertaking a systematic examination of biocatalytic processing outside of the cell (i.e., by using a reconstituted fatty acid pathway). There are four objectives: (i) to identify kinetically coupled controls of fatty acid synthesis, (ii) to examine the structural basis of functional compatibility between enzymes, (iii) to assess the functional advantage of catalytic branching (the replacement of a single enzyme with multiple specialized enzymes), and (iv) to measureÑ and tuneÑthe response fatty acid synthesis to stimuli (e.g., changes in temperature or inhibitor concentration). These efforts will require the construction of a detailed kinetic model of fatty acid synthesis, the reconstitution of a fatty acid pathway (in vitro) to testÑand validate Ñmodel predictions, the use of sophisticated biophysical tools (e.g., isothermal titration calorimetry, X-ray crystallography, NMR spectroscopy, and molecular dynamics simulations) to analyze the structural basis and thermodynamic origin of substrate specificity in pathway enzymes, and the use of site-directed mutagenesis to modify the behavior (i.e., activity, temperature sensitivity, and/or susceptibility to inhibition) of pathway enzymes. The overarching goal of this work is the development of a general framework for building self-regulating, stable, and/or stimuli-responsive biocatalytic networks.
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Feb 14, 2019
- Source ID
- W911NF1810159
Entities
People
- Jerome M Fox
Organizations
- Army Contracting Command
- United States Army
- University of Colorado Boulder