Theses and Dissertations at Montana State University (MSU)
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Item New insights into radical initiation by radical S-adenosylmethionine enzymes and activation of [FeFe]-hydrogenase(Montana State University - Bozeman, College of Letters & Science, 2020) Impano, Stella; Chairperson, Graduate Committee: Joan B. Broderick; Hao Yang, Adrien Pagnier, Richard Jodts, Ryan Swimley, Eric M. Shepard, Sarah M. Hill, Christopher D. James, William E. Broderick, Brian M. Hoffman and Joan B. Broderick were co-authors of the article, 'Photolytic cleavage of S-adenosylmethionine' which is contained within this dissertation.; Eric M. Shepard, Hao Yang, Adrien Pagnier, Ryan Swimley, Emma Dolen, William E. Broderick, Brian M. Hoffman and Joan B. Broderick were co-authors of the article, 'Generation of an ethyl radical trapped in active sites of [FeFe]-hydrogenase maturase enzymes HydE AND HydG' which is contained within this dissertation.; Eric M. Shepard, Hao Yang, Jeremiah N. Betz, Adrien Pagnier, William E. Broderick, Brian M. Hoffman and Joan B. Broderick were co-authors of the article, 'EPR and ENDOR spectroscopic evidence of an ammonium binding site in HydE' which is contained within this dissertation.; Adrien Pagnier, Eric M. Shepard, William E. Broderick and Joan B. Broderick were co-authors of the article, 'Investigation into all the necessary components required for [FeFe]-hydrogenase H-cluster maturation' which is contained within this dissertation.; Dissertations contains two articles of which Stella Impano is not the main author.Radical S-adenosylmethionine (SAM) enzymes harbor a [4Fe-4S] cluster in their active sites that coordinates a catalytically relevant small molecule SAM. During catalysis the S-5'C bond of SAM is reductively cleaved to generate a 5'-deoxyadenosyl radical that subsequently abstracts an H atom from substrate, allowing functionally diverse reactions to be achieved. Trapping of the 5'-deoxyadenosyl radical intermediate during turnover had proven difficult likely due to the formation of omega intermediate resulting from the oxidative addition of the 5'-deoxyadenosyl radical to the unique iron of the cluster. Recently, our laboratory showed that this elusive 5'-deoxyadenosyl can be liberated, captured, and characterized, in the absence of substrate, via photoinduced electron transfer (ET)-mediated reductive cleavage of SAM. Further, photolysis of [4Fe-4S] +-SAM complexes in different radical SAM enzymes revealed that the regioselective bond cleavage of SAM is dependent on the active site environment where either a 5'-deoxyadenosyl or a *CH 3, depending on the enzyme. When Sadenosyl- ethionine is used in place of SAM in the [4Fe-4S] +-SAM complex of HydE or HydG an ethyl radical is trapped. In either case, annealing of the methyl and ethyl radicals yields corresponding omega-like species, omega M and omega E, respectively. Functionally, HydE and HydG work together with a third protein HydF, to synthesize the H-cluster of [FeFe]-hydrogenase enzymes. HydG lyses tyrosine to generate CO and CN - ligands of the diiron core of the H-cluster, while the role and substrate of HydE are yet to be elucidated; however, it is hypothesized that this enzyme is responsible for dithiomethylamine (DTMA) bridge assembly. Our hypothesis is that HydE uses ammonium as a co-substrate and we propose that this polyatomic ion condenses with two CH 2S- like species to assemble the DTMA. We demonstrate for the first time via EPR and ENDOR spectroscopic techniques that HydE harbors an ammonium binding site; this NH 4 + would be stored in the active site of HydE prior to DTMA synthesis. Additionally, through in vitro [FeFe]-hydrogenase assays, we investigate what component of the essential E. coli lysate is required for H-cluster assembly. Results from this work suggest that the Hyd maturases are not the only proteins needed for H-cluster biosynthesis.Item How biological catalysts activate oxygen to realize its full potential(Montana State University - Bozeman, College of Letters & Science, 2021) Ellis, Emerald Sue; Chairperson, Graduate Committee: Jennifer DuBois; Daniel J. Hinchen, Alissa Bleem, Lintao Bu, Bennett R. Streit, Quinlan V. Doolin, William E. Michener and Brandon C. Knott were authors and Sam J.B. Mallinson, Mark D. Allen, Melodie M. Machovina, Christopher W. Johnson, Gregg T. Beckham, John E. McGeehan, Jennifer L. DuBois were co-authors of the article, 'Engineering a biocatalyst for demethylation of lignin-derived aromatic aldehydes' in the journal 'Journal of the American Chemical Society Au' which is contained within this dissertation.; Luke MacHale, Robert K. Szilagyi and Jennifer L. DuBois were co-authors of the article, 'How chemical environment activates anthralin and molecular oxygen for direct reaction' in the journal 'Journal of organic chemistry' which is contained within this dissertation.; Dissertation contains an article of which Emerald Sue Ellis is not the main author.Dioxygen is a potent oxidant, inexpensive, and environmentally-friendly compared with most industrial oxidants, but intrinsic energy barriers to reaction limit its utility. Biological catalysts can activate O 2 by generating dangerous reactive oxygen species intermediates. The fundamental chemistry of two diverse O 2-utilizing enzyme systems were examined: GcoAB, a cytochrome P450 which catalyzes the O-demethylation of aromatic alcohols using heme to activate O 2, and NMO, an antibiotic biosynthesis monooxygenase which catalyzes cofactor-independent monooxygenation of an organic substrate. The enzyme active site environments and the reactions catalyzed therein were investigated with mutagenesis, X-ray crystallography, molecular dynamics simulations, fluorescence and UV/visible spectroscopy, cyclic voltammetry, electrode-based measurement of O 2 consumption, high-performance liquid chromatography, and simulations of homogenous solvation using quantum chemistry composite methods. The substrate range of GcoAB was expanded by rational design engineering to include two aromatic aldehydes commonly found in chemically-processed lignin. Only a single-point mutation was needed for GcoAB to catalyze demethylation of each new substrate. The reaction catalyzed by NMO can be called 'substrate-assisted' because the substrate mimics the role of the organic cofactor flavin in activating O 2. The physics of this reaction were probed using Marcus Theory, which relates the activation energy of the reaction to the free energy and the reorganization energy. By measuring the differences in the activation energy and free energy of the reaction within and without the enzyme, we found that the enzyme mainly acts on the reorganization energy term. The reaction was then examined in several homogenous solvents chosen based on their chemical similarity to individual amino acids. Homogenous solvation is much less computationally expensive to model than a protein active site, especially at higher levels of theory. By this approach, we discovered a plausible mechanism by which the chemical environment alone can boost the O 2-activating capacity of NMO's substrate--particularly by stabilizing the deprotonated anion which can transfer an electron to O 2 more easily than the neutral molecule. In summary, this work demonstrates that, while cofactors are responsible for activating O 2 in most oxidases, full appreciation of how an oxidase catalyzes reactions requires that neither the enzyme environment nor the substrate be ignored.Item Biochemical and biophysical characterization of plastic degrading aromatic polyesterases(Montana State University - Bozeman, College of Letters & Science, 2019) Topuzlu, Ece; Chairperson, Graduate Committee: Valerie Copie; Brandon C. Knott and Mark D. Allen were authors and Japheth Gado, Harry P. Austin, Erika Erickson, Bryon S. Donohoe, Nicholas A. Rorrer, Fiona L. Kearns, Graham Dominick, Christopher W. Johnson, Valerie Copie, Christina M. Payne, H. Lee Woodcock, Gregg T. Beckham and John E. McGeehan were co-authors of the article, 'Structural and biochemical characterization of MHETASE' submitted to the journal 'Proceedings of the National Academy of Sciences of the United States of America' which is contained within this dissertation.As the world is producing more plastics than it can recycle, accumulation of manmade polymers in the environment is becoming one of the greatest global threats humanity is facing today. One of the major contributors to the plastics pollution problem is polyethylene terephthalate (PET), an aromatic polyester widely used in the packaging, beverage, garment and carpeting industries. As a response to the onslaught of plastics in the environment, fungi and bacteria are evolving metabolic pathways to convert plastics into useable energy sources. One of these organisms, a bacterium, Ideonella sakaiensis 201-F6, has recently been identified to convert PET into its monomers, terephthalic acid (TPA) and ethylene glycol (EG), and to use these compounds for energy and growth. I. sakaiensis' ability to convert PET is made possible by two enzymes, named PETase and MHETase. As a first step, PETase breaks down the insoluble substrate PET into a soluble major hydrolysis product - mono-(2- hydroxyethyl) terephthalate (MHET), which is then further hydrolyzed by MHETase into TPA and EG. Crystal structure of PETase, as well as some of its biochemical features, have been reported several times to date, but MHETase has remained largely uncharacterized. This work focuses on further discovery-driven biophysical and biochemical characterization of PETase, visualization of PETase activity on various polyester surfaces, as well as the structural and biochemical characterizations of the MHETase enzyme. We have found that several aspects of PETase-mediated substrate surface modification hydrolysis mechanisms differ depending on the specific mechanical and material characteristics of the substrate. We have also found that PETase is inhibited by BHET. Additionally, we have solved the crystal structure of MHETase. MHETase consists of an alpha/beta hydrolase domain, and a 'lid' domain, commonly seen in lipases. Molecular dynamics simulations revealed the mechanism of MHETase action. Through bioinformatics approaches, we have also identified mutants of interest for improved MHETase activity. Coincubation of MHETase with PETase affects PET turnover in a synergistic fashion. Taken together, this work provides additional insights into the mechanisms of action of the PETase and MHETase enzymes, which may open new avenue for bioremediation and removing plastics from the environment in a sustainable manner.Item The reactive form of a C-S bond-cleaving CO 2-fixing flavoenzyme(Montana State University - Bozeman, College of Letters & Science, 2019) Mattice, Jenna Rose; Chairperson, Graduate Committee: Jennifer DuBois; Thesis includes a paper of which Jenna R. Mattice is not the main author.Atmospheric carbon dioxide (CO 2) is used as a carbon source for building biomass in plants and most engineered synthetic microbes. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme on earth, is used by these organisms to catalyze the first step in CO 2 fixation. 1,2 Microbial processes that also fix carbon dioxide or bicarbonate have more recently been discovered. My research focuses on a reaction catalyzed by 2-KPCC (NADPH:2-ketopropyl-coenzyme M oxidorectuase/ carboxylase), a bacterial enzyme that is part of the flavin and cysteine-disulfide containing oxidoreductase family (DSORs) which are best known for reducing metallic or disulfide substrates. 2-KPCC is unique because it breaks a comparatively strong C-S bond, leading to the generation of a reactive enolacetone intermediate which can directly attack and fix CO 2. 2-KPCC contains a phenylalanine in the place where most other DSOR members have a catalytically essential histidine. This research focuses on studying the unique reactive form of 2-KPCC in presence of an active site phenylalanine.Item The coenzyme M biosynthetic pathway in proteobacterium Xanthobacter autotrophicus Py2(Montana State University - Bozeman, College of Letters & Science, 2018) Partovi, Sarah Eve; Chairperson, Graduate Committee: John W. Peters; Florence Mus, Andrew E. Gutknecht, Hunter A. Martinez, Brian P. Tripet, Bernd Markus Lange, Jennifer L. DuBois and John W. Peters were co-authors of the article, 'Coenzyme M biosynthesis in bacteria involves phosphate elimination by a unique member of the aspartase/fumarase superfamily' submitted to the journal 'Journal of biological chemistry' which is contained within this thesis.The metabolically versatile bacterium Xanthobacter autotrophicus Py2 has been the focus of many studies within the field of bioenergy sciences, as it contains two unique CO 2 fixing enzymes, and can utilize unconventional substrates such as propylene and acetone as the sole supplemented carbon source while fixing CO 2 in the process. Unexpectedly, coenzyme M (CoM) was found to play a crucial role as a C 3 carrier in the pathway for propylene metabolism in the late 1990s. Previously, CoM was thought to be present solely as a C 1 carrier in methanogenic archaea for nearly 30 years. Though CoM biosynthesis has been characterized in methanogenic archaea, bacterial CoM biosynthesis remained uncharacterized. In X. autotrophicus Py2, four putative CoM biosynthetic enzymes encoded by xcbB1, C1, D1, and E1 have been identified through informatics and proteomic approaches. XcbB1 is homologous to the archaeal ComA which catalyzes the addition of sulfite to phosphoenolpyruvate, and forms the initial intermediate, phosphosulfolactate, in one of the methanogen CoM biosynthetic pathways. The remaining genes do not encode homologues of any of the previously characterized enzymes in methanogen CoM biosynthesis, suggesting bacteria have a unique pathway. The production of phosphosulfolactate by ComA homolog XcbB1 was verified, indicating that bacterial CoM biosynthesis is initiated in an analogous fashion to the PEP-dependent methanogenic archaeal CoM biosynthesis pathway. XcbC1 and D1 are members of the aspartase/fumarase superfamily (AFS), and XcbE1 is a pyridoxal 5'-phosphate-containing enzyme with homology to D-cysteine desulfhydrases. Direct demonstration of activities for XcbB1 and C1 strengthens their hypothetical assignment to a CoM biosynthetic pathway, and puts firm contraints on our proposed functions for XcbD1 and E1. Known AFS members catalyze beta-elimination reactions of succinyl-containing substrates, yielding fumarate as the common unsaturated elimination product. We demonstrate herein that XcbC1 catalyzes a beta-elimination reaction on the substrate phosphosulfolactate to yield sulfoacrylic acid and inorganic phosphate. To our knowledge, beta-elimination reactions releasing phosphate is unprecedented among the AFS, indicating XcbC1 is a unique phosphatase. This work will serve as the framework for future studies aimed at uncovering the final stages of the biosynthetic pathway. By elucidating the XcbB1 and XcbC1 reactions, we have made significant strides towards understanding bacterial CoM biosynthesis which evaded characterization in previous years.Item Biochemical characterization of the six-transmembrane epithelial antigen of the prostate family of metalloreductases(Montana State University - Bozeman, College of Letters & Science, 2015) Kleven, Mark Daniel; Chairperson, Graduate Committee: C. Martin Lawrence; George H. Gauss was the main author, and Mark D. Kleven, Anoop K. Sendamarai, Mark D. Fleming and C. Martin Lawrence were co-authors of the article, 'The crystal structure of six-transmembrane epithelial antigen of the prostate 4 (Steap4), a ferri/cuprireductase, suggests a novel interdomain flavin-binding site' in the journal 'Journal of biological chemistry' which is contained within this thesis.; Mark D. Fleming and C. Martin Lawrence were co-authors of the article, 'Characterization of a single B-type heme, FAD and metal binding sites in the transmembrane domain of six trans-membrane epithelial antigen of the prostate (Steap) family proteins' submitted to the journal 'Journal of biological chemistry' which is contained within this thesis.Iron and copper are the two most abundant transition metals in humans and are mediators of many essential cellular processes. The entry of these metals into cells require controlled processes, including their reduction prior to uptake. A group of integral membrane enzymes, the six-transmembrane epithelial antigen of the prostate (Steap) family, are able to perform this function. Steap3, in particular, functions as the primary ferric reductase in the transferrin cycle, the dominant mode of erythrocyte iron uptake. How these enzymes perform these functions has remained ill-defined. Here, the biochemical underpinnings of Steap metalloreductase activity have been investigated. To elucidate these mechanisms, expression systems for Steap3 and Steap4 have been developed in bacterial, insect, and human cell lines and purified to varying degrees. By analyzing the truncated cytoplasmic oxidoreductase domain of Steap4, it was found that NADPH is oxidized by transferring a pair of electrons to a flavin. With this truncation, however, flavin only binds weakly and the construct shows no ability to preferentially bind one type of flavin. In contrast, when the full length Steap3 was partially purified, it exhibits high-affinity FAD-binding, indicating that the transmembrane region of the protein contains the major structural features of the FAD binding site. Further, it was found that the cytoplasm-oriented loops between transmembrane helices formed the site. The next cofactor in the electron transport chain is a single b-type heme. Two strictly conserved histidines were identified that coordinate the heme and both are required for heme incorporation. The metal binding site at the extracellular face of the membrane was also characterized. Here, it was found that Steap3 and Steap4 share a conserved high-affinity iron binding site. Additionally, iron and copper both bind with similar affinities to Steap4. Two critical residues of the metal binding site were determined and their predicted proximity to the heme cofactor suggests that the electron is transfer is direct between cofactor and metal. Finally, it was found that Steap's are able to dimerize in the cells, forming homo- and heterodimers Together, the enzymatic mechanism has been characterized in-depth for the first time for these physiologically-significant enzymes.Item Effect of iodine on the biochemical and immunochemical properties of the toxic lecithinase of clostridium hemolyticum(Montana State University - Bozeman, College of Letters & Science, 1949) Parmelee, Edwin T.Item The location and identification of the enzyme system responsible for the fermentation of isomaltose in Candida utilis(Montana State University - Bozeman, College of Letters & Science, 1963) Robbins, John EdwardItem Molecular structure and reactivity of Vitamin B6/salicylaldehyde containing model enzymes(Montana State University - Bozeman, College of Letters & Science, 1984) Sykes, Andrew GilchristItem The isolation and purification of Brassica juncea myrosinase and a study of its glycoprotein nature(Montana State University - Bozeman, College of Letters & Science, 1966) Thompson, Kenneth Nordahl