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- All Subjects: Chemistry
- Creators: School of Molecular Sciences
- Status: Published
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
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
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
The transmembrane subunit (gp41) of the envelope glycoprotein of HIV-1 associates noncovalently with the surface subunit (gp120) and together they play essential roles in viral mucosal transmission and infection of target cells. The membrane proximal region (MPR, residues 649-683) of gp41 is highly conserved and contains epitopes of broadly neutralizing antibodies. The transmembrane (TM) domain (residues 684-705) of gp41 not only anchors the envelope glycoprotein complex in the viral membrane but also dynamically affects the interactions of the MPR with the membrane. While high-resolution X-ray structures of some segments of the MPR were solved in the past, they represent the pre-fusion and post-fusion conformations, most of which could not react with the broadly neutralizing antibodies 2F5 and 4E10. Structural information on the TM domain of gp41 is scant and at low resolution.
This thesis describes the structural studies of MPR-TM (residues 649-705) of HIV-1 gp41 by X-ray crystallography. MPR-TM was fused with different fusion proteins to improve the membrane protein overexpression. The expression level of MPR-TM was improved by fusion to the C-terminus of the Mistic protein, yielding ∼1 mg of pure MPR-TM protein per liter cell culture. The fusion partner Mistic was removed for final crystallization. The isolated MPR-TM protein was biophysically characterized and is a monodisperse candidate for crystallization. However, no crystal with diffraction quality was obtained even after extensive crystallization screens. A novel construct was designed to overexpress MPR-TM as a maltose binding protein (MBP) fusion. About 60 mg of MBP/MPR-TM recombinant protein was obtained from 1 liter of cell culture. Crystals of MBP/MPR-TM recombinant protein could not be obtained when MBP and MPR-TM were separated by a 42 amino acid (aa)-long linker but were obtained after changing the linker to three alanine residues. The crystals diffracted to 2.5 Å after crystallization optimization. Further analysis of the diffraction data indicated that the crystals are twinned. The final structure demonstrated that MBP crystallized as a dimer of trimers, but the electron density did not extend beyond the linker region. We determined by SDS-PAGE and MALDI-TOF MS that the crystals contained MBP only. The MPR-TM of gp41 might be cleaved during or after the process of crystallization. Comparison of the MBP trimer reported here with published trimeric MBP fusion structures indicated that MBP might form such a trimeric conformation under the effect of MPR-TM.
This thesis describes the structural studies of MPR-TM (residues 649-705) of HIV-1 gp41 by X-ray crystallography. MPR-TM was fused with different fusion proteins to improve the membrane protein overexpression. The expression level of MPR-TM was improved by fusion to the C-terminus of the Mistic protein, yielding ∼1 mg of pure MPR-TM protein per liter cell culture. The fusion partner Mistic was removed for final crystallization. The isolated MPR-TM protein was biophysically characterized and is a monodisperse candidate for crystallization. However, no crystal with diffraction quality was obtained even after extensive crystallization screens. A novel construct was designed to overexpress MPR-TM as a maltose binding protein (MBP) fusion. About 60 mg of MBP/MPR-TM recombinant protein was obtained from 1 liter of cell culture. Crystals of MBP/MPR-TM recombinant protein could not be obtained when MBP and MPR-TM were separated by a 42 amino acid (aa)-long linker but were obtained after changing the linker to three alanine residues. The crystals diffracted to 2.5 Å after crystallization optimization. Further analysis of the diffraction data indicated that the crystals are twinned. The final structure demonstrated that MBP crystallized as a dimer of trimers, but the electron density did not extend beyond the linker region. We determined by SDS-PAGE and MALDI-TOF MS that the crystals contained MBP only. The MPR-TM of gp41 might be cleaved during or after the process of crystallization. Comparison of the MBP trimer reported here with published trimeric MBP fusion structures indicated that MBP might form such a trimeric conformation under the effect of MPR-TM.
ContributorsGong, Zhen (Author) / Fromme, Petra (Thesis advisor) / Mor, Tsafrir (Thesis advisor) / Ros, Alexandra (Committee member) / Redding, Kevin (Committee member) / Arizona State University (Publisher)
Created2014
Description
Time-resolved serial femtosecond crystallography is an emerging method that allows for structural discovery to be performed on biomacromolecules during their dynamic trajectory through a reaction pathway after activation. This is performed by triggering a reaction on an ensemble of molecules in nano- or microcrystals and then using femtosecond X-ray laser pulses produced by an X-ray free electron laser to collect near-instantaneous data on the crystal. A full data set can be collected by merging a sufficient number of these patterns together and multiple data sets can be collected at different points along the reaction pathway by manipulating the delay time between reaction initiation and the probing X-rays. In this way, these ‘snapshot’ structures can be viewed in series to make a molecular movie, allowing for atomic visualization of a molecule in action and, thereby, a structural basis for the mechanism and function of a given biomacromolecule.
This dissertation presents results towards this end, including the successful implementations of the first diffusive mixing chemoactivated reactions and ultrafast dynamics in the femtosecond regime. The primary focus is on photosynthetic membrane proteins and enzymatic drug targets, in pursuit of strategies for sustainable energy and medical advancement by gaining understanding of the structure-function relationships evolved in nature. In particular, photosystem I, photosystem II, the complex of photosystem I and ferredoxin, and 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase are reported on, from purification and isolation, to crystallogenesis, to experimental design and data collection and subsequent interpretation of results and novel insights gained.
This dissertation presents results towards this end, including the successful implementations of the first diffusive mixing chemoactivated reactions and ultrafast dynamics in the femtosecond regime. The primary focus is on photosynthetic membrane proteins and enzymatic drug targets, in pursuit of strategies for sustainable energy and medical advancement by gaining understanding of the structure-function relationships evolved in nature. In particular, photosystem I, photosystem II, the complex of photosystem I and ferredoxin, and 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase are reported on, from purification and isolation, to crystallogenesis, to experimental design and data collection and subsequent interpretation of results and novel insights gained.
ContributorsCoe, Jesse (Author) / Fromme, Petra (Thesis advisor) / Sayres, Scott (Thesis advisor) / Mujica, Vladimiro (Committee member) / Redding, Kevin (Committee member) / Arizona State University (Publisher)
Created2018
Description
The free-base tetra-tolyl-porphyrin and the corresponding cobalt and iron porphyrin complexes were synthesized and characterized to show that this class of compound can be promising, tunable catalysts for carbon dioxide reduction. During cyclic voltammetry experiments, the iron porphyrin showed an on-set of ‘catalytic current’ at an earlier potential than the cobalt porphyrin’s in organic solutions gassed with carbon dioxide. The cobalt porphyrin yielded larger catalytic currents, but at the same potential as the electrode. This difference, along with the significant changes in the porphyrin’s electronic, optical and redox properties, showed that its capabilities for carbon dioxide reduction can be controlled by metal ions, allotting it unique opportunities for applications in solar fuels catalysis and photochemical reactions.
ContributorsSkibo, Edward Kim (Author) / Moore, Gary (Thesis director) / Woodbury, Neal (Committee member) / School of Molecular Sciences (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Iron (Fe) scarcity limits biological productivity in high-nutrient low-chlorophyll (HNLC) ocean regions. Thus, the input, output and abundance of Fe in seawater likely played a critical role in shaping the development of modern marine ecosystems and perhaps even contributed to past changes in Earth’s climate. Three sources of Fe—wind-blown dust, hydrothermal activity, and sediment dissolution—carry distinct Fe isotopic fingerprints, and can therefore be used to track Fe source variability through time. However, establishing the timing of this source variability through Earth’s history remains challenging because the major depocenters for dissolved Fe in the ocean lack well-established chronologies. This is due to the fact that they are difficult to date with traditional techniques such as biostratigraphy and radiometric dating. Here, I develop age models for sediments collected from the International Drilling Program Expedition 329 by measuring the Os (osmium) isotopic composition of the hydrogenous portion of the clays. These extractions enable dating of the clays by aligning the Os isotope patterns observed in the clays to those in a reference curve with absolute age constraints through the Cenozoic. Our preliminary data enable future development of chronologies for three sediment cores from the high-latitude South Pacific and Southern Oceans, and demonstrate a wider utility of this method to establish age constraints on pelagic sediments worldwide. Moreover, the preliminary Os isotopic data provides a critical first step needed to examine the changes in Fe (iron) sources and cycling on millions of years timescales. Fe isotopic analysis was conducted at the same sites in the South Pacific and demonstrates that there are significant changes in the sources of Fe to the Southern Ocean over the last 90 Ma. These results lay the groundwork for the exploration of basin-scale sources to Fe source changes, which will have implications for understanding how biological productivity relates to Fe source variability over geological timescales.
ContributorsTegler, Logan Ashley (Author) / Anbar, Ariel (Thesis director) / Herckes, Pierre (Committee member) / Romaniello, Stephen (Committee member) / Department of English (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
As a child passes through the birth canal, they become inoculated with vital gram positive and gram-negative bacteria, aerobes and anaerobes. Breast milk helps to support this growing microbiome by providing oligosaccharides that support its proliferation. Breast milk can be considered the most nutritious source of food available to a growing infant by providing the necessary nutrients, growth hormones and antibodies to promote digestive health, growth, and a strong immune system. The Developmental Origins of Health and Disease Theory (DOHaD) is a theory that suggests a growing fetus and nursing child's nutrients and immune system are dependent on the mother's exposure to nutrients and toxins. Studies have shown a positive correlation between the length of nursing and a child's overall health through life. In addition, consuming an enriched diet after weaning builds a strong immunological and nutritional basis from which the child can grow. This leads to improvements in a child's overall health, which has beneficial long-term effects on morbidity and mortality. This project applied the theory to two Middle Horizon (AD500-1100) individuals from Akapana, Tiwanaku, in the Lake Titicaca Basin, Bolivia. Stable nitrogen and carbon isotope analysis was applied to first molar serial samples of these two individuals to determine weaning age and early childhood diet. Both individuals were male; one male died in adolescence between the age of 9-15 years, and the other died as an elderly adult around the age of 50-59 years. The results showed that the male who died in adulthood was provisioned with supplemental and post-weaning foods high in animal protein, and received breast milk until around 37 months of age. The adolescent male was weaned between 11-12 months and consumed a diet dominated by C4 plants \u2014 most likely maize \u2014 with much less protein. The correlation between prolonged access to breast milk and a healthier and more nutritious childhood diet and longevity are consistent with the theory discussed above.
ContributorsCampbell, Sibella Sweelin (Author) / Knudson, Kelly (Thesis director) / Marsteller, Sara (Committee member) / Greenwald, Alexandra (Committee member) / School of Human Evolution & Social Change (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
Description
This study seeks to determine whether female and male students in general chemistry courses differ in exam and course-based performance. Using data from previous semesters of CHM 101 (Marks), CHM 101 (Bauer), CHM 114 (Seo, Windman), CHM 113/116 (Cabirac), and CHM 117/118 (Williams) courses taught at Arizona State University, the total exam scores and final course grades for each student were recorded and analyzed. The results of this study differ greatly by course type, as each course corresponded to a different STEM major. While CHM 113/116, the pre-medicinal majors course, saw evidence of stereotype threat via lower female exam performance, the other courses saw no statistical difference between male and female performance on their exam scores or overall course grades. For CHM 101, this was understandable, as the majority of students were nursing majors, who likely did not experience tokenism or feel stereotyped negatively in their science classes. However, CHM 114, the engineering majors course, and CHM 117/118, the research science course, saw parity with respect to male and female student performance. This suggests the possibility that female students face adversity in science and math courses before college that cause only those with high self-efficacy to advance to a career in these fields.
ContributorsWoner, Victoria Elaine (Author) / Gould, Ian (Thesis director) / Saenz, Delia (Committee member) / Austin, Ara (Committee member) / Department of Psychology (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Biomolecules can easily recognize its corresponding partner and get bound to it, resulting in controlling various processes (immune system, inter or intracellular signaling) in biology and physiology. Bonding between two partners can be a result of electrostatic, hydrophobic interactions or shape complementarity. It is of great importance to study these kinds of biomolecular interactions to have a detailed knowledge of above mentioned physiological processes. These studies can also open avenues for other aspects of science such as drug development. Discussed in the first part of Chapter 1 are the biotin-streptavidin biomolecular interaction studies by atomic force microscopy (AFM) and surface plasmon resonance (SPR) instrument. Also, the basic working principle of AFM and SPR has been discussed.
The second part of Chapter 1 is discussed about site-specific chemical modification of peptides and proteins. Proteins have been used to generate therapeutic materials, proteins-based biomaterials. To achieve all these properties in protein there is a need for site-specific protein modification.
To be able to successfully monitor biomolecular interaction using AFM there is a need for organic linker molecule which helps one of the investigating molecules to get attached to the AFM tip. Most of the linker molecules available are capable of investigating one type of interaction at a time. Therefore, it is significant to have linker molecule which can monitor multiple interactions (same or different type) at the same time. Further, these linker molecules are modified so that biomolecular interactions can also be monitored using SPR instrument. Described in Chapter 2 are the synthesis of organic linker molecules and their use to study biomolecular interaction through AFM and SPR.
In Chapter 3, N-terminal chemical modification of peptides and proteins has been discussed. Further, modified peptides are attached to DNA thread for their translocation through the solid-state nanopore to identify them. Synthesis of various peptide-DNA conjugates and their nanopore studies have been discussed in this chapter.
The second part of Chapter 1 is discussed about site-specific chemical modification of peptides and proteins. Proteins have been used to generate therapeutic materials, proteins-based biomaterials. To achieve all these properties in protein there is a need for site-specific protein modification.
To be able to successfully monitor biomolecular interaction using AFM there is a need for organic linker molecule which helps one of the investigating molecules to get attached to the AFM tip. Most of the linker molecules available are capable of investigating one type of interaction at a time. Therefore, it is significant to have linker molecule which can monitor multiple interactions (same or different type) at the same time. Further, these linker molecules are modified so that biomolecular interactions can also be monitored using SPR instrument. Described in Chapter 2 are the synthesis of organic linker molecules and their use to study biomolecular interaction through AFM and SPR.
In Chapter 3, N-terminal chemical modification of peptides and proteins has been discussed. Further, modified peptides are attached to DNA thread for their translocation through the solid-state nanopore to identify them. Synthesis of various peptide-DNA conjugates and their nanopore studies have been discussed in this chapter.
ContributorsBiswas, Sudipta (Author) / Lindsay, Stuart (Thesis advisor) / Zhang, Peiming (Thesis advisor) / Redding, Kevin (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2016