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Description
Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.
ContributorsLi, Dianfan (Author) / Stansfeld, Phillip J. (Author) / Sansom, Mark S. P. (Author) / Keogh, Aaron (Author) / Vogeley, Lutz (Author) / Howe, Nicole (Author) / Lyons, Joseph A. (Author) / Aragao, David (Author) / Fromme, Petra (Author) / Fromme, Raimund (Author) / Basu, Shibom (Author) / Grotjohann, Ingo (Author) / Kupitz, Christopher (Author) / Rendek, Kimberley (Author) / Weierstall, Uwe (Author) / Zatsepin, Nadia (Author) / Cherezov, Vadim (Author) / Liu, Wei (Author) / Bandaru, Sateesh (Author) / English, Niall J. (Author) / Gati, Cornelius (Author) / Barty, Anton (Author) / Yefanov, Oleksandr (Author) / Chapman, Henry N. (Author) / Diederichs, Kay (Author) / Messerschmidt, Marc (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Seibert, M. Marvin (Author) / Caffrey, Martin (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2015-12-17
Description
Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.
ContributorsEdlund, Petra (Author) / Takala, Heikki (Author) / Claesson, Elin (Author) / Henry, Leocadie (Author) / Dods, Robert (Author) / Lehtivuori, Heli (Author) / Panman, Matthijs (Author) / Pande, Kanupriya (Author) / White, Thomas (Author) / Nakane, Takanori (Author) / Berntsson, Oskar (Author) / Gustavsson, Emil (Author) / Bath, Petra (Author) / Modi, Vaibhav (Author) / Roy Chowdhury, Shatabdi (Author) / Zook, James (Author) / Berntsen, Peter (Author) / Pandey, Suraj (Author) / Poudyal, Ishwor (Author) / Tenboer, Jason (Author) / Kupitz, Christopher (Author) / Barty, Anton (Author) / Fromme, Petra (Author) / Koralek, Jake D. (Author) / Tanaka, Tomoyuki (Author) / Spence, John (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Boutet, Sebastien (Author) / Nango, Eriko (Author) / Moffat, Keith (Author) / Groenhof, Gerrit (Author) / Ihalainen, Janne (Author) / Stojkovic, Emina A. (Author) / Schmidt, Marius (Author) / Westenhoff, Sebastian (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2016-10-19
Description
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
ContributorsNogly, Przemyslaw (Author) / Panneels, Valerie (Author) / Nelson, Garrett (Author) / Gati, Cornelius (Author) / Kimura, Tetsunari (Author) / Milne, Christopher (Author) / Milathianaki, Despina (Author) / Kubo, Minoru (Author) / Wu, Wenting (Author) / Conrad, Chelsie (Author) / Coe, Jesse (Author) / Bean, Richard (Author) / Zhao, Yun (Author) / Bath, Petra (Author) / Dods, Robert (Author) / Harimoorthy, Rajiv (Author) / Beyerlein, Kenneth R. (Author) / Rheinberger, Jan (Author) / James, Daniel (Author) / Deponte, Daniel (Author) / Li, Chufeng (Author) / Sala, Leonardo (Author) / Williams, Garth J. (Author) / Hunter, Mark S. (Author) / Koglin, Jason E. (Author) / Berntsen, Peter (Author) / Nango, Eriko (Author) / Iwata, So (Author) / Chapman, Henry N. (Author) / Fromme, Petra (Author) / Frank, Matthias (Author) / Abela, Rafael (Author) / Boutet, Sebastien (Author) / Barty, Anton (Author) / White, Thomas A. (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Neutze, Richard (Author) / Schertler, Gebhard (Author) / Standfuss, Jorg (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Molecular Sciences (Contributor)
Created2016-08-22
Description
I have conducted a creative that captures the power of women through an artistic perspective. The title of the creative project is “A Tribute to the Women Among us,” because this project’s purpose is to express gratitude for the women that fought for the rights I have today, and for the women I encounter in marches, continuing the fight. I have taken photographs of women and children at women's marches in the United States and in France, yielding a total of 10 photographs I will be presenting at my defense, and printing out to sell. All the profits made from the photographs will be donated to planned parenthood.
ContributorsMiss Ozuna, Alejandra Miss (Author) / Anand, Julia (Thesis director) / Mesch, Claudia (Committee member) / School of Politics and Global Studies (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
This thesis explores the relationship between sustainability, the fashion industry, and fashion exhibitions. Sustainability has been a driving force in the fashion industry in recent years as designers attempt to combat staggering textile waste statistics in order to lessen the damage the industry has on the environment. Producers must rethink human engagement with nature based on a new ethic of ecosystem stewardship, which proposes that humans have ethical obligations to one another in their mutual relationship with non-human species and nature (Schmitz 13). Enhancing a socio-ecological perspective garners new ways of consuming and appreciating clothing design while focusing on lessening impacts on the environment through using less materials, reusing materials in new textile developments, and projecting a sustainable identity that can be followed by the public in order to be more conscious of spending habits, annual waste, and how sustainably ethical companies are. Removing natural resources or transforming landscapes to enhance human well-being paradoxically stands to diminish human well being over time (Schmitz 12), and this is something that humans face with the inevitability of climate change affecting future generations. In mapping the relationship between sustainability, fashion designer's design process, and the way curators communicate sustainable themes, an overall understanding of sustainable culture can be understood in the industry.
ContributorsLord, Nicolas K (Author) / Sewell, Dennita (Thesis director) / Mesch, Claudia (Committee member) / School of Art (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
X-ray Free Electron Lasers (XFELs) are used for diffractive x-ray imaging of the structure of many biological particles, such as viruses and proteins. The ultimate goal for XFEL-based microscopy is atomic resolution images of non-crystalline particles. However, data collection efficiency as well as the limited amount of measurement time given annually to researchers, such high-resolution images are presently impossible to attain. Here, we consider two potential solutions to the single-particle hit rate problem; the first looks at applying static electric fields to existing aerodynamic particle injectors, and the second looks at the viability of using time-varying electric fields associated with ion traps to create high-density regions of particles. For the static solution, we looked at applying a constant electric potential to the nozzle, as well as applying a high voltage to a ring electrode in close proximity to a grounded nozzle. We considered the breakdown field strength of the helium gas used to determine how closely the ring electrode could be placed without creating an arc that could potentially destroy expensive equipment. Then, we considered the possibility of using electrodynamic ion traps to increase particle densities. We first characterized how charged particles behave in oscillating electric fields using a simple electrode geometry. Using the general results from this, we then constructed a rudimentary ion trap to test if our experiment agreed with the theory. Finally, we conducted a literature review to determine what particle densities other scientists have been able to measure using ion traps. We then compared existing ion traps to what we expect from the nozzle injectors to determine which method may be the better solution.
ContributorsBradshaw, Layne Nicholas (Author) / Kirian, Richard (Thesis director) / Weierstall, Uwe (Committee member) / Department of Physics (Contributor, Contributor) / School of Earth and Space Exploration (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
The dissertation focuses on several Romanian avant-garde magazines, such as Contimporanul, Integral, and 75HP, that Romanian artists and writers created in Romania in the 1920s, after Romanian Dadaists Tristan Tzara and Marcel Iancu disbanded from Zurich Dada in the 1910s. The Romanian avant-garde magazines launched the Romanian avant-garde movement—the most intense period of artistic production in the country. The Romanian avant-gardists established Integralism in an attempt to differentiate themselves from other European avant-garde groups and to capture the intense and innovative creative spirit of their modern era by uniting and condensing avant-garde and modern styles on the pages of their magazines. However, I argue that instead of Integralism, what the Romanian avant-garde magazines put forth were Romanian avant-garde versions of Constructivism and Cubism conveyed in the magazines’ constructivist prints and reproductions of cubist paintings. The originality of the Romanian avant-garde magazines, thus, is concentrated in their appropriation and reinterpretation of Constructivism and Cubism rather than in their Integralism. Moreover, in their rebellion and resistance to Romania’s social, political, and artistic status quo, the Romanian avant-garde magazines functioned as an instrument with which the Romanian avant-gardists expressed their complex relationship with their Jewish identity. The magazines were not on the periphery of artistic production, as art history discourse on modern and avant-garde art has situated them, but were an important player in the global network of avant-garde magazines that traversed across eastern and western Europe, South America, the United States, and Japan.
ContributorsMiholca, Amelia (Author) / Mesch, Claudia (Thesis advisor) / Orlich, Ileana (Committee member) / Holian, Anna (Committee member) / Navarro, Rudy (Committee member) / Arizona State University (Publisher)
Created2021
Description
Traditional Reinforcement Learning (RL) assumes to learn policies with respect to reward available from the environment but sometimes learning in a complex domain requires wisdom which comes from a wide range of experience. In behavior based robotics, it is observed that a complex behavior can be described by a combination of simpler behaviors. It is tempting to apply similar idea such that simpler behaviors can be combined in a meaningful way to tailor the complex combination. Such an approach would enable faster learning and modular design of behaviors. Complex behaviors can be combined with other behaviors to create even more advanced behaviors resulting in a rich set of possibilities. Similar to RL, combined behavior can keep evolving by interacting with the environment. The requirement of this method is to specify a reasonable set of simple behaviors. In this research, I present an algorithm that aims at combining behavior such that the resulting behavior has characteristics of each individual behavior. This approach has been inspired by behavior based robotics, such as the subsumption architecture and motor schema-based design. The combination algorithm outputs n weights to combine behaviors linearly. The weights are state dependent and change dynamically at every step in an episode. This idea is tested on discrete and continuous environments like OpenAI’s “Lunar Lander” and “Biped Walker”. Results are compared with related domains like Multi-objective RL, Hierarchical RL, Transfer learning, and basic RL. It is observed that the combination of behaviors is a novel way of learning which helps the agent achieve required characteristics. A combination is learned for a given state and so the agent is able to learn faster in an efficient manner compared to other similar approaches. Agent beautifully demonstrates characteristics of multiple behaviors which helps the agent to learn and adapt to the environment. Future directions are also suggested as possible extensions to this research.
ContributorsVora, Kevin Jatin (Author) / Zhang, Yu (Thesis advisor) / Yang, Yezhou (Committee member) / Praharaj, Sarbeswar (Committee member) / Arizona State University (Publisher)
Created2021
Description
The Hong Kong-born Canadian photographer and performance artist Tseng Kwong Chi mostly worked in the United States until the year he died in 1990. Upon arriving in New York in 1979, he started his career with a new name. By dropping his anglicized name Joseph and replacing it with his Chinese given name Kwong Chi, Tseng made a clear statement: this is my staged persona who refuses to assimilate to Western culture. This thesis deconstructs Tseng’s key works, including his party-crashing Met series, the decade-long East Meets West series, and the extended Expeditionary series. With his persona disguised by wearing a Mao suit and a pair of sunglasses, I argue that Tseng was a pioneer in the genre of Asian American performance photography and that his work foreshadowed the cultural jamming movement in his innovative use of détournement while it also critically comments on orientalism, cultural fetish, and Asian identity politics. Additionally, Tseng’s work served as a bridge, connecting art history with issues of Asian American identity. As a gay artist who worked mostly in the United States, his work was an early example of what Jachinson Chan has suggested as an alternative model of masculinity for Asian American men: that Asian American men can be free, independent, expressive, and willing to embrace femininity with their masculinity. As David Eng has argued, Tseng also bridged the fields of Asian American queer studies and diaspora studies. Moreover, Tseng carried the legacy of the first-generation Chinese American artists in the medium of photography and inspired the next generation of diasporic artists to explore Asian identity, and to contest the image of Mao and the power dynamics between East and West.
ContributorsWei, Xin (Author) / Mesch, Claudia (Thesis advisor) / Hoy, Meredith (Committee member) / Kuo, Karen (Committee member) / Arizona State University (Publisher)
Created2022
Description
The self-assembly of strongly-coupled nanocrystal superlattices, as a convenient bottom-up synthesis technique featuring a wide parameter space, is at the forefront of next-generation material design. To realize the full potential of such tunable, functional materials, a more complete understanding of the self-assembly process and the artificial crystals it produces is required. In this work, we discuss the results of a hard coherent X-ray scattering experiment at the Linac Coherent Light Source, observing superlattices long after their initial nucleation. The resulting scattering intensity correlation functions have dispersion suggestive of a disordered crystalline structure and indicate the occurrence of rapid, strain-relieving events therein. We also present real space reconstructions of individual superlattices obtained via coherent diffractive imaging. Through this analysis we thus obtain high-resolution structural and dynamical information of self-assembled superlattices in their native liquid environment.
ContributorsHurley, Matthew (Author) / Teitelbaum, Samuel (Thesis director) / Ginsberg, Naomi (Committee member) / Kirian, Richard (Committee member) / Barrett, The Honors College (Contributor) / Department of Physics (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Historical, Philosophical & Religious Studies, Sch (Contributor)
Created2023-05