Theses and Dissertations
This collection includes both ASU Theses and Dissertations, submitted by graduate students, and the Barrett, Honors College theses submitted by undergraduate students.
Displaying 1 - 10 of 90
Description
Membrane proteins are a vital part of cellular structure. They are directly involved in many important cellular functions, such as uptake, signaling, respiration, and photosynthesis, among others. Despite their importance, however, less than 500 unique membrane protein structures have been determined to date. This is due to several difficulties with macromolecular crystallography, primarily the difficulty of growing large, well-ordered protein crystals. Since the first proof of concept for femtosecond nanocrystallography showing that diffraction patterns can be collected on extremely small crystals, thus negating the need to grow larger crystals, there have been many exciting advancements in the field. The technique has been proven to show high spatial resolution, thus making it a viable method for structural biology. However, due to the ultrafast nature of the technique, which allows for a lack of radiation damage in imaging, even more interesting experiments are possible, and the first temporal and spatial images of an undamaged structure could be acquired. This concept was denoted as time-resolved femtosecond nanocrystallography.
This dissertation presents on the first time-resolved data set of Photosystem II where structural changes can actually be seen without radiation damage. In order to accomplish this, new crystallization techniques had to be developed so that enough crystals could be made for the liquid jet to deliver a fully hydrated stream of crystals to the high-powered X-ray source. These changes are still in the preliminary stages due to the slightly lower resolution data obtained, but they are still a promising show of the power of this new technique. With further optimization of crystal growth methods and quality, injection technique, and continued development of data analysis software, it is only a matter of time before the ability to make movies of molecules in motion from X-ray diffraction snapshots in time exists. The work presented here is the first step in that process.
This dissertation presents on the first time-resolved data set of Photosystem II where structural changes can actually be seen without radiation damage. In order to accomplish this, new crystallization techniques had to be developed so that enough crystals could be made for the liquid jet to deliver a fully hydrated stream of crystals to the high-powered X-ray source. These changes are still in the preliminary stages due to the slightly lower resolution data obtained, but they are still a promising show of the power of this new technique. With further optimization of crystal growth methods and quality, injection technique, and continued development of data analysis software, it is only a matter of time before the ability to make movies of molecules in motion from X-ray diffraction snapshots in time exists. The work presented here is the first step in that process.
ContributorsKupitz, Christopher (Author) / Fromme, Petra (Thesis advisor) / Spence, John C. (Thesis advisor) / Redding, Kevin (Committee member) / Ros, Alexandra (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
Cyanovirin-N (CVN) is a cyanobacterial lectin with potent anti-HIV activity, mediated by binding to the N-linked oligosaccharide moiety of the envelope protein gp120. CVN offers a scaffold to develop multivalent carbohydrate-binding proteins with tunable specificities and affinities. I present here biophysical calculations completed on a monomeric-stabilized mutant of cyanovirin-N, P51G-m4-CVN, in which domain A binding activity is abolished by four mutations; with comparisons made to CVNmutDB, in which domain B binding activity is abolished. Using Monte Carlo calculations and docking simulations, mutations in CVNmutDB were considered singularly, and the mutations E41A/G and T57A were found to impact the affinity towards dimannose the greatest. 15N-labeled proteins were titrated with Manα(1-2)Manα, while following chemical shift perturbations in NMR spectra. The mutants, E41A/G and T57A, had a larger Kd than P51G-m4-CVN, matching the trends predicted by the calculations. We also observed that the N42A mutation affects the local fold of the binding pocket, thus removing all binding to dimannose. Characterization of the mutant N53S showed similar binding affinity to P51G-m4-CVN. Using biophysical calculations allows us to study future iterations of models to explore affinities and specificities. In order to further elucidate the role of multivalency, I report here a designed covalent dimer of CVN, Nested cyanovirin-N (Nested CVN), which has four binding sites. Nested CVN was found to have comparable binding affinity to gp120 and antiviral activity to wt CVN. These results demonstrate the ability to create a multivalent, covalent dimer that has comparable results to that of wt CVN.
WW domains are small modules consisting of 32-40 amino acids that recognize proline-rich peptides and are found in many signaling pathways. We use WW domain sequences to explore protein folding by simulations using Zipping and Assembly Method. We identified five crucial contacts that enabled us to predict the folding of WW domain sequences based on those contacts. We then designed a folded WW domain peptide from an unfolded WW domain sequence by introducing native contacts at those critical positions.
WW domains are small modules consisting of 32-40 amino acids that recognize proline-rich peptides and are found in many signaling pathways. We use WW domain sequences to explore protein folding by simulations using Zipping and Assembly Method. We identified five crucial contacts that enabled us to predict the folding of WW domain sequences based on those contacts. We then designed a folded WW domain peptide from an unfolded WW domain sequence by introducing native contacts at those critical positions.
ContributorsWoodrum, Brian William (Author) / Ghirlanda, Giovanna (Thesis advisor) / Redding, Kevin (Committee member) / Wang, Xu (Committee member) / Arizona State University (Publisher)
Created2014
Description
With the increasing user demand for low latency, elastic provisioning of computing resources coupled with ubiquitous and on-demand access to real-time data, cloud computing has emerged as a popular computing paradigm to meet growing user demands. However, with the introduction and rising use of wear- able technology and evolving uses of smart-phones, the concept of Internet of Things (IoT) has become a prevailing notion in the currently growing technology industry. Cisco Inc. has projected a data creation of approximately 403 Zetabytes (ZB) by 2018. The combination of bringing benign devices and connecting them to the web has resulted in exploding service and data aggregation requirements, thus requiring a new and innovative computing platform. This platform should have the capability to provide robust real-time data analytics and resource provisioning to clients, such as IoT users, on-demand. Such a computation model would need to function at the edge-of-the-network, forming a bridge between the large cloud data centers and the distributed connected devices.
This research expands on the notion of bringing computational power to the edge- of-the-network, and then integrating it with the cloud computing paradigm whilst providing services to diverse IoT-based applications. This expansion is achieved through the establishment of a new computing model that serves as a platform for IoT-based devices to communicate with services in real-time. We name this paradigm as Gateway-Oriented Reconfigurable Ecosystem (GORE) computing. Finally, this thesis proposes and discusses the development of a policy management framework for accommodating our proposed computational paradigm. The policy framework is designed to serve both the hosted applications and the GORE paradigm by enabling them to function more efficiently. The goal of the framework is to ensure uninterrupted communication and service delivery between users and their applications.
This research expands on the notion of bringing computational power to the edge- of-the-network, and then integrating it with the cloud computing paradigm whilst providing services to diverse IoT-based applications. This expansion is achieved through the establishment of a new computing model that serves as a platform for IoT-based devices to communicate with services in real-time. We name this paradigm as Gateway-Oriented Reconfigurable Ecosystem (GORE) computing. Finally, this thesis proposes and discusses the development of a policy management framework for accommodating our proposed computational paradigm. The policy framework is designed to serve both the hosted applications and the GORE paradigm by enabling them to function more efficiently. The goal of the framework is to ensure uninterrupted communication and service delivery between users and their applications.
ContributorsDsouza, Clinton (Author) / Ahn, Gail-Joon (Thesis advisor) / Doupe, Adam (Committee member) / Dasgupta, Partha (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
Android is currently the most widely used mobile operating system. The permission model in Android governs the resource access privileges of applications. The permission model however is amenable to various attacks, including re-delegation attacks, background snooping attacks and disclosure of private information. This thesis is aimed at understanding, analyzing and performing forensics on application behavior. This research sheds light on several security aspects, including the use of inter-process communications (IPC) to perform permission re-delegation attacks.
Android permission system is more of app-driven rather than user controlled, which means it is the applications that specify their permission requirement and the only thing which the user can do is choose not to install a particular application based on the requirements. Given the all or nothing choice, users succumb to pressures and needs to accept permissions requested. This thesis proposes a couple of ways for providing the users finer grained control of application privileges. The same methods can be used to evade the Permission Re-delegation attack.
This thesis also proposes and implements a novel methodology in Android that can be used to control the access privileges of an Android application, taking into consideration the context of the running application. This application-context based permission usage is further used to analyze a set of sample applications. We found the evidence of applications spoofing or divulging user sensitive information such as location information, contact information, phone id and numbers, in the background. Such activities can be used to track users for a variety of privacy-intrusive purposes. We have developed implementations that minimize several forms of privacy leaks that are routinely done by stock applications.
Android permission system is more of app-driven rather than user controlled, which means it is the applications that specify their permission requirement and the only thing which the user can do is choose not to install a particular application based on the requirements. Given the all or nothing choice, users succumb to pressures and needs to accept permissions requested. This thesis proposes a couple of ways for providing the users finer grained control of application privileges. The same methods can be used to evade the Permission Re-delegation attack.
This thesis also proposes and implements a novel methodology in Android that can be used to control the access privileges of an Android application, taking into consideration the context of the running application. This application-context based permission usage is further used to analyze a set of sample applications. We found the evidence of applications spoofing or divulging user sensitive information such as location information, contact information, phone id and numbers, in the background. Such activities can be used to track users for a variety of privacy-intrusive purposes. We have developed implementations that minimize several forms of privacy leaks that are routinely done by stock applications.
ContributorsGollapudi, Narasimha Aditya (Author) / Dasgupta, Partha (Thesis advisor) / Xue, Guoliang (Committee member) / Doupe, Adam (Committee member) / Arizona State University (Publisher)
Created2014
Description
The increasing number of continually connected mobile persons has created an environment conducive to real time user data gathering for many uses both public and private in nature. Publicly, one can envision no longer requiring a census to determine the demographic composition of the country and its sub regions. The information provided is vastly more up to date than that of a census and allows civil authorities to be more agile and preemptive with planning. Privately, advertisers take advantage of a persons stated opinions, demographics, and contextual (where and when) information in order to formulate and present pertinent offers.
Regardless of its use this information can be sensitive in nature and should therefore be under the control of the user. Currently, a user has little say in the manner that their information is processed once it has been released. An ad-hoc approach is currently in use, where the location based service providers each maintain their own policy over personal information usage.
In order to allow more user control over their personal information while still providing for targeted advertising, a systematic approach to the release of the information is needed. It is for that reason we propose a User-Centric Context Aware Spatiotemporal Anonymization framework. At its core the framework will unify the current spatiotemporal anonymization with that of traditional anonymization so that user specified anonymization requirement is met or exceeded while allowing for more demographic information to be released.
Regardless of its use this information can be sensitive in nature and should therefore be under the control of the user. Currently, a user has little say in the manner that their information is processed once it has been released. An ad-hoc approach is currently in use, where the location based service providers each maintain their own policy over personal information usage.
In order to allow more user control over their personal information while still providing for targeted advertising, a systematic approach to the release of the information is needed. It is for that reason we propose a User-Centric Context Aware Spatiotemporal Anonymization framework. At its core the framework will unify the current spatiotemporal anonymization with that of traditional anonymization so that user specified anonymization requirement is met or exceeded while allowing for more demographic information to be released.
ContributorsSanchez, Michael Andrew (Author) / Ahn, Gail-Joon (Thesis advisor) / Doupe, Adam (Committee member) / Dasgupta, Partha (Committee member) / Arizona State University (Publisher)
Created2014
Description
The rate at which new malicious software (Malware) is created is consistently increasing each year. These new malwares are designed to bypass the current anti-virus countermeasures employed to protect computer systems. Security Analysts must understand the nature and intent of the malware sample in order to protect computer systems from these attacks. The large number of new malware samples received daily by computer security companies require Security Analysts to quickly determine the type, threat, and countermeasure for newly identied samples. Our approach provides for a visualization tool to assist the Security Analyst in these tasks that allows the Analyst to visually identify relationships between malware samples.
This approach consists of three steps. First, the received samples are processed by a sandbox environment to perform a dynamic behavior analysis. Second, the reports of the dynamic behavior analysis are parsed to extract identifying features which are matched against other known and analyzed samples. Lastly, those matches that are determined to express a relationship are visualized as an edge connected pair of nodes in an undirected graph.
This approach consists of three steps. First, the received samples are processed by a sandbox environment to perform a dynamic behavior analysis. Second, the reports of the dynamic behavior analysis are parsed to extract identifying features which are matched against other known and analyzed samples. Lastly, those matches that are determined to express a relationship are visualized as an edge connected pair of nodes in an undirected graph.
ContributorsHolmes, James Edward (Author) / Ahn, Gail-Joon (Thesis advisor) / Dasgupta, Partha (Committee member) / Doupe, Adam (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
Rhodoferax antarcticus strain ANT.BR, a purple nonsulfur bacterium isolated from a microbial mat in Ross Island, Antarctica, is the first described anoxygenic phototrophic bacterium that is adapted to cold habitats and is the first beta-proteobacterium to undergo complete genome sequencing. R. antarcticus has unique absorption spectra and there are no obvious intracytoplasmic membranes in cells grown phototrophically, even under low light intensity. Analysis of the finished genome sequence reveals a single chromosome (3,809,266 bp) and a large plasmid (198,615 bp) that together harbor 4,262 putative genes. The genome contains two types of Rubiscos, Form IAq and Form II, which are known to exhibit quite different kinetic properties in other bacteria. The presence of multiple Rubisco forms could give R. antarcticus high metabolic flexibility in diverse environments. Annotation of the complete genome sequence along with previous experimental results predict the presence of structural genes for three types of light-harvesting (LH) complexes, LH I (B875), LH II (B800/850), and LH III (B800/820). There is evidence that expression of genes for the LH II complex might be inhibited when R. antarcticus is under low temperature and/or low light intensity. These interesting condition-dependent light-harvesting apparatuses and the control of their expression are very valuable for the further understanding of photosynthesis in cold environments. Finally, R. antarcticus exhibits a highly motile lifestyle. The genome content and organization of all putative polar flagella genes are characterized and discussed.
ContributorsZhao, Tingting, M.S (Author) / Touchman, Jeffrey (Thesis advisor) / Rosenberg, Michael (Committee member) / Redding, Kevin (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2011