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Genetically encoded non-canonical amino acids (NCAAs) have allowed researchers to access functionalities that would be otherwise unavailable with the naturally-occurring amino acids. The metal-chelating NCAA (2,2'-bipyridin-5yl)alanine (Bpy-ala) has recently been employed, in tandem with computational modeling, to drive the assembly of a homotrimeric protein complex in the presence of a metal ion, specifically Fe(II). While a successful design was identified to form a homotrimeric complex with an iron-trisbipyridyl [Fe(Bpy-ala)3]2+ core when expressed in E. coli, its subsequent utility was marred by an excessively strong protein-protein interaction thus leading to a lack of metal-dependency. This thesis describes principles of protein design and characterization used to reduce the favorability of the apo protein complex in solution, resulting in the experimental verification of a mutant that undergoes facile, reversible complex assembly and disassembly in the presence or absence of Fe(II), respectively. The addition of other metal ions, such as Co(II) or Ni(II), yields products that show some level of assembly, although not with the same efficiency as Fe(II) addition, necessitating a better description of the energetics and kinetics of the system. Current studies are ongoing to examine the redox properties of the complex, as well as the kinetics of the metal-mediated self-assembly. Attempts to nucleate the trimer with Ru(II), forming a [Ru(Bpy)3]2+ complex with its interesting photophysical, photochemical, and photoredox properties, have not been met with substantial success, as coordination of the low-spin d6 metal ion often requires harsh conditions. However, due to the unique stability of the TRI_05 complexes, many approaches are available to this end, and experiments are underway to elucidate the proper conditions.
ContributorsAlmhjell, Patrick James (Author) / Mills, Jeremy H. (Thesis director) / Moore, Gary F. (Committee member) / Department of Psychology (Contributor) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Proteins are, arguably, the most complicated molecular machines found in nature. From the receptor proteins that decorate the exterior of cell membranes to enzymes that catalyze the slowest of chemical reactions, proteins perform a wide variety of essential biological functions. A reductionist view of proteins as a macromolecular group, however, may hold that they simply interact with other chemical species. Notably, proteins interact with other proteins, other biological macromolecules, small molecules, and ions. This in turn makes proteins uniquely qualified for use technological use as sensors of said chemical species (biosensors). Several methods have been developed to convert proteins into biosensors. Many of these techniques take advantage of fluorescence spectroscopy because it is a fast, non-invasive, non-destructive and highly sensitive method that also allows for spatiotemporal control. This, however, requires that first a fluorophore be added to a target protein. Several methods for achieving this have been developed from large, genetically encoded autofluorescent protein tags, to labeling with small molecule fluorophores using bioorthogonal chemical handles, to genetically encoded fluorescent non-canonical amino acids (fNCAA). In recent years, the fNCAA, L-(7-hydroxycoumarin-4yl)ethylglycine (7-HCAA) has been used in to develop several types of biosensors.
The dissertation I present here specifically addresses the use of the fNCAA L-(7-hydroxycoumarin-4-yl)ethylglycine (7-HCAA) in protein-based biosensors. I demonstrate 7-HCAA’s ability to act as a Förster resonance energy transfer (FRET) acceptor with tryptophan as the FRET donor in a single protein containing multiple tryptophans. I the describe efforts to elucidate—through both spectroscopic and structural characterization—interactions within a 7-HCAA containing protein that governs 7-HCAA fluorescence. Finally, I present a top-down computational design strategy for incorporating 7-HCAA into proteins that takes advantage of previously described interactions. These reports show the applicability of 7-HCAA and the wider class of fNCAAs as a whole for their use of rationally designed biosensors.
The dissertation I present here specifically addresses the use of the fNCAA L-(7-hydroxycoumarin-4-yl)ethylglycine (7-HCAA) in protein-based biosensors. I demonstrate 7-HCAA’s ability to act as a Förster resonance energy transfer (FRET) acceptor with tryptophan as the FRET donor in a single protein containing multiple tryptophans. I the describe efforts to elucidate—through both spectroscopic and structural characterization—interactions within a 7-HCAA containing protein that governs 7-HCAA fluorescence. Finally, I present a top-down computational design strategy for incorporating 7-HCAA into proteins that takes advantage of previously described interactions. These reports show the applicability of 7-HCAA and the wider class of fNCAAs as a whole for their use of rationally designed biosensors.
ContributorsGleason, Patrick Ray (Author) / Mills, Jeremy H (Thesis advisor) / Hecht, Sidney M. (Committee member) / Fromme, Petra (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2020