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- All Subjects: Chemistry
- Creators: Ghirlanda, Giovanna
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Description
A major goal of synthetic biology is to recapitulate emergent properties of life. Despite a significant body of work, a longstanding question that remains to be answered is how such a complex system arose? In this dissertation, synthetic nucleic acid molecules with alternative sugar-phosphate backbones were investigated as potential ancestors of DNA and RNA. Threose nucleic acid (TNA) is capable of forming stable helical structures with complementary strands of itself and RNA. This provides a plausible mechanism for genetic information transfer between TNA and RNA. Therefore TNA has been proposed as a potential RNA progenitor. Using molecular evolution, functional sequences were isolated from a pool of random TNA molecules. This implicates a possible chemical framework capable of crosstalk between TNA and RNA. Further, this shows that heredity and evolution are not limited to the natural genetic system based on ribofuranosyl nucleic acids. Another alternative genetic system, glycerol nucleic acid (GNA) undergoes intrasystem pairing with superior thermalstability compared to that of DNA. Inspired by this property, I demonstrated a minimal nanostructure composed of both left- and right-handed mirro image GNA. This work suggested that GNA could be useful as promising orthogonal material in structural DNA nanotechnology.
ContributorsZhang, Su (Author) / Chaut, John C (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2011
Description
Hydrogenases, the enzymes that reversibly convert protons and electrons to hydrogen, are used in all three domains of life. [NiFe]-hydrogenases are considered best suited for biotechnological applications because of their reversible inactivation with oxygen. Phylogenetically, there are four groups of [NiFe]-hydrogenases. The best characterized group, "uptake" hydrogenases, are membrane-bound and catalyze hydrogen oxidation in vivo. In contrast, the group 3 [NiFe]-hydrogenases are heteromultimeric, bifunctional enzymes that fulfill various cellular roles. In this dissertation, protein film electrochemistry (PFE) is used to characterize the catalytic properties of two group 3 [NiFe]-hydrogenases: HoxEFUYH from Synechocystsis sp. PCC 6803 and SHI from Pyrococcus furiosus. First, HoxEFUYH is shown to be biased towards hydrogen production. Upon exposure to oxygen, HoxEFUYH inactivates to two states, both of which can be reactivated on the timescale of seconds. Second, we show that PfSHI is the first example of an oxygen tolerant [NiFe]-hydrogenase that produces two inactive states upon exposure to oxygen. Both inactive states are analogous to those characterized for HoxEFUYH, but oxygen exposed PfSHI produces a greater fraction that reactivates at high potentials, enabling hydrogen oxidation in the presence of oxygen. Third, it is shown that removing the NAD(P)-reducing subunits from PfSHI leads to a decrease in bias towards hydrogen oxidation and renders the enzyme oxygen sensitive. Both traits are likely due to impaired intramolecular electron transfer. Mechanistic hypotheseses for these functional differences are considered.
ContributorsMcIntosh, Chelsea Lee (Author) / Jones, Anne K (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Buttry, Daniel (Committee member) / Arizona State University (Publisher)
Created2012
Description
A novel small metal-binding protein (SmbP), with only 93 residues and no similarity to other known proteins, has been isolated from the periplasm of Nitrosomonas europaea. It is characterized by its high percentage (17%) of histidines, a motif of ten repeats of seven residues, a four α-helix bundle structure, and a high binding affinity to about six equivalents of Cu2+. The goal of this study is to investigate the Cu2+ binding sites in SmbP and to understand how Cu2+ stabilizes the protein. Preliminary folding experiments indicated that Cu2+ greatly stabilizes SmbP. In this study, protein folding data from circular dichroism (CD) spectroscopy was used to elucidate the role of Cu2+ in stabilizing SmbP structure against unfolding induced by decreased pH, increased temperature, and chemical denaturants. The significant stabilization effects of Cu2+ were demonstrated by the observation that Cu2+-SmbP remained fully folded under extreme environmental conditions, such as acidic pH, 96 °C, and 8 M urea. Also, it was shown that Cu2+ is able to induce the refolding of unfolded SmbP in acidic solutions. These findings imply that the coordination of Cu2+ to histidine residues is responsible for the stabilization effects. The crystal structure of SmbP without Cu2+ has been determined. However, attempts to crystallize Cu2+-SmbP have not been successful. In this study, multidimensional NMR experiments were conducted in order to gain additional information regarding the Cu2+-SmbP structure, in particular its metal binding sites. Unambiguous resonance assignments were successfully made. Cα secondary chemical shifts confirmed that SmbP has a four α-helical structure. A Cu2+-protein titration experiment monitored by NMR indicated a top-to-bottom, sequential metal binding pattern for SmbP. In addition, several bioinformatics tools were used to complement the experimental approach and identity of the ligands in Cu2+-binding sites in SmbP is proposed.
ContributorsYan, Qin (Author) / Francisco, Wilson A (Thesis advisor) / Allen, James (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2010
Description
In eukaryotes, DNA is packed in a highly condensed and hierarchically organized structure called chromatin, in which DNA tightly wraps around the histone octamer consisting of one histone 3-histone 4 (H3-H4) tetramer and two histone 2A- histone 2B (H2A-H2B) dimers with 147 base pairs in an almost two left handed turns. Almost all DNA dependent cellular processes, such as DNA duplication, transcription, DNA repair and recombination, take place in the chromatin form. Based on the critical importance of appropriate chromatin condensation, this thesis focused on the folding behavior of the nucleosome array reconstituted using different templates with various controllable factors such as histone tail modification, linker DNA length, and DNA binding proteins. Firstly, the folding behaviors of wild type (WT) and nucleosome arrays reconstituted with acetylation on the histone H4 at lysine 16 (H4K16 (Ac)) were studied. In contrast to the sedimentation result, atomic force microscopy (AFM) measurements revealed no apparent difference in the compact nucleosome arrays between WT and H4K16 (Ac) and WT. Instead, an optimal loading of nucleosome along the template was found necessary for the Mg2+ induced nucleosome array compaction. This finding leads to the further study on the role of linker DNA in the nucleosome compaction. A method of constructing DNA templates with varied linker DNA lengths was developed, and uniformly and randomly spaced nucleosome arrays with average linker DNA lengths of 30 bp and 60 bp were constructed. After comprehensive analyses of the nucleosome arrays' structure in mica surface, the lengths of the linker DNA were found playing an important role in controlling the structural geometries of nucleosome arrays in both their extended and compact forms. In addition, higher concentration of the DNA binding domain of the telomere repeat factor 2 (TRF2) was found to stimulate the compaction of the telomeric nucleosome array. Finally, AFM was successfully applied to investigate the nucleosome positioning behaviors on the Mouse Mammary Tumor Virus (MMTV) promoter region, and two highly positioned region corresponded to nucleosome A and B were identified by this method.
ContributorsFu, Qiang (Author) / Lindsay, Stuart M (Thesis advisor) / Yan, Hao (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2010
Description
Non-canonical amino acids (NCAAs) can be used in protein chemistry to determine their structures. A common method for imaging proteins is cryo-electron microscopy (cryo-EM) which is ideal for imaging proteins that cannot be obtained in large quantities. Proteins with indistinguishable features are difficult to image using this method due to the large size requirements, therefore antibodies designed specifically for binding these proteins have been utilized to better identify the proteins. By using an existing antibody that binds to stilbene, NCAAs containing this molecule can be used as a linker between proteins and an antibody. Stilbene containing amino acids can be integrated into proteins to make this process more access able. In this paper, synthesis methods for various NCAAs containing stilbene were proposed. The resulting successfully synthesized NCAAs were E)-N6-(5-oxo-5-((4-styrylphenyl) amino) pentanoyl) lysine, (R,E)-2-amino-3-(5-oxo-5-((4-styrylphenyl)amino)pentanamido)propanoic acid, (E)-2-amino-5-(5-oxo-5-((4-styrylphenyl) amino) pentanamido) pentanoic acid. A synthesis for three more shorter amino acids, (R,E)-2-amino-3-(3-oxo-3-((4-styrylphenyl) amino) propanamido) propanoic acid, (E)-2-amino-5-(3-oxo-3-((4-styrylphenyl) amino) propanamido) pentanoic acid, and (E)-N6-(3-oxo-3-((4-styrylphenyl) amino) propanoyl) lysine, is also proposed.
ContributorsJenkins, Bryll (Author) / Mills, Jeremy (Thesis director) / Ghirlanda, Giovanna (Committee member) / Nannenga, Brent (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor)
Created2022-05
Description
Proteins are among the important macromolecules in living systems, with diverse biological functions and properties that make them greatly interesting to study in both structure and function. The chemical synthesis of proteins allows researchers to incorporate a wide variety of post-translation modifications that can diversify protein functions. It also allows the incorporation of many noncanonical amino acids that enable the study of protein structure and function, as well as the control of their activity in living cells. The work presented in this dissertation focuses on two DNA-templated chemical synthesis approaches for the synthesis of proteins: i) DNA-templated native chemical ligation (NCL), and ii) DNA-templated click chemistry. NCL and its extended version has been used as a powerful tool to obtain proteins; however, it still struggles to make longer proteins due to aggregation and poor yield. To address these issues, a DNA-templated approach is being developed where two peptide fragments are brought into proximity by an oligonucleotide to facilitate the NCL reaction. The sequential ligation of the peptide fragments will result in full-length proteins with increased yield and improved solubility. This research involves synthesis of small molecule auxiliaries, thioester peptides, DNA-peptide conjugates, and ligation of peptides through NCL. This method has the potential to be applied to synthesize large hydrophobic proteins.
A DNA-templated click chemistry method was also reported where duplex DNA was utilized as a template for enhancing the copper click reaction between peptide fragments into functional mini-proteins. As a proof of principle, peptide fragments were synthesized with click functional groups and conjugated with distinct DNA handles through a disulfide exchange bioconjugation reaction. The DNA-peptide conjugates were assembled with the template to bring the two peptides into proximity and enhance the effective molarities of the functional groups. The peptides were coupled efficiently using a copper click reaction. The designed DNA-templated method is being implemented to synthesize a designed mini-protein (called LCB1), which can bind tightly to the spike protein of SARS-CoV-2 and inhibit its interaction with the human angiotensin-converting enzyme 2 (ACE2) receptor. This method allows researchers to introduce multiple non-natural amino acids in the protein and has the potential to extend to larger proteins, synthetic polymers, and DNA-peptide biomaterials.
ContributorsAl-Amin, Md (Author) / Stephanopoulos, Nicholas (Thesis advisor) / Gould, Ian (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2024
Description
The addition of aminoalkyl-substituted 2,6-bis(imino)pyridine (or pyridine diimine, PDI) ligands to [(COD)RhCl]2 (COD = 1,5-cyclooctadiene) resulted in the formation of rhodium monochloride complexes with the general formula (NPDI)RhCl (NPDI = iPr2NEtPDI or Me2NPrPDI). The investigation of (iPr2NEtPDI)RhCl and (Me2NPrPDI)RhCl by single crystal X-ray diffraction verified the absence of amine arm coordination and a pseudo square planar geometry about rhodium. Replacement of the chloride ligand with an outer-sphere anion was achieved by adding AgBF4 directly to (iPr2NEtPDI)RhCl to form [(iPr2NEtPDI)Rh][BF4]. Alternatively, this complex was prepared upon chelate addition following the salt metathesis reaction between AgBF4 and [(COD)RhCl]2. Using the latter method, both [(NPDI)Rh][BF4] complexes were isolated and found to exhibit κ4-N,N,N,N-PDI coordination regardless of arm length or steric bulk. In contrast, the metallation of PPDI chelates featuring alkylphosphine imine substituents (PPDI = Ph2PEtPDI or Ph2PPrPDI) resulted in the formation of cationic complexes featuring κ5-N,N,N,P,P-PDI coordination in all instances, [(PPDI)Rh][X] (X = Cl, BF4). Adjusting the metallation stoichiometry allowed the preparation of [(Ph2PPrPDI)Rh][(COD)RhCl2], which was characterized by multinuclear NMR spectroscopy and single crystal X-ray diffraction.
ContributorsLevin, Hagit Ben-Daat (Author) / Trovitch, Ryan J (Thesis advisor) / Gould, Ian R (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2016
Description
Natural hydrogenases catalyze the reduction of protons to molecular hydrogen reversibly under mild conditions; these enzymes have an unusual active site architecture, in which a diiron site is connected to a cubane type [4Fe-4S] cluster. Due to the relevance of this reaction to energy production, and in particular to sustainable fuel production, there have been substantial amount of research focused on developing biomimetic organometallic models. However, most of these organometallic complexes cannot revisit the structural and functional fine-tuning provided by the protein matrix as seen in the natural enzyme. The goal of this thesis is to build a protein based functional mimic of [Fe-Fe] hydrogenases. I used a 'retrosynthetic' approach that separates out two functional aspects of the natural enzyme. First, I built an artificial electron transfer domain by engineering two [4Fe-4S] cluster binding sites into an existing protein, DSD, which is a de novo designed domain swapped dimer. The resulting protein, DSD-bis[4Fe-4S], contains two clusters at a distance of 36 Å . I then varied distance between two clusters using vertical translation along the axis of the coiled coil; the resulting protein demonstrates efficient electron transfer to/from redox sites. Second, I built simple, functional artificial hydrogenases by using an artificial amino acid comprising a 1,3 dithiol moiety to anchor a biomimetic [Fe-Fe] active site within the protein scaffold Correct incorporation of the cluster into a model helical peptide was verified by UV-Vis, FTIR, ESI-MS and CD spectroscopy. This synthetic strategy is extended to the de novo design of more complex protein architectures, four-helix bundles that host the di-iron cluster within the hydrophobic core. In a separate approach, I developed a generalizable strategy to introduce organometallic catalytic sites into a protein scaffold. I introduced a biomimetic organometallic complex for proton reduction by covalent conjugation to biotin. The streptavidin-bound complex is significantly more efficient in photocatalytic hydrogen production than the catalyst alone. With these artificial proteins, it will be possible to explore the effect of second sphere interactions on the activity of the diiron center, and to include in the design properties such as compatibility with conductive materials and electrodes.
ContributorsRoy, Anindya (Author) / Ghirlanda, Giovanna (Thesis advisor) / Yan, Hao (Committee member) / Gust, Devens (Committee member) / Arizona State University (Publisher)
Created2014
Description
The utilization of solar energy requires an efficient means of its storage as fuel. In bio-inspired artificial photosynthesis, light energy can be used to drive water oxidation, but catalysts that produce molecular oxygen from water are required. This dissertation demonstrates a novel complex utilizing earth-abundant Ni in combination with glycine as an efficient catalyst with a modest overpotential of 0.475 ± 0.005 V for a current density of 1 mA/cm2 at pH 11. The production of molecular oxygen at a high potential was verified by measurement of the change in oxygen concentration, yielding a Faradaic efficiency of 60 ± 5%. This Ni species can achieve a current density of 4 mA/cm2 that persists for at least 10 hours. Based upon the observed pH dependence of the current amplitude and oxidation/reduction peaks, the catalysis is an electron-proton coupled process. In addition, to investigate the binding of divalent metals to proteins, four peptides were designed and synthesized with carboxylate and histidine ligands. The binding of the metals was characterized by monitoring the metal-induced changes in circular dichroism spectra. Cyclic voltammetry demonstrated that bound copper underwent a Cu(I)/Cu(II) oxidation/reduction change at a potential of approximately 0.32 V in a quasi-reversible process. The relative binding affinity of Mn(II), Fe(II), Co(II), Ni(II) and Cu(II) to the peptides is correlated with the stability constants of the Irving-Williams series for divalent metal ions. A potential application of these complexes of transition metals with amino acids or peptides is in the development of artificial photosynthetic cells.
ContributorsWang, Dong (Author) / Allen, James P. (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Redding, Kevin (Committee member) / Arizona State University (Publisher)
Created2014
Description
Atomic force microscopy (AFM) has become an important tool to characterize and image surfaces with nanoscale resolution. AFM imaging technique has been utilized to study a wide range of substances such as DNA, proteins, cells, silicon surfaces, nanowires etc. Hence AFM has become extremely important in the field of biochemistry, cell biology and material science. Functionalizing the AFM tip made it possible to detect molecules and their interaction using recognition imaging at single molecule level. Also the unbinding force of two molecules can be investigated based on AFM based single molecule force spectroscopy.
In the first study, a new chemical approach to functionalize the AFM tip in a simple and user-friendly way has been described. Copper-free click chemistry and a vinyl sulfone PEG linker have been utilized during the process. Using this technique, human thrombin and integrin were detected in separate experiments. Then a novel tri-arm linker with two recognition molecules on it was designed and two proteins (human thrombin and integrin) were detected simultaneously in the same experiment using recognition imaging. This technique can be applied to understand many multivalent interactions taking place in nature. Using the same tri-arm linker functionalized with two biotin molecules, the interaction of streptavidin with mono-biotin and bis-biotin ligands were investigated. The thermal stability of streptavidin-biotin complex was also studied using SDS-PAGE analysis.
In the final study, structure of native chromatin extracted from normal and cancer cell lines were analyzed using AFM imaging and agarose gel electrophoresis. Different salt fractions were used to extract chromatin region depending on their solubility. Mnase sensitivity of the chromatin sample was used to understand the open and closed structures of chromatin from different sources. The amount of chromatin in different salt fractions could act as an indicator of amount of open and condensed chromatin in normal and cancer cells. Eventually this ratio of closed and open structure of chromatin could be an indicator of tumorigenic nature of particular cell lines.
In the first study, a new chemical approach to functionalize the AFM tip in a simple and user-friendly way has been described. Copper-free click chemistry and a vinyl sulfone PEG linker have been utilized during the process. Using this technique, human thrombin and integrin were detected in separate experiments. Then a novel tri-arm linker with two recognition molecules on it was designed and two proteins (human thrombin and integrin) were detected simultaneously in the same experiment using recognition imaging. This technique can be applied to understand many multivalent interactions taking place in nature. Using the same tri-arm linker functionalized with two biotin molecules, the interaction of streptavidin with mono-biotin and bis-biotin ligands were investigated. The thermal stability of streptavidin-biotin complex was also studied using SDS-PAGE analysis.
In the final study, structure of native chromatin extracted from normal and cancer cell lines were analyzed using AFM imaging and agarose gel electrophoresis. Different salt fractions were used to extract chromatin region depending on their solubility. Mnase sensitivity of the chromatin sample was used to understand the open and closed structures of chromatin from different sources. The amount of chromatin in different salt fractions could act as an indicator of amount of open and condensed chromatin in normal and cancer cells. Eventually this ratio of closed and open structure of chromatin could be an indicator of tumorigenic nature of particular cell lines.
ContributorsSenapati, Subhadip (Author) / Lindsay, Stuart (Thesis advisor) / Zhang, Peiming (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2015
Description
A vast amount of energy emanates from the sun, and at the distance of Earth, approximately 172,500 TW reaches the atmosphere. Of that, 80,600 TW reaches the surface with 15,600 TW falling on land. Photosynthesis converts 156 TW in the form of biomass, which represents all food/fuel for the biosphere with about 20 TW of the total product used by humans. Additionally, our society uses approximately 20 more TW of energy from ancient photosynthetic products i.e. fossil fuels. In order to mitigate climate problems, the carbon dioxide must be removed from the human energy usage by replacement or recycling as an energy carrier. Proposals have been made to process biomass into biofuels; this work demonstrates that current efficiencies of natural photosynthesis are inadequate for this purpose, the effects of fossil fuel replacement with biofuels is ecologically irresponsible, and new technologies are required to operate at sufficient efficiencies to utilize artificial solar-to-fuels systems. Herein a hybrid bioderived self-assembling hydrogen-evolving nanoparticle consisting of photosystem I (PSI) and platinum nanoclusters is demonstrated to operate with an overall efficiency of 6%, which exceeds that of land plants by more than an order of magnitude. The system was limited by the rate of electron donation to photooxidized PSI. Further work investigated the interactions of natural donor acceptor pairs of cytochrome c6 and PSI for the thermophilic cyanobacteria Thermosynechococcus elogantus BP1 and the red alga Galderia sulphuraria. The cyanobacterial system is typified by collisional control while the algal system demonstrates a population of prebound PSI-cytochrome c6 complexes with faster electron transfer rates. Combining the stability of cyanobacterial PSI and kinetics of the algal PSI:cytochrome would result in more efficient solar-to-fuel conversion. A second priority is the replacement of platinum with chemically abundant catalysts. In this work, protein scaffolds are employed using host-guest strategies to increase the stability of proton reduction catalysts and enhance the turnover number without the oxygen sensitivity of hydrogenases. Finally, design of unnatural electron transfer proteins are explored and may introduce a bioorthogonal method of introducing alternative electron transfer pathways in vitro or in vivo in the case of engineered photosynthetic organisms.
ContributorsVaughn, Michael David (Author) / Moore, Thomas (Thesis advisor) / Fromme, Petra (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Redding, Kevin (Committee member) / Arizona State University (Publisher)
Created2014
Description
As sunlight is an ideal source of energy on a global scale, there are several approaches being developed to harvest it and convert it to a form that can be used. One of these is though mimicking the processes in natural photosynthesis. Artificial photosynthetic systems include dye sensitized solar cells for the conversion of sunlight to electricity, and photoelectrosynthetic cells which use sunlight to drive water oxidation and hydrogen production to convert sunlight to energy stored in fuel. Both of these approaches include the process of the conversion of light energy into chemical potential in the form of a charge-separated state via molecular compounds. Porphyrins are commonly used as sensitizers as they have well suited properties for these applications. A high potential porphyrin with four nitrile groups at the beta positions, a β-cyanoporphyrin (CyP), was investigated and found to be an excellent electron acceptor, as well as have the necessary properties to be used as a sensitizer for photoelectrosynthetic cells for water oxidation. A new synthetic method was developed which allowed for the CyP to be used in a number of studies in artificial photosynthetic systems. This dissertation reports the theories behind, and the results of four studies utilizing a CyP for the first time; as a sensitizer in a DSSC for an investigation of its use in light driven water oxidation photoelectrosynthetic cells, as an electron acceptor in a proton coupled electron transfer system, in a carotene-CyP dyad to study energy and electron transfer processes between these moieties, and in a molecular triad to study a unique electron transfer process from a C60 radical anion to the CyP. It has been found that CyPs can be used as powerful electron acceptors in molecular systems to provide a large driving force for electron transfer that can aid in the process of the conversion of light to electrochemical potential. The results from these studies have led to a better understanding of the properties of CyPs, and have provided new insight into several electron transfer reactions.
ContributorsAntoniuk-Pablant, Antaeres' Dawn (Author) / Gust, Devens (Thesis advisor) / Moore, Ana L (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2015
Description
The AAA+ ATPase Rubisco activase (Rca) regulates the activity of Rubisco, the photosynthetic enzyme responsible for catalyzing biological carbon fixation. However, the detailed mechanism by which Rca self-association controls Rubisco reactivation activity remains poorly understood. In this work, we are using fluorescence correlation spectroscopy (FCS) to better characterize the thermodynamics of the assembly process of cotton Rca. We present FCS data for Rca in the presence of Mg*ATPgS and Mg*ADP and for the D173N Walker B motif mutant in the presence of Mg*ATP. Our data are consistent with promotion and stabilization of hexamers by Mg*ATPgS and Mg*ATP, whereas Mg*ADP facilitates continuous assembly. We find that in the presence of Mg·ADP, Rca self-associates in a step-wise fashion to form oligomeric and higher order forms, with a strong size dependence on subunit concentration. The monomer is the dominant species below 0.5 micromolar, whereas the hexamer appears to be most populated in the 10-30 micromolar range. Large assemblies containing on the order of 24 subunits become dominant above 40 micromolar, with continued assembly at even higher concentrations. Our data are consistent with a highly dynamic exchange of subunits among oligomeric species of diverse sizes. The most likely ADP-mediated assembly mechanism seems to involve the formation of spiral supra-molecular structures that grow along the helical axis by the step-wise addition of dimeric units. To examine the effect of Mg·ATP on oligomerization, we have generated the D173N mutant of Rca, which binds but does not hydrolyze ATP. In range of 8 and 70 micromolar, 60-80% of Rca is predicted to form hexamers in the presence of Mg*ATP compared to just 30-40% with Mg*ADP. We see a clear trend at which hexamerization occurs at high ATP:ADP ratios and in addition, at increasing concentrations of free magnesium ions to 5 milimolar that results in formation of six subunits. We present an assembly model where Mg*ATP promotes and stabilizes hexamerization at low micromolar Rca concentrations relative to Mg*ADP, and suggest that this results from closed ring hexamer formation in Mg*ATP and open hexameric spiral formation in Mg*ADP .
ContributorsKuriata, Agnieszka (Author) / Wachter, Rebekka (Thesis advisor) / Redding, Kevin (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2014
Description
Since the discovery of graphene, two dimensional materials (2D materials) have become a focus of interest for material research due to their many unique physical properties embedded in their 2D structure. While they host many exciting potential applications, some of these 2D materials are subject to environmental instability issues induced by interaction between material and gas molecules in air, which poses a barrier to further application and manufacture. To overcome this, it is necessary to understand the origin of material instability and interaction with molecules commonly found in air, as well as developing a reproducible and manufacturing compatible method to post-process these materials to extend their lifetime. In this work, the very first investigation on environmental stability on Te containing anisotropic 2D materials such as GaTe and ZrTe3 is reported. Experimental results have demonstrated that freshly exfoliated GaTe quickly deteriorate in air, during which the Raman spectrum, surface morphology, and surface chemistry undergo drastic changes. Environmental Raman spectroscopy and XPS measurements demonstrate that H2O molecules in air interact strongly on the surface while O2, N2, and inert gases don't show any detrimental effects on GaTe surface. Moreover, the anisotropic properties of GaTe slowly disappear during the aging process. To prevent this gas/material interaction based surface transformation, diazonium based surface functionalization is adopted on these Te based 2D materials. Environmental Raman spectroscopy results demonstrate that the stability of functionalized Te based 2D materials exhibit much higher stability both in ambient and extreme conditions. Meanwhile, PL spectroscopy, angle resolved Raman spectroscopy, atomic force microscopy measurements confirm that many attractive physical properties of the material are not affected by surface functionalization. Overall, these findings unveil the degradation mechanism of Te based 2D materials as well as provide a way to significantly enhance their environmental stability through an inexpensive and reproducible surface chemical functionalization route.
ContributorsYang, Sijie (Author) / Tongay, Sefaattin (Thesis advisor) / Gould, Ian (Thesis advisor) / Trovitch, Ryan (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2017
Description
Continuing and increasing reliance on fossil fuels to satisfy our population’s energy demands has encouraged the search for renewable carbon-free and carbon-neutral sources, such as hydrogen gas or CO2 reduction products. Inspired by nature, one of the objectives of this dissertation was to develop protein-based strategies that can be applied in the production of green fuels. The first project of this dissertation aimed at developing a controllable strategy to incorporate domains with different functions (e. g. catalytic sites, electron transfer modules, light absorbing subunits) into a single multicomponent system. This was accomplished through the rational design of 2,2’-bipyridine modified dimeric peptides that allowed their metal-directed oligomerization by forming tris(bipyridine) complexes, thus resulting in the formation of a hexameric assembly.
Additionally, two different approaches to incorporate non-natural organometallic catalysts into protein matrix are discussed. First, cobalt protoporphyrin IX was incorporated into cytochrome b562 to produce a water-soluble proton and CO2 reduction catalyst that is active upon irradiation in the presence of a photosensitizer. The effect of the porphyrin axial ligands provided by the protein environment has been investigated by introducing mutations into the native scaffold, indicating that catalytic activity of proton reduction is dependent on axial coordination to the porphyrin. It is also shown that effects of the protein environment are not directly transferred when applied to other reactions, such as CO2 reduction.
Inspired by the active site of [FeFe]-hydrogenases, the second approach is based on the stereoselective preparation of a novel amino acid bearing a 1,2-benzenedithiol side chain. This moiety can serve as an anchoring point for the introduction of metal complexes into protein matrices. By doing so, this strategy enables the study of protein interactions with non-natural cofactors and the effects that it may have on catalysis. The work developed herein lays a foundation for furthering the study of the use of proteins as suitable environments for tuning the activity of organometallic catalysts in aqueous conditions, and interfacing these systems with other supporting units into supramolecular assemblies.
Additionally, two different approaches to incorporate non-natural organometallic catalysts into protein matrix are discussed. First, cobalt protoporphyrin IX was incorporated into cytochrome b562 to produce a water-soluble proton and CO2 reduction catalyst that is active upon irradiation in the presence of a photosensitizer. The effect of the porphyrin axial ligands provided by the protein environment has been investigated by introducing mutations into the native scaffold, indicating that catalytic activity of proton reduction is dependent on axial coordination to the porphyrin. It is also shown that effects of the protein environment are not directly transferred when applied to other reactions, such as CO2 reduction.
Inspired by the active site of [FeFe]-hydrogenases, the second approach is based on the stereoselective preparation of a novel amino acid bearing a 1,2-benzenedithiol side chain. This moiety can serve as an anchoring point for the introduction of metal complexes into protein matrices. By doing so, this strategy enables the study of protein interactions with non-natural cofactors and the effects that it may have on catalysis. The work developed herein lays a foundation for furthering the study of the use of proteins as suitable environments for tuning the activity of organometallic catalysts in aqueous conditions, and interfacing these systems with other supporting units into supramolecular assemblies.
ContributorsAlcala-Torano, Rafael de Jesus (Author) / Ghirlanda, Giovanna (Thesis advisor) / Moore, Ana L (Committee member) / Mills, Jeremy H (Committee member) / Arizona State University (Publisher)
Created2019
Description
Palladium metal in its various forms has been heavily studied for many catalytic, hydrogen storage and sensing applications and as an electrocatalyst in fuel cells. A short review on various applications of palladium and the mechanism of Pd nanoparticles synthesis will be discussed in chapter 1. Size dependent properties of various metal nanoparticles and a thermodynamic theory proposed by Plieth to predict size dependent redox properties of metal nanoparticles will also be discussed in chapter 1.
To evaluate size dependent stability of metal nanoparticles using electrochemical techniques in aqueous media, a synthetic route was designed to produce water soluble Pd nanoparticles. Also, a purification technique was developed to obtain monodisperse metal nanoparticles to study size dependent stability using electrochemical methods. Chapter 2 will describe in detail the synthesis, characterization and size dependent anodic dissolution studies of water soluble palladium nanoparticles.
The cost associated with using expensive metal catalysts can further decreased by using the underpotential deposition (UPD) technique, in which one metal is electrodeposited in monolayer or submonolayer form on a different metal substrate. Electrochemically, this process can be detected by the presence of a deposition peak positive to the bulk deposition potential in a cyclic voltammetry (CV) experiment. The difference between the bulk deposition potential and underpotential deposition peak (i.e. the UPD shift), which is a measure of the energetics of the monolayer deposition step, depends on the work function difference between the metal pairs. Chapter 3 will explore how metal nanoparticles of different sizes will change the energetics of the UPD phenomenon, using the UPD of Cu on palladium nanoparticles as an example. It will be shown that the UPD shift depends on the size of the nanoparticle substrate in a way that is understandable based on the Plieth model.
High electrocatalytic activity of palladium towards ethanol oxidation in an alkaline medium makes it an ideal candidate for the anode electrocatalyst in direct ethanol based fuel cells (DEFCs). Chapter 4 will explore the poisoning of the catalytic activity of palladium in the presence of halide impurities, often used in synthesis of palladium nanoparticles as precursors or shape directing agents.
To evaluate size dependent stability of metal nanoparticles using electrochemical techniques in aqueous media, a synthetic route was designed to produce water soluble Pd nanoparticles. Also, a purification technique was developed to obtain monodisperse metal nanoparticles to study size dependent stability using electrochemical methods. Chapter 2 will describe in detail the synthesis, characterization and size dependent anodic dissolution studies of water soluble palladium nanoparticles.
The cost associated with using expensive metal catalysts can further decreased by using the underpotential deposition (UPD) technique, in which one metal is electrodeposited in monolayer or submonolayer form on a different metal substrate. Electrochemically, this process can be detected by the presence of a deposition peak positive to the bulk deposition potential in a cyclic voltammetry (CV) experiment. The difference between the bulk deposition potential and underpotential deposition peak (i.e. the UPD shift), which is a measure of the energetics of the monolayer deposition step, depends on the work function difference between the metal pairs. Chapter 3 will explore how metal nanoparticles of different sizes will change the energetics of the UPD phenomenon, using the UPD of Cu on palladium nanoparticles as an example. It will be shown that the UPD shift depends on the size of the nanoparticle substrate in a way that is understandable based on the Plieth model.
High electrocatalytic activity of palladium towards ethanol oxidation in an alkaline medium makes it an ideal candidate for the anode electrocatalyst in direct ethanol based fuel cells (DEFCs). Chapter 4 will explore the poisoning of the catalytic activity of palladium in the presence of halide impurities, often used in synthesis of palladium nanoparticles as precursors or shape directing agents.
ContributorsKumar, Ashok (Author) / Buttry, Daniel A. (Thesis advisor) / Gould, Ian R. (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2016