Controlling bioenergetic systems using protein design and synthetic biology.

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dc.contributor.advisorSilberg, Jonathan J.en_US
dc.contributor.committeeMemberBennett, George N.en_US
dc.creatorAtkinson, Joshua Ten_US
dc.date.accessioned2019-05-17T18:34:20Zen_US
dc.date.available2020-05-01T05:01:08Zen_US
dc.date.created2019-05en_US
dc.date.issued2019-03-27en_US
dc.date.submittedMay 2019en_US
dc.date.updated2019-05-17T18:34:20Zen_US
dc.description.abstractAn 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.en_US
dc.embargo.terms2020-05-01en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationAtkinson, 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>.en_US
dc.identifier.urihttps://hdl.handle.net/1911/105935en_US
dc.language.isoengen_US
dc.rightsCopyright 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.en_US
dc.subjectprotein engineeringen_US
dc.subjectsynthetic biologyen_US
dc.subjectbioinformaticsen_US
dc.subjectadenylate kinaseen_US
dc.subjectcircular permutationen_US
dc.subjectferredoxinen_US
dc.subjectelectron transporten_US
dc.subjectextracellular electron transporten_US
dc.titleControlling bioenergetic systems using protein design and synthetic biology.en_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentSystems, Synthetic and Physical Biologyen_US
thesis.degree.disciplineNatural Sciencesen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelDoctoralen_US
thesis.degree.nameDoctor of Philosophyen_US
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