Matching Items (510)
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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

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
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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

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
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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.

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
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Description

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices.

ContributorsOberthuer, Dominik (Author) / Knoska, Juraj (Author) / Wiedorn, Max O. (Author) / Beyerlein, Kenneth R. (Author) / Bushnell, David A. (Author) / Kovaleva, Elena G. (Author) / Heymann, Michael (Author) / Gumprecht, Lars (Author) / Kirian, Richard (Author) / Barty, Anton (Author) / Mariani, Valerio (Author) / Tolstikova, Aleksandra (Author) / Adriano, Luigi (Author) / Awel, Salah (Author) / Barthelmess, Miriam (Author) / Dorner, Katerina (Author) / Xavier, P. Lourdu (Author) / Yefanov, Oleksandr (Author) / James, Daniel (Author) / Nelson, Garrett (Author) / Wang, Dingjie (Author) / Calvey, George (Author) / Chen, Yujie (Author) / Schmidt, Andrea (Author) / Szczepek, Michael (Author) / Frielingsdorf, Stefan (Author) / Lenz, Oliver (Author) / Snell, Edward (Author) / Robinson, Philip J. (Author) / Sarler, Bozidar (Author) / Belsak, Grega (Author) / Macek, Marjan (Author) / Wilde, Fabian (Author) / Aquila, Andrew (Author) / Boutet, Sebastien (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Scheerer, Patrick (Author) / Lipscomb, John D. (Author) / Weierstall, Uwe (Author) / Kornberg, Roger D. (Author) / Spence, John (Author) / Pollack, Lois (Author) / Chapman, Henry N. (Author) / Bajt, Sasa (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2017-03-16
Description

A survey was created to help gain some insight on the opinions of homeowners across the <br/>Phoenix Metro Area. This survey consisted of 7 questions relating to personal experiences and <br/>the homeowners’ opinions or concerns. The results of the survey showed that there are a few <br/>concerns surrounding solar energy

A survey was created to help gain some insight on the opinions of homeowners across the <br/>Phoenix Metro Area. This survey consisted of 7 questions relating to personal experiences and <br/>the homeowners’ opinions or concerns. The results of the survey showed that there are a few <br/>concerns surrounding solar energy with an emphasis on the cost of maintenance of panels and <br/>the payback period where the homeowners would see a return on their investment. Most of the <br/>homeowners answered that they do not use solar energy but have thought about using it for their <br/>main source of energy before. The homeowners in the survey also thought that solar energy was <br/>overall too expensive and that it would take a long time before they would see any payoff or <br/>savings from the solar panels. It was found that the payback period for panels is around 7 years <br/>and that depending on the size of the solar system installed or on the model used, solar panels <br/>cost much less than many people think. This was found by researching non-biased resources <br/>from government websites and from local energy companies’ websites. To combat the concerns <br/>found from the survey, an infographic was created to help inform the public about solar energy <br/>and allow the homeowners to make decisions that are well informed and not based on <br/>misinformation. The infographic included information related to the survey by explaining the <br/>survey and explaining topics that were of concern to the homeowners who took the survey. In <br/>addition, the infographic displayed information about solar energy and that the decision to use <br/>solar is ultimately up to the audience.

ContributorsGobiel, Erin (Author) / Taylor, David (Thesis director) / Koster, Auriane (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

This paper outlines the design and testing of a z-scan spectrometer capable of measuring the third order refraction index of liquids. The spectrometer underwent multiple redesigns, with each explored in this paper with their benefits and drawbacks discussed. The first design was capable of measuring the third order

This paper outlines the design and testing of a z-scan spectrometer capable of measuring the third order refraction index of liquids. The spectrometer underwent multiple redesigns, with each explored in this paper with their benefits and drawbacks discussed. The first design was capable of measuring the third order refraction index for glass, and found a value of 8.43 +- 0.392 x 10^(-16) cm^2/W for the glass sample, with the literature stating glass has a refraction index between 1-100 x 10^(-16) cm^2/W. The second design was capable of measuring the third order refraction index of liquids, and found values of 1.23 $\pm$ 0.121 $\e{-16}$ and 9.43 +- 1.00 x 10^(-17) cm^2/W for water and ethanol respectively, with literature values of 2.7 x 10^(-16) and 5.0 x 10^(-17) cm^2/W respectively. The third design gave inconclusive results due to extreme variability in testing, and and the fourth design outlined has not been tested yet due to time constraints.

ContributorsClark, Brian Vincent (Author) / Sayres, Scott (Thesis director) / Steimle, Timothy (Committee member) / Keeler, Cynthia (Committee member) / School of Molecular Sciences (Contributor) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

Temperature swing adsorption is a commonly used gas separation technique, and is being<br/>further researched as a method of carbon capture. Carbon capture is becoming increasingly<br/>important as a potential way to slow global warming. In this study, algae-derived activated<br/>carbon adsorbents were analyzed for their carbon dioxide adsorption effectiveness.<br/>Algae-derived carbon adsorbents were

Temperature swing adsorption is a commonly used gas separation technique, and is being<br/>further researched as a method of carbon capture. Carbon capture is becoming increasingly<br/>important as a potential way to slow global warming. In this study, algae-derived activated<br/>carbon adsorbents were analyzed for their carbon dioxide adsorption effectiveness.<br/>Algae-derived carbon adsorbents were synthesized and then studied for their adsorption<br/>isotherms and adsorption breakthrough behavior. From the generated isotherm plots, it was<br/>determined that the carbonization temperature was not high enough and that more batches of<br/>adsorbent would have to be made to more accurately analyze the adsorptive potential of the<br/>algae-derived carbon adsorbent.

ContributorsCiha, Trevor (Author) / Deng, Shuguang (Thesis director) / Taylor, David (Committee member) / Chemical Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

This research endeavor explores the 1964 reasoning of Irish physicist John Bell and how it pertains to the provoking Einstein-Podolsky-Rosen Paradox. It is necessary to establish the machinations of formalisms ranging from conservation laws to quantum mechanical principles. The notion that locality is unable to be reconciled with the quantum

This research endeavor explores the 1964 reasoning of Irish physicist John Bell and how it pertains to the provoking Einstein-Podolsky-Rosen Paradox. It is necessary to establish the machinations of formalisms ranging from conservation laws to quantum mechanical principles. The notion that locality is unable to be reconciled with the quantum paradigm is upheld through analysis and the subsequent Aspect experiments in the years 1980-1982. No matter the complexity, any local hidden variable theory is incompatible with the formulation of standard quantum mechanics. A number of strikingly ambiguous and abstract concepts are addressed in this pursuit to deduce quantum's validity, including separability and reality. `Elements of reality' characteristic of unique spaces are defined using basis terminology and logic from EPR. The discussion draws directly from Bell's succinct 1964 Physics 1 paper as well as numerous other useful sources. The fundamental principle and insight gleaned is that quantum physics is indeed nonlocal; the door into its metaphysical and philosophical implications has long since been opened. Yet the nexus of information pertaining to Bell's inequality and EPR logic does nothing but assert the impeccable success of quantum physics' ability to describe nature.

ContributorsRapp, Sean R (Author) / Foy, Joseph (Thesis director) / Martin, Thomas (Committee member) / School of Earth and Space Exploration (Contributor) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

The ongoing Global Coronavirus Pandemic has been upheving social norms for over a year at this point. For countless people, our lives look very different at this point in time than they did before the pandemic began. Quarantine, Shelter in Place, Work from Home, and Online classes have led global

The ongoing Global Coronavirus Pandemic has been upheving social norms for over a year at this point. For countless people, our lives look very different at this point in time than they did before the pandemic began. Quarantine, Shelter in Place, Work from Home, and Online classes have led global populations to become less active leading to an increase in sedentary lifestyles. The final impact of this consequence is unknown, but emerging studies have led to concrete evidence of decreased physical and mental wellbeing, particularly in children. VirusFreeSports was the brainchild of three ASU Honors students who sought to remedy these devastating consequences by creating environments where children can participate in sports and exercise safely, free of the threat COVID-19 or other transmissible illnesses. The ultimate goal for the project team was to build traction for their idea, which culminated in a video pitch sent to potential investors. Although largely created as an exercise and we did not create a full certification course, merely a prototype through a website with sample questions to gauge interest, the project was a success as a large target market for this product was identified that showed great promise. Our team believes that early entrance to the market, as well as the lack of any other competitors would give the team a tremendous advantage in creating an impactful and influential service.

ContributorsVrbanac, Matthew Thomas (Co-author) / Tanveer, Samad (Co-author) / Israel, Natasha (Co-author) / Byrne, Jared (Thesis director) / Lee, Chris (Committee member) / Kunowski, Jeff (Committee member) / Chemical Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

Human beings have long sought to conquer the unconquerable and to push the boundaries of human endurance. There are few such endeavors more challenging than venturing into the coldest and harshest environments on the planet. The challenges these adventurers face are nearly countless, but one that is often underestimated is

Human beings have long sought to conquer the unconquerable and to push the boundaries of human endurance. There are few such endeavors more challenging than venturing into the coldest and harshest environments on the planet. The challenges these adventurers face are nearly countless, but one that is often underestimated is the massive risk of dehydration in high mountains and the lack of sufficient technology to meet this important need. Astronauts and mountaineers of NASA's Johnson Space Center have created a technology that solves this problem: a freeze-resistant hydration system that helps stop water from freezing at sub-zero temperatures by using cutting-edge technology and materials science to insulate and heat enough water to prevent dehydration over the course of the day, so that adventurers no longer need to worry about their equipment stopping them. This patented technology is the basis of the founding of Aeropak, an advanced outdoor hydration brand developed by three ASU students (Kendall Robinson, Derek Stein, and Thomas Goers) in collaboration with W.P. Carey’s Founder’s Lab. The primary goal was to develop traction among winter sport enthusiasts to create a robust customer base and evaluate the potential for partnership with hydration solution companies as well as direct sales through online and brick-and-mortar retail avenues. To this end, the Aeropak team performed market research to determine the usefulness and need for the product through a survey sent out to a number of outdoor sporting clubs on Arizona State University’s campus. After determining an interest in a potential product, the team developed a marketing strategy and business model which was executed through Instagram as well as a standalone website, with the goal of garnering interest and traction for a future product. Future goals of the project will be to bring a product to market and expand Aeropak’s reach into a variety of winter sport subcommunities, as well as evaluate the potential for further expansion into large-scale retailers and collaboration with established companies.

ContributorsStein, Derek W (Co-author) / Robinson, Kendall (Co-author) / Goers, Thomas (Co-author) / Byrne, Jared (Thesis director) / Sebold, Brent (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05