Matching Items (115)
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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
Antibodies are essential for structural determinations and functional studies of membrane proteins, but antibody generation is limited by the availability of properly-folded and purified antigen. We describe the first application of genetic immunization to a structurally diverse set of membrane proteins to show that immunization of mice with DNA alone

Antibodies are essential for structural determinations and functional studies of membrane proteins, but antibody generation is limited by the availability of properly-folded and purified antigen. We describe the first application of genetic immunization to a structurally diverse set of membrane proteins to show that immunization of mice with DNA alone produced antibodies against 71% (n = 17) of the bacterial and viral targets. Antibody production correlated with prior reports of target immunogenicity in host organisms, underscoring the efficiency of this DNA-gold micronanoplex approach. To generate each antigen for antibody characterization, we also developed a simple in vitro membrane protein expression and capture method. Antibody specificity was demonstrated upon identifying, for the first time, membrane-directed heterologous expression of the native sequences of the FopA and FTT1525 virulence determinants from the select agent Francisella tularensis SCHU S4. These approaches will accelerate future structural and functional investigations of therapeutically-relevant membrane proteins.
ContributorsHansen, Debra (Author) / Robida, Mark (Author) / Craciunescu, Felicia (Author) / Loskutov, Andrey (Author) / Dorner, Katerina (Author) / Rodenberry, John-Charles (Author) / Wang, Xiao (Author) / Olson, Tien (Author) / Patel, Hetal (Author) / Fromme, Petra (Author) / Sykes, Kathryn (Author) / Biodesign Institute (Contributor) / Innovations in Medicine (Contributor) / Applied Structural Discovery (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor)
Created2016-02-24
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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
Description

Video games are packed full of endless potential. They are the telling of impossible narratives with something for every type of person. So then why has the industry historically been one of the worst for representations of race and gender? In this thesis, I define "good" media representation and engage

Video games are packed full of endless potential. They are the telling of impossible narratives with something for every type of person. So then why has the industry historically been one of the worst for representations of race and gender? In this thesis, I define "good" media representation and engage in the analysis of both Overwatch (2016) and Detroit Become Human (2018) to observe the ways these two video games, which so outwardly market their diversity, have failed marginalized groups. Accompanying the research paper is a video game poster representing a woman of color designed by the author which is meant to learn from the mistakes of its predecessors.

ContributorsBateman, Phoebe Jasmine (Author) / Dove-Viebahn, Aviva (Thesis director) / Holmes, Jeffrey (Committee member) / School of Humanities, Arts, and Cultural Studies (Contributor) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

My thesis focuses on the use of American Sign Language in popular movies. My paper analyzes the intersection between popular media and language, a subject I find personally interesting. My project addresses how and when ASL is used in movies, including technical components such as lighting, framing, visibility, and subtitling.

My thesis focuses on the use of American Sign Language in popular movies. My paper analyzes the intersection between popular media and language, a subject I find personally interesting. My project addresses how and when ASL is used in movies, including technical components such as lighting, framing, visibility, and subtitling. It also looks at the function of ASL, as well as Deafness and how it is portrayed. It focuses on three popular films: Children of a Lesser God (1986), The Shape of Water (2017), and A Quiet Place (2018). It also studies a fourth film, No Ordinary Hero: The SuperDeafy Movie (2013), which provides a Deaf perspective when it comes to filmmaking. These films are studies from technical and representational perspectives.

ContributorsEllis, Lucy Anne (Author) / Quinn, Paul (Thesis director) / Dove-Viebahn, Aviva (Committee member) / Sanford School of Social and Family Dynamics (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
My creative thesis project is titled “NOTEworthy HERstory: A Feminist Exploration of Prominent Women in Pop Music.” Specifically, I seek to answer this research question: what is the dynamic, reciprocal relationship between these prominent female artists’ music and careers with feminist theory? In other words, I am exploring how feminist

My creative thesis project is titled “NOTEworthy HERstory: A Feminist Exploration of Prominent Women in Pop Music.” Specifically, I seek to answer this research question: what is the dynamic, reciprocal relationship between these prominent female artists’ music and careers with feminist theory? In other words, I am exploring how feminist theory influenced their work, and also how their work influenced feminist theory and our societal understanding and appreciation of women’s lives. This topic incorporates history, sociology, musicology, and feminist theory. I have presented my findings about specific female artists through a series of four podcast episodes. I selected Carole King, Tina Turner, Beyoncé, and Taylor Swift as the subjects for the episodes because they each jumped out to me as being highly connected to specific feminist themes: waves of feminism, patriarchy, intersectionality, and power, respectively.
ContributorsHott, Sydney (Author) / Carrasco, Clare (Thesis director) / Dove-Viebahn, Aviva (Committee member) / Espaillat Lizardo, Mónica (Committee member) / Barrett, The Honors College (Contributor) / Sanford School of Social and Family Dynamics (Contributor) / Historical, Philosophical & Religious Studies, Sch (Contributor) / School of Social Transformation (Contributor)
Created2024-05
DescriptionA TV adaptation of the classic book The Count of Monte Cristo by Alexandre Dumas, set-in modern-day Los Angeles with a Latinx based cast. The project includes a 45-page script, episode descriptions for the first season, and a page with brief descriptions of the characters.
ContributorsFlores, Czarina (Author) / Bradley, Christoper (Thesis director) / Dove-Viebahn, Aviva (Committee member) / Barrett, The Honors College (Contributor) / Department of English (Contributor)
Created2024-05
Description

This Creative Project involves developing Acceptance--an original, feature-length screenplay--from prior outlining material using methods from David Snyder's "Save The Cat!". Upon realizing the strikingly iterative nature of screenplay development, parallels began to arise concerning software development. Said parallels led to a synopsis of how screenplay development can offer insight into

This Creative Project involves developing Acceptance--an original, feature-length screenplay--from prior outlining material using methods from David Snyder's "Save The Cat!". Upon realizing the strikingly iterative nature of screenplay development, parallels began to arise concerning software development. Said parallels led to a synopsis of how screenplay development can offer insight into ways the software development process can improve iteration.

ContributorsWalker, Garrison (Author) / Scott Lynch, Jacquie (Thesis director) / Dove-Viebahn, Aviva (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2023-05
Description
“They told us that if your brain was less developed than others, less fit, more cruel, you were more likely to mutate due to the virus.” Drew can’t remember her life before she woke up on the cold concrete floor of the hospital, chained up alongside several others. All she– and

“They told us that if your brain was less developed than others, less fit, more cruel, you were more likely to mutate due to the virus.” Drew can’t remember her life before she woke up on the cold concrete floor of the hospital, chained up alongside several others. All she– and anyone else in the facility– knows is what the guards have told her: they’ve been exposed to the Insects, prior humans who caught an airborne virus that turned them into zombie-like creatures. To prevent a mutation into an insect, Drew and the others must quarantine inside the abandoned hospital, training their minds and bodies against the virus living dormant inside of them. The virus that is triggered by one’s cruelty. As time goes on, lines begin to blur between being kept safe and being kept a prisoner, and it becomes hard for Drew to know who to trust. Combining elements of sci-fi and horror, Operation Insect serves as a cautionary tale of current incarceration issues in America.
ContributorsAscherl, Adelyn (Author) / Miller, April (Thesis director) / Dove-Viebahn, Aviva (Committee member) / Barrett, The Honors College (Contributor) / Walter Cronkite School of Journalism and Mass Comm (Contributor) / School of Art (Contributor)
Created2024-05