Silberg, Jonathan J.2019-05-172020-05-012019-052019-03-27May 2019Atkinson, Joshua T. "Controlling bioenergetic systems using protein design and synthetic biology.." (2019) Diss., Rice University. <a href="https://hdl.handle.net/1911/105935">https://hdl.handle.net/1911/105935</a>.https://hdl.handle.net/1911/105935An understanding of the mechanisms that life uses to regulate this flow of energy and how to program them at different scales is becoming of great importance for the field of synthetic biology as researches build living systems with ever increasing complexity. My thesis goals are to determine design rules for programming the function of proteins that control energy charge and electron transfer in cells. Herein, I describe my efforts in developing a computational pipeline for analyzing sequencing data from bacterial growth selections that depend on the function of adenylate kinase, a protein that controls cellular energy charge, applying this pipeline to libraries of topological mutants to uncover trends in how the energetic frustration in an allosteric domain relates to tolerance to increased local conformational entropy, developing a high-throughput growth selection for monitoring the efficiency of an electron transfer pathway in vivo, design of synthetic allosteric metalloprotein switches to control electron transfer in the cytosol of cells, and finally coupling cytosolic metabolism to a synthetic extracellular respiratory circuit that enables the transfer of intracellular electrons to surface of cells for reduction of conductive materials. These studies help enable synthetic biology strategies for the control of bioenergetics across a variety of length scales including from local energetics of protein structures to the energy charge of the cell to the energetic interface of cells and materials.application/pdfengCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.protein engineeringsynthetic biologybioinformaticsadenylate kinasecircular permutationferredoxinelectron transportextracellular electron transportThesis2019-05-17