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Description
Exoelectrogenic microorganisms can grow by transferring electrons from their internal metabolism to extracellular substrates in a process known as extracellular electron transfer (EET). This dissertation explores the mechanisms of EET by both chemotrophic and phototrophic organisms and constructs a novel supramolecular structure that can be used as a model for microbial, long-range electron transfer. Geobacter sulfurreducens has been hypothesized to secrete and use riboflavin as a soluble, extracellular redox shuttle in conjunction with multi-heme, outer membrane, c-type cytochromes, but the required proteins and their properties have not been defined. To address the mechanism of extracellular electron transfer by G. sulfurreducens, the first part of this work explores the interaction between an outer membrane, octaheme, c-type cytochrome OmcZs from G. sulfurreducens and riboflavin. Interrogation via multiple physical techniques shows that OmcZs transfers electrons to riboflavin. By analogy to other characterized systems, riboflavin then likely interacts with extracellular acceptors directly. The second part of this work addresses the mechanisms of EET by the model cyanobacterium Synechocystis sp. PCC 6803. It has been hypothesized that Synechocystis employs conductive pili for production of extracellular current. However, the results herein show that a strain that does not have pili produces extracellular photocurrent in a direct electrochemical cell at a level similar to that by wild type cells. Furthermore, conductive atomic force microscopy (AFM) imaging is used to show that pili produced by the wild type organism are not conductive. Thus, an alternative EET mechanism must be operable. In the third part of this work, a supramolecular structure comprised of peptide and cytochromes designed to serve as a model for long-range electron transfer through cytochrome rich environments is described. The c-type cytochromes in this synthetic nanowire retain their redox activity after assembly and have suitable characteristics for long-range electron transfer. Taken together, the results of this dissertation not only inform on natural microbial mechanisms for EET but also provide a starting point to develop novel, synthetic systems.
ContributorsThirumurthy, Miyuki (Author) / Jones, Anne K (Thesis advisor) / Redding, Kevin (Committee member) / Torres, Cesar (Committee member) / Arizona State University (Publisher)
Created2019
Description
Quantifying molecular interactions is pivotal for understanding biological processes at molecular scale and for screening drugs. Although various detection technologies have been developed, it is still challenging to quantify the binding kinetics of small molecules because the sensitivities of the mainstream technologies scale down with the size of the molecule. To address this problem, two different optical detection methods, charge sensitive optical detection (CSOD) and virion
ano-oscillators, are developed to measure the binding-induced charge change instead of the mass change, which enables quantification of the binding kinetics for both large and small molecules.
In particular, the nano-oscillator approach provides a unique capability to image individual nanoparticles and measure the size and charge of each nanoparticle simultaneously. This approach is applied to measure one of the smallest biological particles - single protein molecules. By tracking the oscillation of each protein molecule, the size, charge, and mobility are measured in real-time with high precision. This capability also allows to monitor the conformation and charge changes of single protein molecules upon ligand binding. Measuring the size and charge of single proteins opens a new revenue to protein analysis and disease biomarker detection at the single molecule level.
The virion
ano-oscillators and the single protein approach employ a scheme where a particle is tethered to the surface with a polymer molecule. The dynamics of the particle is governed by two important forces: One is entropic force arising from the conformational change of the molecular tether, and the other is solvent damping on the particle and the molecule. The dynamics is studied by varying the type of the tether molecule, size of the particle, and viscosity of the solvent. The findings provide insights into single molecule studies using not only tethered particles, but also other approaches, including force spectroscopy using atomic force microscopy and nanopores.
ano-oscillators, are developed to measure the binding-induced charge change instead of the mass change, which enables quantification of the binding kinetics for both large and small molecules.
In particular, the nano-oscillator approach provides a unique capability to image individual nanoparticles and measure the size and charge of each nanoparticle simultaneously. This approach is applied to measure one of the smallest biological particles - single protein molecules. By tracking the oscillation of each protein molecule, the size, charge, and mobility are measured in real-time with high precision. This capability also allows to monitor the conformation and charge changes of single protein molecules upon ligand binding. Measuring the size and charge of single proteins opens a new revenue to protein analysis and disease biomarker detection at the single molecule level.
The virion
ano-oscillators and the single protein approach employ a scheme where a particle is tethered to the surface with a polymer molecule. The dynamics of the particle is governed by two important forces: One is entropic force arising from the conformational change of the molecular tether, and the other is solvent damping on the particle and the molecule. The dynamics is studied by varying the type of the tether molecule, size of the particle, and viscosity of the solvent. The findings provide insights into single molecule studies using not only tethered particles, but also other approaches, including force spectroscopy using atomic force microscopy and nanopores.
ContributorsMa, Guangzhong, Ph.D (Author) / Tao, Nongjian (Thesis advisor) / Wang, Shaopeng (Thesis advisor) / Ros, Alexandra (Committee member) / Guo, Jia (Committee member) / Arizona State University (Publisher)
Created2019
Description
Air pollution has been linked to various health problems but how different air pollutants and exposure levels contribute to those diseases remain largely unknown. Researchers have mainly relied on data from government air monitoring stations to study the health effects of air pollution exposure. The limited information provided by sparse stations has low spatial and temporal resolution, which is not able to represent the actual exposure of individuals. A tool that can accurately monitor personal exposure provides valuable data for epidemiologists to understand the relationship between air pollution and certain diseases. It also allows individuals to be aware of any ambient air quality issues and prevent air pollution exposure. To build such a tool, sensors with features of fast response, small size, long lifetime, high sensitivity, high selectivity, and multi-analyte sensing are of great importance.
In order to meet these requirements, three generations of novel colorimetric sensors have been developed. The first generation is mosaic colorimetric sensors based on tiny sensor blocks and by detecting absorbance change after each air sample injection, the target analyte concentration can be measured. The second generation is a gradient-based colorimetric sensor. Lateral transport of analytes across the colorimetric sensor surface creates a color gradient that shifts along the transport direction over time, and the sensor tracks the gradient shift and converts it into analyte concentration in real-time. The third generation is gradient-based colorimetric arrays fabricated by inkjet-printing method that integrates multiple sensors on a miniaturized sensor chip. Unlike traditional colorimetric sensors, such as detection tubes and optoelectronic nose, that are typically for one-time use, the presented three generations of colorimetric sensors aim to continuously monitor multiple air pollutants and the sensor lifetime and fabrication methods have been improved over each generation. Ozone, nitrogen dioxide, formaldehyde and carbon monoxide are chosen as analytes of interest. The performance of sensors has been validated in the lab and field tests, proving the capability of the sensors to be used for personal exposure monitoring.
In order to meet these requirements, three generations of novel colorimetric sensors have been developed. The first generation is mosaic colorimetric sensors based on tiny sensor blocks and by detecting absorbance change after each air sample injection, the target analyte concentration can be measured. The second generation is a gradient-based colorimetric sensor. Lateral transport of analytes across the colorimetric sensor surface creates a color gradient that shifts along the transport direction over time, and the sensor tracks the gradient shift and converts it into analyte concentration in real-time. The third generation is gradient-based colorimetric arrays fabricated by inkjet-printing method that integrates multiple sensors on a miniaturized sensor chip. Unlike traditional colorimetric sensors, such as detection tubes and optoelectronic nose, that are typically for one-time use, the presented three generations of colorimetric sensors aim to continuously monitor multiple air pollutants and the sensor lifetime and fabrication methods have been improved over each generation. Ozone, nitrogen dioxide, formaldehyde and carbon monoxide are chosen as analytes of interest. The performance of sensors has been validated in the lab and field tests, proving the capability of the sensors to be used for personal exposure monitoring.
ContributorsLin, Chenwen (Author) / Tao, Nongjian (Thesis advisor) / Borges, Chad R (Committee member) / Hayes, Mark A. (Committee member) / Arizona State University (Publisher)
Created2019
Description
An evolving understanding of elastomeric polymer nanocomposites continues to expand commercial, defense, and industrial products and applications. This work explores the thermomechanical properties of elastomeric nanocomposites prepared from bisphenol A diglycidyl ether (BADGE) and three amine-terminated poly(propylene oxides) (Jeffamines). The Jeffamines investigated include difunctional crosslinkers with molecular weights of 2,000 and 4,000 g/mol and a trifunctional crosslinker with a molecular weight of 3,000 g/mol. Additionally, carbon nanotubes (CNTs) were added, up to 1.25 wt%, to each thermoset. The findings indicate that the Tg and storage modulus of the polymer nanocomposites can be controlled independently within narrow concentration windows, and that effects observed following CNT incorporation are dependent on the crosslinker molecular weight.
Polymer matrix composites (PMCs) offer design solutions to produce smart sensing, conductive, or high performance composites for a number of critical applications. Nanoparticle additives, in particular, carbon nanotubes and metallic quantum dots, have been investigated for their ability to improve the conductivity, thermal stability, and mechanical strength of traditional composites. Herein we report the use of quantum dots (QDs) and fluorescently labeled carbon nanotubes (CNTs) to modify the thermomechanical properties of PMCs. Additionally, we find that pronounced changes in fluorescence emerge following plastic deformation, indicating that in these polymeric materials the transduction of mechanical force into the fluorescence occurs in response to mechanical activation.
Segmented ionenes are a class of thermoplastic elastomers that contain a permanent charged group within the polymer backbone and a spacer segment with a low glass transition temperature (Tg) to provide flexibility. Ionenes are of interest because of their synthetic versatility, unique morphologies, and ionic nature. Using phase changing ionene-based nanocomposites could be extended to create reversible mechanically, electrically, optically, and/or thermally responsive materials depending on constituent nanoparticles and polymers. This talk will discuss recent efforts to utilize the synthetic versatility of ionenes (e.g., spacer composition of PTMO or PEG) to prepare percolated ionic domains in microphase separated polymers that display a range of thermomechanical properties. Furthermore, by synthesizing two series of ionene copolymers with either PEG or PTMO spacers at various ratios with 1,12-dibromododecane will yield a range of ion contents (hard contents) and will impact nanoparticle dispersion.
Polymer matrix composites (PMCs) offer design solutions to produce smart sensing, conductive, or high performance composites for a number of critical applications. Nanoparticle additives, in particular, carbon nanotubes and metallic quantum dots, have been investigated for their ability to improve the conductivity, thermal stability, and mechanical strength of traditional composites. Herein we report the use of quantum dots (QDs) and fluorescently labeled carbon nanotubes (CNTs) to modify the thermomechanical properties of PMCs. Additionally, we find that pronounced changes in fluorescence emerge following plastic deformation, indicating that in these polymeric materials the transduction of mechanical force into the fluorescence occurs in response to mechanical activation.
Segmented ionenes are a class of thermoplastic elastomers that contain a permanent charged group within the polymer backbone and a spacer segment with a low glass transition temperature (Tg) to provide flexibility. Ionenes are of interest because of their synthetic versatility, unique morphologies, and ionic nature. Using phase changing ionene-based nanocomposites could be extended to create reversible mechanically, electrically, optically, and/or thermally responsive materials depending on constituent nanoparticles and polymers. This talk will discuss recent efforts to utilize the synthetic versatility of ionenes (e.g., spacer composition of PTMO or PEG) to prepare percolated ionic domains in microphase separated polymers that display a range of thermomechanical properties. Furthermore, by synthesizing two series of ionene copolymers with either PEG or PTMO spacers at various ratios with 1,12-dibromododecane will yield a range of ion contents (hard contents) and will impact nanoparticle dispersion.
ContributorsWang, Meng, Ph.D (Author) / Green, Matthew D (Thesis advisor) / Green, Alexander (Committee member) / Yarger, Jeffery (Committee member) / Arizona State University (Publisher)
Created2019
Description
The highly specialized telomerase ribonucleoprotein enzyme is composed minimally of telomerase reverse transcriptase (TERT) and telomerase RNA (TR) for catalytic activity. Telomerase is an RNA-dependent DNA polymerase that syntheizes DNA repeats at chromosome ends to maintain genome stability. While TERT is highly conserved among various groups of species, the TR subunit exhibits remarkable divergence in primary sequence, length, secondary structure and biogenesis, making TR identification extremely challenging even among closely related groups of organisms.
A unique computational approach combined with in vitro telomerase activity reconstitution studies was used to identify 83 novel TRs from 10 animal kingdom phyla spanning 18 diverse classes from the most basal sponges to the late evolving vertebrates. This revealed that three structural domains, pseudoknot, a distal stem-loop moiety and box H/ACA, are conserved within TRs from basal groups to vertebrates, while group-specific elements emerge or disappear during animal TR evolution along different lineages.
Next the corn-smut fungus Ustilago maydis TR was identified using an RNA-immunoprecipitation and next-generation sequencing approach followed by computational identification of TRs from 19 additional class Ustilaginomycetes fungi, leveraging conserved gene synteny among TR genes. Phylogenetic comparative analysis, in vitro telomerase activity and TR mutagenesis studies reveal a secondary structure of TRs from higher fungi, which is also conserved with vertebrates and filamentous fungi, providing a crucial link in TR evolution within the opisthokonta super-kingdom.
Lastly, work by collabarotors from Texas A&M university and others identified the first bona fide TR from the model plant Arabidopsis thaliana. Computational analysis was performed to identify 85 novel AtTR orthologs from three major plant clades: angiosperms, gymnosperms and lycophytes, which facilitated phylogenetic comparative analysis to infer the first plant TR secondary structural model. This model was confirmed using site-specific mutagenesis and telomerase activity assays of in vitro reconstituted enzyme. The structures of plant TRs are conserved across land plants providing an evolutionary bridge that unites the disparate structures of previously characterized TRs from ciliates and vertebrates.
A unique computational approach combined with in vitro telomerase activity reconstitution studies was used to identify 83 novel TRs from 10 animal kingdom phyla spanning 18 diverse classes from the most basal sponges to the late evolving vertebrates. This revealed that three structural domains, pseudoknot, a distal stem-loop moiety and box H/ACA, are conserved within TRs from basal groups to vertebrates, while group-specific elements emerge or disappear during animal TR evolution along different lineages.
Next the corn-smut fungus Ustilago maydis TR was identified using an RNA-immunoprecipitation and next-generation sequencing approach followed by computational identification of TRs from 19 additional class Ustilaginomycetes fungi, leveraging conserved gene synteny among TR genes. Phylogenetic comparative analysis, in vitro telomerase activity and TR mutagenesis studies reveal a secondary structure of TRs from higher fungi, which is also conserved with vertebrates and filamentous fungi, providing a crucial link in TR evolution within the opisthokonta super-kingdom.
Lastly, work by collabarotors from Texas A&M university and others identified the first bona fide TR from the model plant Arabidopsis thaliana. Computational analysis was performed to identify 85 novel AtTR orthologs from three major plant clades: angiosperms, gymnosperms and lycophytes, which facilitated phylogenetic comparative analysis to infer the first plant TR secondary structural model. This model was confirmed using site-specific mutagenesis and telomerase activity assays of in vitro reconstituted enzyme. The structures of plant TRs are conserved across land plants providing an evolutionary bridge that unites the disparate structures of previously characterized TRs from ciliates and vertebrates.
ContributorsLogeswaran, Dhenugen (Author) / Chen, Julian J-L (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Borges, Chad R (Committee member) / Arizona State University (Publisher)
Created2019
Description
In the past decade, technological breakthroughs have facilitated structure determination of so many difficult-to-study membrane protein targets. In this thesis research, three techniques were investigated to enable the structural determination of such challenging targets, polychromatic pink-beam serial crystallography with high-viscous sample, lipidic cubic phase (LCP)-based microcrystal electron diffraction (MicroED), and single-particle cryogenic electron microscopy targeting (cryoEM).
Inspired by the successful serial crystallography (SX) experiment at a synchrotron radiation source, it is first-time equipping the high-viscosity injector to X-ray fluxes increased at 100 times by a moderate increased in bandwidth to perform the pink beam SX experiments. The structure of proteinase K (PK) was determined to 1.8 Å resolution with 4 consecutive 100 ps X-ray pink beam pulse exposures. The structure of human A2A adenosine receptor (A2AAR) reached to a 4.2 Å resolution using 24 consecutive X-ray pink beam pulse exposures. It has proven the feasibility to utilize such storage-ring synchrotron sources complemented to serial femtosecond crystallography, presenting new opportunities for microcrystallography and the time-resolved experiments.
As an alternative approach to serial femtosecond crystallography, a novel protocol was developed to combine the lipidic cubic phase crystallization approach and microED strategy and solved the structure from LCP-embedded proteinase K microcrystals with the comparable high resolution to conventional crystallographic method.
It cannot be neglected that only very few portions of membrane proteins were able to be successfully crystallized for structure determination. Single particle cryoEM method allows the structural studies from protein molecules detour away from crystallization. An atomic resolution structure of the β1-AR bound with agonist in complex with Gs protein, with particle size of less than 200 kDa, was determined by cryoEM, reaching to an atomic resolution of 3.8 Å. The complex structure captured a fully active conformation and revealed the important mechanisms of how the agonist bound receptor activated Gs protein.
These technological developments provide more opportunities to the structural biology community to discover mechanisms underlying such complicated machinery network, which would eventually benefit the structure-based drug discovery.
Inspired by the successful serial crystallography (SX) experiment at a synchrotron radiation source, it is first-time equipping the high-viscosity injector to X-ray fluxes increased at 100 times by a moderate increased in bandwidth to perform the pink beam SX experiments. The structure of proteinase K (PK) was determined to 1.8 Å resolution with 4 consecutive 100 ps X-ray pink beam pulse exposures. The structure of human A2A adenosine receptor (A2AAR) reached to a 4.2 Å resolution using 24 consecutive X-ray pink beam pulse exposures. It has proven the feasibility to utilize such storage-ring synchrotron sources complemented to serial femtosecond crystallography, presenting new opportunities for microcrystallography and the time-resolved experiments.
As an alternative approach to serial femtosecond crystallography, a novel protocol was developed to combine the lipidic cubic phase crystallization approach and microED strategy and solved the structure from LCP-embedded proteinase K microcrystals with the comparable high resolution to conventional crystallographic method.
It cannot be neglected that only very few portions of membrane proteins were able to be successfully crystallized for structure determination. Single particle cryoEM method allows the structural studies from protein molecules detour away from crystallization. An atomic resolution structure of the β1-AR bound with agonist in complex with Gs protein, with particle size of less than 200 kDa, was determined by cryoEM, reaching to an atomic resolution of 3.8 Å. The complex structure captured a fully active conformation and revealed the important mechanisms of how the agonist bound receptor activated Gs protein.
These technological developments provide more opportunities to the structural biology community to discover mechanisms underlying such complicated machinery network, which would eventually benefit the structure-based drug discovery.
ContributorsZhu, Lan, Ph.D (Author) / Liu, Wei (Thesis advisor) / Mills, Jeremy (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2019
Temperature and polarizability effects on electron transfer in biology and artificial photosynthesis
Description
This study aims to address the deficiencies of the Marcus model of electron transfer
(ET) and then provide modifications to the model. A confirmation of the inverted energy
gap law, which is the cleanest verification so far, is presented for donor-acceptor complexes.
In addition to the macroscopic properties of the solvent, the physical properties of the solvent
are incorporated in the model via the microscopic solvation model. For the molecules
studied in this dissertation, the rate constant first increases with cooling, in contrast to the
prediction of the Arrhenius law, and then decreases at lower temperatures. Additionally,
the polarizability of solute, which was not considered in the original Marcus theory, is included
by the Q-model of ET. Through accounting for the polarizability of the reactants, the
Q-model offers an important design principle for achieving high performance solar energy
conversion materials. By means of the analytical Q-model of ET, it is shown that including
molecular polarizability of C60 affects the reorganization energy and the activation barrier
of ET reaction.
The theory and Electrochemistry of Ferredoxin and Cytochrome c are also investigated.
By providing a new formulation for reaction reorganization energy, a long-standing disconnect
between the results of atomistic simulations and cyclic voltametery experiments is
resolved. The significant role of polarizability of enzymes in reducing the activation energy
of ET is discussed. The binding/unbinding of waters to the active site of Ferredoxin leads
to non-Gaussian statistics of energy gap and result in a smaller activation energy of ET.
Furthermore, the dielectric constant of water at the interface of neutral and charged
C60 is studied. The dielectric constant is found to be in the range of 10 to 22 which is
remarkably smaller compared to bulk water( 80). Moreover, the interfacial structural
crossover and hydration thermodynamic of charged C60 in water is studied. Increasing the
charge of the C60 molecule result in a dramatic structural transition in the hydration shell,
which lead to increase in the population of dangling O-H bonds at the interface.
(ET) and then provide modifications to the model. A confirmation of the inverted energy
gap law, which is the cleanest verification so far, is presented for donor-acceptor complexes.
In addition to the macroscopic properties of the solvent, the physical properties of the solvent
are incorporated in the model via the microscopic solvation model. For the molecules
studied in this dissertation, the rate constant first increases with cooling, in contrast to the
prediction of the Arrhenius law, and then decreases at lower temperatures. Additionally,
the polarizability of solute, which was not considered in the original Marcus theory, is included
by the Q-model of ET. Through accounting for the polarizability of the reactants, the
Q-model offers an important design principle for achieving high performance solar energy
conversion materials. By means of the analytical Q-model of ET, it is shown that including
molecular polarizability of C60 affects the reorganization energy and the activation barrier
of ET reaction.
The theory and Electrochemistry of Ferredoxin and Cytochrome c are also investigated.
By providing a new formulation for reaction reorganization energy, a long-standing disconnect
between the results of atomistic simulations and cyclic voltametery experiments is
resolved. The significant role of polarizability of enzymes in reducing the activation energy
of ET is discussed. The binding/unbinding of waters to the active site of Ferredoxin leads
to non-Gaussian statistics of energy gap and result in a smaller activation energy of ET.
Furthermore, the dielectric constant of water at the interface of neutral and charged
C60 is studied. The dielectric constant is found to be in the range of 10 to 22 which is
remarkably smaller compared to bulk water( 80). Moreover, the interfacial structural
crossover and hydration thermodynamic of charged C60 in water is studied. Increasing the
charge of the C60 molecule result in a dramatic structural transition in the hydration shell,
which lead to increase in the population of dangling O-H bonds at the interface.
ContributorsWaskasi, Morteza M (Author) / Matyushov, Dmitry (Thesis advisor) / Richert, Ranko (Committee member) / Heyden, Matthias (Committee member) / Beckstein, Oliver (Committee member) / Arizona State University (Publisher)
Created2019
Description
Nanostructured zeolites, in particular nanocrystalline zeolites, are of great interest due to their efficient use in conventional catalysis, separations, and emerging applications. Despite the recent advances, fewer than 20 zeolite framework types have been synthesized in the form of nanocrystallites and their scalable synthesis has yet to be developed and understood. Geopolymers, claimed to be “amorphous cousins of zeolites”, are a class of ceramic-like aluminosilicate materials with prominent application in construction due to their unique chemical and mechanical properties. Despite the monolith form, geopolymers are fundamentally nanostructured materials and contain zeolite nanocrystallites.
Herein, a new cost-effective and scalable synthesis of various types of nanocrystalline zeolites based on geopolymer chemistry is presented. The study includes the synthesis of highly crystalline discrete nanorods of a CAN zeolite framework structure that had not been achieved hitherto, the exploration of the Na−Al−Si−H2O kinetic phase diagram of hydrogels that gives SOD, CAN and FAU nanocrystalline zeolites, and the discovery of a unique formation mechanism of highly crystalline nanostructured FAU zeolite with intermediate gel products that possess an unprecedented uniform distribution of elements. This study demonstrated the possibility of using high-concentration hydrogels for the synthesis of nanocrystalline zeolites of additional framework structures.
Moreover, a comprehensive study on nanostructured FAU zeolites ion-exchanged with Ag+, Zn2+, Cu2+ and Fe2+ for antibacterial applications is presented, which comprises metal ion release kinetics, antibacterial properties, and cytotoxicity. For the first time, superior metal ion release performance was confirmed for the nanostructured zeolites compared to their micron-sized counterparts. The metal ion-exchanged FAU nanostructured zeolites were established as new effective antibacterial materials featuring their unique physiochemical, antibacterial, and cytotoxic properties.
Herein, a new cost-effective and scalable synthesis of various types of nanocrystalline zeolites based on geopolymer chemistry is presented. The study includes the synthesis of highly crystalline discrete nanorods of a CAN zeolite framework structure that had not been achieved hitherto, the exploration of the Na−Al−Si−H2O kinetic phase diagram of hydrogels that gives SOD, CAN and FAU nanocrystalline zeolites, and the discovery of a unique formation mechanism of highly crystalline nanostructured FAU zeolite with intermediate gel products that possess an unprecedented uniform distribution of elements. This study demonstrated the possibility of using high-concentration hydrogels for the synthesis of nanocrystalline zeolites of additional framework structures.
Moreover, a comprehensive study on nanostructured FAU zeolites ion-exchanged with Ag+, Zn2+, Cu2+ and Fe2+ for antibacterial applications is presented, which comprises metal ion release kinetics, antibacterial properties, and cytotoxicity. For the first time, superior metal ion release performance was confirmed for the nanostructured zeolites compared to their micron-sized counterparts. The metal ion-exchanged FAU nanostructured zeolites were established as new effective antibacterial materials featuring their unique physiochemical, antibacterial, and cytotoxic properties.
ContributorsChen, Shaojiang (Author) / Seo, Dong Kyun (Thesis advisor) / Trovitch, Ryan (Committee member) / Thomas, MaryLaura Lind (Committee member) / Arizona State University (Publisher)
Created2019
Description
Redox enzymes represent a big group of proteins and they serve as catalysts for
biological processes that involve electron transfer. These proteins contain a redox center
that determines their functional properties, and hence, altering this center or incorporating
non-biological redox cofactor to proteins has been used as a means to generate redox
proteins with desirable activities for biological and chemical applications. Porphyrins and
Fe-S clusters are among the most common cofactors that biology employs for electron
transfer processes and there have been many studies on potential activities that they offer
in redox reactions.
In this dissertation, redox activity of Fe-S clusters and catalytic activity of porphyrins
have been explored with regard to protein scaffolds. In the first part, modular property of
repeat proteins along with previously established protein design principles have been
used to incorporate multiple Fe-S clusters within the repeat protein scaffold. This study is
the first example of exploiting a single scaffold to assemble a determined number of
clusters. In exploring the catalytic activity of transmetallated porphyrins, a cobalt-porphyrin
binding protein known as cytochrome c was employed in a water oxidation
photoelectrochemical cell. This system can be further coupled to a hydrogen production
electrode to achieve a full water splitting tandem cell. Finally, a cobalt-porphyrin binding
protein known as cytochrome b562 was employed to design a whole cell catalysis system,
and the activity of the surface-displayed protein for hydrogen production was explored
photochemically. This system can further be expanded for directed evolution studies and
high-throughput screening.
biological processes that involve electron transfer. These proteins contain a redox center
that determines their functional properties, and hence, altering this center or incorporating
non-biological redox cofactor to proteins has been used as a means to generate redox
proteins with desirable activities for biological and chemical applications. Porphyrins and
Fe-S clusters are among the most common cofactors that biology employs for electron
transfer processes and there have been many studies on potential activities that they offer
in redox reactions.
In this dissertation, redox activity of Fe-S clusters and catalytic activity of porphyrins
have been explored with regard to protein scaffolds. In the first part, modular property of
repeat proteins along with previously established protein design principles have been
used to incorporate multiple Fe-S clusters within the repeat protein scaffold. This study is
the first example of exploiting a single scaffold to assemble a determined number of
clusters. In exploring the catalytic activity of transmetallated porphyrins, a cobalt-porphyrin
binding protein known as cytochrome c was employed in a water oxidation
photoelectrochemical cell. This system can be further coupled to a hydrogen production
electrode to achieve a full water splitting tandem cell. Finally, a cobalt-porphyrin binding
protein known as cytochrome b562 was employed to design a whole cell catalysis system,
and the activity of the surface-displayed protein for hydrogen production was explored
photochemically. This system can further be expanded for directed evolution studies and
high-throughput screening.
ContributorsBahrami Dizicheh, Zahra (Author) / Ghirlanda, Giovanna (Thesis advisor) / Allen, James P. (Committee member) / Seo, Dong Kyun (Committee member) / Arizona State University (Publisher)
Created2019
Description
Transient receptor potential vanilloid member 1 (TRPV1) is a membrane protein ion channel that functions as a heat and capsaicin receptor. In addition to activation by hot temperature and vanilloid compounds such as capsaicin, TRPV1 is modulated by various stimuli including acidic pH, endogenous lipids, diverse biological and synthetic chemical ligands, and modulatory proteins. Due to its sensitivity to noxious stimuli such as high temperature and pungent chemicals, there has been significant evidence that TRPV1 participates in a variety of human physiological and pathophysiological pathways, raising the potential of TRPV1 as an attractive therapeutic target. However, the polymodal nature of TRPV1 function has complicated clinical application because the TRPV1 activation mechanisms from different modes have generally been enigmatic. Consequently, tremendous efforts have put into dissecting the mechanisms of different activation modes, but numerous questions remain to be answered.
The studies conducted in this dissertation probed the role of the S1-S4 membrane domain in temperature and ligand activation of human TRPV1. Temperature-dependent solution nuclear magnetic resonance (NMR) spectroscopy for thermodynamic and mechanistic studies of the S1-S4 domain. From these results, a potential temperature sensing mechanism of TRPV1, initiated from the S1-S4 domain, was proposed. Additionally, direct binding of various ligands to the S1-S4 domain were used to ascertain the interaction site and the affinities (Kd) of various ligands to this domain. These results are the first to study the isolated S1-S4 domain of human TRPV1 and many results indicate that the S1-S4 domain is crucial for both temperature-sensing and is the general receptor binding site central to chemical activation.
The studies conducted in this dissertation probed the role of the S1-S4 membrane domain in temperature and ligand activation of human TRPV1. Temperature-dependent solution nuclear magnetic resonance (NMR) spectroscopy for thermodynamic and mechanistic studies of the S1-S4 domain. From these results, a potential temperature sensing mechanism of TRPV1, initiated from the S1-S4 domain, was proposed. Additionally, direct binding of various ligands to the S1-S4 domain were used to ascertain the interaction site and the affinities (Kd) of various ligands to this domain. These results are the first to study the isolated S1-S4 domain of human TRPV1 and many results indicate that the S1-S4 domain is crucial for both temperature-sensing and is the general receptor binding site central to chemical activation.
ContributorsKim, Minjoo (Author) / Van Horn, Wade D (Thesis advisor) / Wang, Xu (Committee member) / Liu, Wei (Committee member) / Arizona State University (Publisher)
Created2019