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In oxygenic photosynthesis, conversion of solar energy to chemical energy is catalyzed by the<br/>pigment-protein complexes Photosystem II (PSII) and Photosystem I (PSI) embedded within the<br/>thylakoid membrane of photoautotrophs. The function of these pigment-protein complexes are<br/>conserved between all photoautotrophs, however, the oligomeric structure, as well as the<br/>spectroscopic properties of the PSI

In oxygenic photosynthesis, conversion of solar energy to chemical energy is catalyzed by the<br/>pigment-protein complexes Photosystem II (PSII) and Photosystem I (PSI) embedded within the<br/>thylakoid membrane of photoautotrophs. The function of these pigment-protein complexes are<br/>conserved between all photoautotrophs, however, the oligomeric structure, as well as the<br/>spectroscopic properties of the PSI complex, differ. In early evolving photoautotrophs, PSI<br/>exists in a trimeric organization, but in later evolving species this was lost and PSI exists solely<br/>as a monomer. While the reasons for a change in oligomerization are not fully understood, one<br/>of the 11 subunits within cyanobacterial PSI, PsaL, is thought to be involved in trimerization<br/>through the coordination of a calcium ion in an adjacent monomer. Recently published<br/>structures have demonstrated that PSI complexes are capable of trimerization without<br/>coordinating the calcium ion within PsaL.<br/>5 Here we explore the role the calcium ion plays in both<br/>the oligomeric and spectroscopic properties in PSI isolated from Synechocystis sp. PCC 6803.

ContributorsVanlandingham, Jackson R (Author) / Mazor, Yuval (Thesis director) / Mills, Jeremy (Committee member) / School of Life Sciences (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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The growing global energy demand coupled with the need for a low-carbon economy requires innovative solutions. Microalgal oxygenic photosynthesis provides a sustainable platform for efficient capture of sunlight and storage of some of the energy in the form of reduced carbon derivatives. Under certain conditions, the photosynthetic reductant can be

The growing global energy demand coupled with the need for a low-carbon economy requires innovative solutions. Microalgal oxygenic photosynthesis provides a sustainable platform for efficient capture of sunlight and storage of some of the energy in the form of reduced carbon derivatives. Under certain conditions, the photosynthetic reductant can be shunted to molecular hydrogen production, yet the efficiency and longevity of such processes are insufficient. In this work, re-engineering of the heterodimeric type I reaction center, also known as photosystem I (PSI), in the green microalga Chlamydomonas reinhardtii was shown to dramatically change algal metabolism and improve photobiological hydrogen production in vivo. First, an internal fusion of the small PsaC subunit of PSI harboring the terminal photosynthetic electron transport chain cofactors with the endogenous algal hydrogenase 2 (HydA2) was demonstrated to assemble on the PSI core in vivo, albeit at ~15% the level of normal PSI accumulation, and make molecular hydrogen from water oxidation. Second, the more physiologically active algal endogenous hydrogenase 1 (HydA1) was fused to PsaC in a similar fashion, resulting in improved levels of accumulation (~75%). Both algal hydrogenases chimeras remained extremely oxygen sensitive and benefited from oxygen removal methods. On the example of PSI-HydA1 chimera, it was demonstrated that the active site of hydrogenase can be reactivated in vivo after complete inactivation by oxygen without the need for new polypeptide synthesis. Third, the hydrogenase domain of Megasphaera elsdenii bacterial hydrogenase (MeHydA) was also fused with psaC, resulting in expression of a PSI-hydrogenase chimera at ~25% the normal level. The heterologous hydrogenase chimera could be activated with the algal maturation system, despite only 32 % sequence identity (43 % similarity). All constructs demonstrated diminished ability to reduce PSI electron acceptors (ferredoxin and flavodoxin) in vitro and indirect evidence indicated that this was true in vivo as well. Finally, chimeric design considerations are discussed in light of the models generated by Alphafold2 and how could they be used to further optimize stability of the PSI-hydrogenase chimeric complexes.
ContributorsKanygin, Andrey (Author) / Redding, Kevin E (Thesis advisor) / Jones, Anne K (Committee member) / Mazor, Yuval (Committee member) / Arizona State University (Publisher)
Created2022
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Description
Cryogenic Electron Microscopy (Cryo-EM) is a method that can be used for studying the structure of biological systems. Biological samples are frozen to cryogenic temperatures and embedded in a vitreous ice when they are imaged by electrons. Due to its ability to preserve biological specimens in near-native conditions, cryo-EM has

Cryogenic Electron Microscopy (Cryo-EM) is a method that can be used for studying the structure of biological systems. Biological samples are frozen to cryogenic temperatures and embedded in a vitreous ice when they are imaged by electrons. Due to its ability to preserve biological specimens in near-native conditions, cryo-EM has a significant contribution to the field of structural biology.Single-particle cryo-EM technique was utilized to investigate the dynamical characteristics of various protein complexes such as the Nogo receptor complex, polymerase ζ (Polζ) in yeast and human integrin ⍺vβ8-pro-TGFβ1-GARP complex. Furthermore, I proposed a new method that can potentially improve the sample preparation for cryo-EM. The Nogo receptor complex was expressed using baculovirus expression system in sf9 insect cells and isolated for structural studies. Nogo receptor complex was found to have various stoichiometries and interactions between individual proteins. A structural investigation of the yeast apo polymerase ζ holoenzyme was also carried out. The apo Polζ displays a concerted motions associated with expansion of the Polζ DNA-binding channel upon DNA binding. Furthermore, a lysine residue that obstructs the DNA-binding channel in apo Polζ was found and suggested a gating mechanism. In addition, cryo-EM studies of the human integrin ⍺vβ8-pro-TGFβ1-GARP complex was conducted to assess its dynamic interactions. The 2D classifications showed the ⍺vβ8-pro-TGFβ1-GARP complex is highly flexible and required several sample preparation techniques such as crosslinking and graphene oxide coating to improve protein homogeneity on the EM grid. To overcome challenges within the cryo-EM technique such as particle adsorption on air-water interface, I have documented a collaborative work on the development and application of lipid monolayer sandwich on cryo-EM grid. Cryogenic electron tomography (cryo-ET) along with cryo-EM were used to study the characteristics of lipid monolayer sandwich as a potential protective layer for EM grid. The cryo-ET results demonstrated that the thickness of lipid monolayer is adequate for single-particle cryo-EM processing. Furthermore, there was no appearance of preferred orientations in cryo-EM and cryo-ET images. To establish that this method is actually beneficial, more data must be collected, and high-resolution structures of protein samples must be obtained using this methodology.
ContributorsTruong, Chloe Du (Author) / Chiu, Po-Lin (Thesis advisor) / Liu, Wei (Committee member) / Mazor, Yuval (Committee member) / Arizona State University (Publisher)
Created2021
Description

Polyketides are a wide ranging class of natural microbial products highly relevant to the pharmacological industry. As chemical synthesis of polyketides is quite challenging, significant effort has been made to understand the polyketide synthases (PKSs) responsible for their natural production. Native to Streptomyces, the aln biosynthetic gene cluster was recently

Polyketides are a wide ranging class of natural microbial products highly relevant to the pharmacological industry. As chemical synthesis of polyketides is quite challenging, significant effort has been made to understand the polyketide synthases (PKSs) responsible for their natural production. Native to Streptomyces, the aln biosynthetic gene cluster was recently characterized and encodes for an iterative type I polyketide synthase (iT1PKS). This iT1PKS produces both , and ,-double bond polyketides named allenomycins; however, the basis in which one bond is chosen over the other is not yet clear. The dehydratase domain, AlnB_DH, is thought to be solely responsible for catalyzing double bond formation. Elucidation of enzyme programming is the first step towards reprogramming AlnB_DH to produce novel industrially relevant products. The Nannenga lab has worked as collaborators to the Zhao lab at the University of Illinois at Urbana-Champaign to unravel AlnB_DH’s structure and mechanism. Here, mutant constructs of AlnB_DH are developed to elucidate enzyme structure and provide insight into active site machinery. The primary focus of this work is on the development of the mutant constructs themselves rather than the methods used for structural or mechanistic determination. Truncated constructs were successfully developed for crystallization and upon x-ray diffraction, a 2.45 Å resolution structure was determined. Point-mutated constructs were then developed based on structural insights, which identified H49, P58, and H62 as critical residues in active site machinery.

ContributorsBlackson, Wyatt (Author) / Nannenga, Brent (Thesis director) / Nielsen, David (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor) / School of Molecular Sciences (Contributor)
Created2023-05