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174 results on '"Botha, Sabine"'

1. A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography.

Author

Liu, Zhongrui, Gu, Kevin, Shelby, Megan, Gilbile, Deepshika, Lyubimov, Artem, Russi, Silvia, Cohen, Aina, Narayanasamy, Sankar, Botha, Sabine, Kupitz, Christopher, Sierra, Raymond, Poitevin, Fredric, Gilardi, Antonio, Lisova, Stella, Coleman, Matthew, Frank, Matthias, and Kuhl, Tonya

Subjects
X-ray crystallography, XFELs, cyclic olefin copolymer, fixed targets, microfluidics, room-temperature SFX, sample delivery, serial crystallography, synchrotrons
Abstract

Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and structure determination. A crucial need to continue advancement is the efficient delivery of fragile and micrometre-sized crystals to the X-ray beam intersection. This paper presents an improved design of an all-polymer microfluidic `chip for room-temperature fixed-target serial crystallography that can be tailored to broadly meet the needs of users at either synchrotron or XFEL light sources. The chips are designed to be customized around different types of crystals and offer users a friendly, quick, convenient, ultra-low-cost and robust sample-delivery platform. Compared with the previous iteration of the chip [Gilbile et al. (2021), Lab Chip, 21, 4831-4845], the new design eliminates cleanroom fabrication. It has a larger imaging area to volume, while maintaining crystal hydration stability for both in situ crystallization or direct crystal slurry loading. Crystals of two model proteins, lysozyme and thaumatin, were used to validate the effectiveness of the design at both synchrotron (lysozyme and thaumatin) and XFEL (lysozyme only) facilities, yielding complete data sets with resolutions of 1.42, 1.48 and 1.70 Å, respectively. Overall, the improved chip design, ease of fabrication and high modifiability create a powerful, all-around sample-delivery tool that structural biologists can quickly adopt, especially in cases of limited sample volume and small, fragile crystals.

Published
2023

2. Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser.

Author

Jernigan, Rebecca J, Logeswaran, Dhenugen, Doppler, Diandra, Nagaratnam, Nirupa, Sonker, Mukul, Yang, Jay-How, Ketawala, Gihan, Martin-Garcia, Jose M, Shelby, Megan L, Grant, Thomas D, Mariani, Valerio, Tolstikova, Alexandra, Sheikh, Michelle Z, Yung, Mimi Cho, Coleman, Matthew A, Zaare, Sahba, Kaschner, Emily K, Rabbani, Mohammad Towshif, Nazari, Reza, Zacks, Michele A, Hayes, Brandon, Sierra, Raymond G, Hunter, Mark S, Lisova, Stella, Batyuk, Alexander, Kupitz, Christopher, Boutet, Sebastien, Hansen, Debra T, Kirian, Richard A, Schmidt, Marius, Fromme, Raimund, Frank, Matthias, Ros, Alexandra, Chen, Julian J-L, Botha, Sabine, and Fromme, Petra

Subjects
Humans, Crystallography, X-Ray, Lasers, Temperature, Electrons, COVID-19, SARS-CoV-2, NSP15, NendoU, X-ray free-electron laser, serial femtosecond crystallography, Prevention, Infectious Diseases, Emerging Infectious Diseases, Vaccine Related, Biodefense, Infection, Chemical Sciences, Biological Sciences, Information and Computing Sciences, Biophysics
Abstract

NendoU from SARS-CoV-2 is responsible for the virus's ability to evade the innate immune system by cleaving the polyuridine leader sequence of antisense viral RNA. Here we report the room-temperature structure of NendoU, solved by serial femtosecond crystallography at an X-ray free-electron laser to 2.6 Å resolution. The room-temperature structure provides insight into the flexibility, dynamics, and other intrinsic properties of NendoU, with indications that the enzyme functions as an allosteric switch. Functional studies examining cleavage specificity in solution and in crystals support the uridine-purine cleavage preference, and we demonstrate that enzyme activity is fully maintained in crystal form. Optimizing the purification of NendoU and identifying suitable crystallization conditions set the benchmark for future time-resolved serial femtosecond crystallography studies. This could advance the design of antivirals with higher efficacy in treating coronaviral infections, since drugs that block allosteric conformational changes are less prone to drug resistance.

Published
2023

3. Co-flow injection for serial crystallography at X-ray free-electron lasers.

Author

Doppler, Diandra, Rabbani, Mohammad, Letrun, Romain, Cruz Villarreal, Jorvani, Kim, Dai, Gandhi, Sahir, Egatz-Gomez, Ana, Sonker, Mukul, Chen, Joe, Koua, Faisal, Yang, Jayhow, Youssef, Mohamed, Mazalova, Victoria, Bajt, Saša, Shelby, Megan, Coleman, Matt, Wiedorn, Max, Knoska, Juraj, Schön, Silvan, Sato, Tokushi, Hunter, Mark, Hosseinizadeh, Ahmad, Kuptiz, Christopher, Nazari, Reza, Alvarez, Roberto, Karpos, Konstantinos, Zaare, Sahba, Dobson, Zachary, Discianno, Erin, Zhang, Shangji, Zook, James, Bielecki, Johan, de Wijn, Raphael, Round, Adam, Vagovic, Patrik, Kloos, Marco, Vakili, Mohammad, Ketawala, Gihan, Stander, Natasha, Olson, Tien, Morin, Katherine, Mondal, Jyotirmory, Nguyen, Jonathan, Meza-Aguilar, José, Kodis, Gerdenis, Vaiana, Sara, Martin-Garcia, Jose, Mariani, Valerio, Schwander, Peter, Schmidt, Marius, Messerschmidt, Marc, Ourmazd, Abbas, Zatsepin, Nadia, Weierstall, Uwe, Bruce, Barry, Mancuso, Adrian, Grant, Thomas, Barty, Anton, Chapman, Henry, Fromme, Raimund, Spence, John, Botha, Sabine, Fromme, Petra, Kirian, Richard, Ros, Alexandra, and Frank, Matthias

Subjects
3D printing, X-ray free-electron lasers, XFELs, microfluidic devices, sample consumption, serial crystallography, viscous media
Abstract

Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macro-molecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.

Published
2022

4. Light-induced Trpin/Metout Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC

Author

Chretien, Anaïs, Nagel, Marius F., Botha, Sabine, de Wijn, Raphaël, Brings, Lea, Dörner, Katerina, Han, Huijong, Koliyadu, Jayanath C.P., Letrun, Romain, Round, Adam, Sato, Tokushi, Schmidt, Christina, Secareanu, Radu-Costin, von Stetten, David, Vakili, Mohammad, Wrona, Agnieszka, Bean, Richard, Mancuso, Adrian, Schulz, Joachim, Pearson, Arwen R., Kottke, Tilman, Lorenzen, Kristina, and Schubert, Robin

Published
2024
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6. Author Correction: Membrane protein megahertz crystallography at the European XFEL

Author

Gisriel, Chris, Coe, Jesse, Letrun, Romain, Yefanov, Oleksandr M, Luna-Chavez, Cesar, Stander, Natasha E, Lisova, Stella, Mariani, Valerio, Kuhn, Manuela, Aplin, Steve, Grant, Thomas D, Dörner, Katerina, Sato, Tokushi, Echelmeier, Austin, Villarreal, Jorvani Cruz, Hunter, Mark S, Wiedorn, Max O, Knoska, Juraj, Mazalova, Victoria, Roy-Chowdhury, Shatabdi, Yang, Jay-How, Jones, Alex, Bean, Richard, Bielecki, Johan, Kim, Yoonhee, Mills, Grant, Weinhausen, Britta, Meza, Jose D, Al-Qudami, Nasser, Bajt, Saša, Brehm, Gerrit, Botha, Sabine, Boukhelef, Djelloul, Brockhauser, Sandor, Bruce, Barry D, Coleman, Matthew A, Danilevski, Cyril, Discianno, Erin, Dobson, Zachary, Fangohr, Hans, Martin-Garcia, Jose M, Gevorkov, Yaroslav, Hauf, Steffen, Hosseinizadeh, Ahmad, Januschek, Friederike, Ketawala, Gihan K, Kupitz, Christopher, Maia, Luis, Manetti, Maurizio, Messerschmidt, Marc, Michelat, Thomas, Mondal, Jyotirmoy, Ourmazd, Abbas, Previtali, Gianpietro, Sarrou, Iosifina, Schön, Silvan, Schwander, Peter, Shelby, Megan L, Silenzi, Alessandro, Sztuk-Dambietz, Jolanta, Szuba, Janusz, Turcato, Monica, White, Thomas A, Wrona, Krzysztof, Xu, Chen, Abdellatif, Mohamed H, Zook, James D, Spence, John CH, Chapman, Henry N, Barty, Anton, Kirian, Richard A, Frank, Matthias, Ros, Alexandra, Schmidt, Marius, Fromme, Raimund, Mancuso, Adrian P, Fromme, Petra, and Zatsepin, Nadia A

Subjects
Biochemistry and Cell Biology, Biological Sciences
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

7. Membrane protein megahertz crystallography at the European XFEL

Author

Gisriel, Chris, Coe, Jesse, Letrun, Romain, Yefanov, Oleksandr M, Luna-Chavez, Cesar, Stander, Natasha E, Lisova, Stella, Mariani, Valerio, Kuhn, Manuela, Aplin, Steve, Grant, Thomas D, Dörner, Katerina, Sato, Tokushi, Echelmeier, Austin, Cruz Villarreal, Jorvani, Hunter, Mark S, Wiedorn, Max O, Knoska, Juraj, Mazalova, Victoria, Roy-Chowdhury, Shatabdi, Yang, Jay-How, Jones, Alex, Bean, Richard, Bielecki, Johan, Kim, Yoonhee, Mills, Grant, Weinhausen, Britta, Meza, Jose D, Al-Qudami, Nasser, Bajt, Saša, Brehm, Gerrit, Botha, Sabine, Boukhelef, Djelloul, Brockhauser, Sandor, Bruce, Barry D, Coleman, Matthew A, Danilevski, Cyril, Discianno, Erin, Dobson, Zachary, Fangohr, Hans, Martin-Garcia, Jose M, Gevorkov, Yaroslav, Hauf, Steffen, Hosseinizadeh, Ahmad, Januschek, Friederike, Ketawala, Gihan K, Kupitz, Christopher, Maia, Luis, Manetti, Maurizio, Messerschmidt, Marc, Michelat, Thomas, Mondal, Jyotirmoy, Ourmazd, Abbas, Previtali, Gianpietro, Sarrou, Iosifina, Schön, Silvan, Schwander, Peter, Shelby, Megan L, Silenzi, Alessandro, Sztuk-Dambietz, Jolanta, Szuba, Janusz, Turcato, Monica, White, Thomas A, Wrona, Krzysztof, Xu, Chen, Abdellatif, Mohamed H, Zook, James D, Spence, John CH, Chapman, Henry N, Barty, Anton, Kirian, Richard A, Frank, Matthias, Ros, Alexandra, Schmidt, Marius, Fromme, Raimund, Mancuso, Adrian P, Fromme, Petra, and Zatsepin, Nadia A

Subjects
Biochemistry and Cell Biology, Biological Sciences, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Crystallography, Cyanobacteria, Electrons, Lasers, Membrane Proteins, Models, Molecular, Photosystem I Protein Complex, Static Electricity, Synchrotrons, Thermosynechococcus, X-Rays
Abstract

The world's first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs.

Published
2019

8. Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature

Author

Ayan, Esra, Yuksel, Busra, Destan, Ebru, Ertem, Fatma Betul, Yildirim, Gunseli, Eren, Meryem, Yefanov, Oleksandr M., Barty, Anton, Tolstikova, Alexandra, Ketawala, Gihan K., Botha, Sabine, Dao, E. Han, Hayes, Brandon, Liang, Mengning, Seaberg, Matthew H., Hunter, Mark S., Batyuk, Alexander, Mariani, Valerio, Su, Zhen, Poitevin, Frederic, Yoon, Chun Hong, Kupitz, Christopher, Cohen, Aina, Doukov, Tzanko, Sierra, Raymond G., Dağ, Çağdaş, and DeMirci, Hasan

Published
2022
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9. Free-electron laser data for multiple-particle fluctuation scattering analysis.

Author

Pande, Kanupriya, Donatelli, Jeffrey J, Malmerberg, Erik, Foucar, Lutz, Poon, Billy K, Sutter, Markus, Botha, Sabine, Basu, Shibom, Bruce Doak, R, Dörner, Katerina, Epp, Sascha W, Englert, Lars, Fromme, Raimund, Hartmann, Elisabeth, Hartmann, Robert, Hauser, Guenter, Hattne, Johan, Hosseinizadeh, Ahmad, Kassemeyer, Stephan, Lomb, Lukas, Montero, Sebastian F Carron, Menzel, Andreas, Rolles, Daniel, Rudenko, Artem, Seibert, Marvin M, Sierra, Raymond George, Schwander, Peter, Ourmazd, Abbas, Fromme, Petra, Sauter, Nicholas K, Bogan, Michael, Bozek, John, Bostedt, Christoph, Schlichting, Ilme, Kerfeld, Cheryl A, and Zwart, Petrus H

Subjects
Phycodnaviridae, X-Ray Diffraction, Scattering, Small Angle
Abstract

Fluctuation X-ray scattering (FXS) is an emerging experimental technique in which solution scattering data are collected using X-ray exposures below rotational diffusion times, resulting in angularly anisotropic X-ray snapshots that provide several orders of magnitude more information than traditional solution scattering data. Such experiments can be performed using the ultrashort X-ray pulses provided by a free-electron laser source, allowing one to collect a large number of diffraction patterns in a relatively short time. Here, we describe a test data set for FXS, obtained at the Linac Coherent Light Source, consisting of close to 100 000 multi-particle diffraction patterns originating from approximately 50 to 200 Paramecium Bursaria Chlorella virus particles per snapshot. In addition to the raw data, a selection of high-quality pre-processed diffraction patterns and a reference SAXS profile are provided.

Published
2018

10. Megahertz serial crystallography

Author

Wiedorn, Max O, Oberthür, Dominik, Bean, Richard, Schubert, Robin, Werner, Nadine, Abbey, Brian, Aepfelbacher, Martin, Adriano, Luigi, Allahgholi, Aschkan, Al-Qudami, Nasser, Andreasson, Jakob, Aplin, Steve, Awel, Salah, Ayyer, Kartik, Bajt, Saša, Barák, Imrich, Bari, Sadia, Bielecki, Johan, Botha, Sabine, Boukhelef, Djelloul, Brehm, Wolfgang, Brockhauser, Sandor, Cheviakov, Igor, Coleman, Matthew A, Cruz-Mazo, Francisco, Danilevski, Cyril, Darmanin, Connie, Doak, R Bruce, Domaracky, Martin, Dörner, Katerina, Du, Yang, Fangohr, Hans, Fleckenstein, Holger, Frank, Matthias, Fromme, Petra, Gañán-Calvo, Alfonso M, Gevorkov, Yaroslav, Giewekemeyer, Klaus, Ginn, Helen Mary, Graafsma, Heinz, Graceffa, Rita, Greiffenberg, Dominic, Gumprecht, Lars, Göttlicher, Peter, Hajdu, Janos, Hauf, Steffen, Heymann, Michael, Holmes, Susannah, Horke, Daniel A, Hunter, Mark S, Imlau, Siegfried, Kaukher, Alexander, Kim, Yoonhee, Klyuev, Alexander, Knoška, Juraj, Kobe, Bostjan, Kuhn, Manuela, Kupitz, Christopher, Küpper, Jochen, Lahey-Rudolph, Janine Mia, Laurus, Torsten, Le Cong, Karoline, Letrun, Romain, Xavier, P Lourdu, Maia, Luis, Maia, Filipe RNC, Mariani, Valerio, Messerschmidt, Marc, Metz, Markus, Mezza, Davide, Michelat, Thomas, Mills, Grant, Monteiro, Diana CF, Morgan, Andrew, Mühlig, Kerstin, Munke, Anna, Münnich, Astrid, Nette, Julia, Nugent, Keith A, Nuguid, Theresa, Orville, Allen M, Pandey, Suraj, Pena, Gisel, Villanueva-Perez, Pablo, Poehlsen, Jennifer, Previtali, Gianpietro, Redecke, Lars, Riekehr, Winnie Maria, Rohde, Holger, Round, Adam, Safenreiter, Tatiana, Sarrou, Iosifina, Sato, Tokushi, Schmidt, Marius, Schmitt, Bernd, Schönherr, Robert, Schulz, Joachim, Sellberg, Jonas A, Seibert, M Marvin, and Seuring, Carolin

Subjects
Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences
Abstract

The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.

Published
2018

11. Minimized Sample Consumption for Time-Resolved Serial Crystallography Applied to the Redox Cycle of Human NQO1

Author

Doppler, Diandra, primary, Grieco, Alice, additional, Koh, Domin, additional, Manna, Abhik, additional, Ansari, Adil, additional, Alvarez, Roberto, additional, Karpos, Konstantinos, additional, Le, Hung, additional, Sonker, Mukul, additional, Ketawala, Gihan, additional, Mahmud, Samira, additional, Quereda Moraleda, Isabel, additional, Pey, Angel Luis, additional, Letrun, Roman, additional, Doerner, Katerina, additional, Koliyadu, Jayanath C. P., additional, de Wijn, Raphael, additional, Bielecki, Johan, additional, Han, Huijong, additional, Kim, Chan, additional, Koua, Faisal, additional, Round, Adam, additional, Sarma, Abhisakh, additional, Sato, Tokushi, additional, Schmidt, Christina, additional, Vakili, Mohammad, additional, Zabelskii, Dmitrii, additional, Bean, Richard, additional, Mancuso, Adrian P., additional, Schulz, Joachim, additional, Fromme, Raimund, additional, Medina, Milagros, additional, Grant, Thomas D, additional, Fromme, Petra, additional, Kirian, Richard A., additional, Botha, Sabine, additional, Martin Garcia, Jose Manuel, additional, and Ros, Alexandra, additional

Published
2024
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12. Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam

Author

Sawaya, Michael R, Cascio, Duilio, Gingery, Mari, Rodriguez, Jose, Goldschmidt, Lukasz, Colletier, Jacques-Philippe, Messerschmidt, Marc M, Boutet, Sébastien, Koglin, Jason E, Williams, Garth J, Brewster, Aaron S, Nass, Karol, Hattne, Johan, Botha, Sabine, Doak, R Bruce, Shoeman, Robert L, DePonte, Daniel P, Park, Hyun-Woo, Federici, Brian A, Sauter, Nicholas K, Schlichting, Ilme, and Eisenberg, David S

Subjects
Generic health relevance, Bacillus thuringiensis, Bacillus thuringiensis Toxins, Bacterial Proteins, Crystallization, Crystallography, X-Ray, Endotoxins, Hemolysin Proteins, Lasers, Spores, Bacterial, Synchrotrons, X-Ray Diffraction, XFEL, Cry3A insecticidal toxin, serial femtosecond crystallography
Abstract

It has long been known that toxins produced by Bacillus thuringiensis (Bt) are stored in the bacterial cells in crystalline form. Here we describe the structure determination of the Cry3A toxin found naturally crystallized within Bt cells. When whole Bt cells were streamed into an X-ray free-electron laser beam we found that scattering from other cell components did not obscure diffraction from the crystals. The resolution limits of the best diffraction images collected from cells were the same as from isolated crystals. The integrity of the cells at the moment of diffraction is unclear; however, given the short time (∼ 5 µs) between exiting the injector to intersecting with the X-ray beam, our result is a 2.9-Å-resolution structure of a crystalline protein as it exists in a living cell. The study suggests that authentic in vivo diffraction studies can produce atomic-level structural information.

Published
2014

13. The Pixel Anomaly Detection Tool: a user‐friendly GUI for classifying detector frames using machine‐learning approaches.

Author

Ketawala, Gihan, Reiter, Caitlin M., Fromme, Petra, and Botha, Sabine

Subjects
FREE electron lasers, MACHINE learning, GRAPHICAL user interfaces, DETECTORS, SUPERVISED learning, MODULAR design, IMAGE recognition (Computer vision)
Abstract

Data collection at X‐ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high‐dynamic‐range gain‐switching X‐ray detectors. This can result in a multitude of data artefacts, which can be detrimental to accurately determining structure‐factor amplitudes for serial crystallography or single‐particle imaging experiments. Here, a new data‐classification tool is reported that offers a variety of machine‐learning algorithms to sort data trained either on manual data sorting by the user or by profile fitting the intensity distribution on the detector based on the experiment. This is integrated into an easy‐to‐use graphical user interface, specifically designed to support the detectors, file formats and software available at most X‐ray free electron laser facilities. The highly modular design makes the tool easily expandable to comply with other X‐ray sources and detectors, and the supervised learning approach enables even the novice user to sort data containing unwanted artefacts or perform routine data‐analysis tasks such as hit finding during an experiment, without needing to write code. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Light-induced Trpin/Metout switching during BLUF domain activation in ATP-bound photoactivatable adenylate cyclase OaPAC

Author

Chretien, Anaïs, primary, Nagel, Marius F., additional, Botha, Sabine, additional, de Wijn, Raphaël, additional, Brings, Lea, additional, Dörner, Katerina, additional, Han, Huijong, additional, Koliyadu, Jayanath C. P., additional, Letrun, Romain, additional, Round, Adam, additional, Sato, Tokushi, additional, Schmidt, Christina, additional, Secareanu, Radu-Costin, additional, von Stetten, David, additional, Vakili, Mohammad, additional, Wrona, Agnieszka, additional, Bean, Richard, additional, Mancuso, Adrian, additional, Schulz, Joachim, additional, Pearson, Arwen R., additional, Kottke, Tilman, additional, Lorenzen, Kristina, additional, and Schubert, Robin, additional

Published
2023
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16. Segmented flow generator for serial crystallography at the European X-ray free electron laser

Author

Echelmeier, Austin, Cruz Villarreal, Jorvani, Messerschmidt, Marc, Kim, Daihyun, Coe, Jesse D., Thifault, Darren, Botha, Sabine, Egatz-Gomez, Ana, Gandhi, Sahir, Brehm, Gerrit, Conrad, Chelsie E., Hansen, Debra T., Madsen, Caleb, Bajt, Saša, Meza-Aguilar, J. Domingo, Oberthür, Dominik, Wiedorn, Max O., Fleckenstein, Holger, Mendez, Derek, Knoška, Juraj, Martin-Garcia, Jose M., Hu, Hao, Lisova, Stella, Allahgholi, Aschkan, Gevorkov, Yaroslav, Ayyer, Kartik, Aplin, Steve, Ginn, Helen Mary, Graafsma, Heinz, Morgan, Andrew J., Greiffenberg, Dominic, Klujev, Alexander, Laurus, Torsten, Poehlsen, Jennifer, Trunk, Ulrich, Mezza, Davide, Schmidt, Bernd, Kuhn, Manuela, Fromme, Raimund, Sztuk-Dambietz, Jolanta, Raab, Natascha, Hauf, Steffen, Silenzi, Alessandro, Michelat, Thomas, Xu, Chen, Danilevski, Cyril, Parenti, Andrea, Mekinda, Leonce, Weinhausen, Britta, Mills, Grant, Vagovic, Patrik, Kim, Yoonhee, Kirkwood, Henry, Bean, Richard, Bielecki, Johan, Stern, Stephan, Giewekemeyer, Klaus, Round, Adam R., Schulz, Joachim, Dörner, Katerina, Grant, Thomas D., Mariani, Valerio, Barty, Anton, Mancuso, Adrian P., Weierstall, Uwe, Spence, John C. H., Chapman, Henry N., Zatsepin, Nadia, Fromme, Petra, Kirian, Richard A., and Ros, Alexandra

Published
2020
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17. Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

Author

Gati, Cornelius, Oberthuer, Dominik, Yefanov, Oleksandr, Bunker, Richard D., Stellato, Francesco, Chiu, Elaine, Yeh, Shin-Mei, Aquila, Andrew, Basu, Shibom, Bean, Richard, Beyerlein, Kenneth R., Botha, Sabine, Boutet, Sébastien, DePonte, Daniel P., Doak, R. Bruce, Fromme, Raimund, Galli, Lorenzo, Grotjohann, Ingo, James, Daniel R., Kupitz, Christopher, Lomb, Lukas, Messerschmidt, Marc, Nass, Karol, Rendek, Kimberly, Shoeman, Robert L., Wang, Dingjie, Weierstall, Uwe, White, Thomas A., Williams, Garth J., Zatsepin, Nadia A., Fromme, Petra, Spence, John C. H., Goldie, Kenneth N., Jehle, Johannes A., Metcalf, Peter, Barty, Anton, and Chapman, Henry N.

Published
2017

18. Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme

Author

National Science Foundation (US), National Institutes of Health (US), Department of Energy (US), Max Planck Institute for Medical Research, Comunidad de Madrid, Ministerio de Ciencia, Innovación y Universidades (España), Junta de Andalucía, Doppler, Diandra [0000-0002-3586-3936], Sonker, Mukul [0000-0001-5816-8410], Egatz-Gomez, Ana [0000-0002-6080-943X], Manna, Abhik [0000-0001-8681-6702], Cruz Villarreal, Jorvani [0000-0002-6762-7348], Pey, Angel L. [0000-0001-7706-3243], Ruiz-Fresneda, Miguel A. [0000-0001-6349-6566], Pacheco-Garcia, Juan Luis [0000-0001-6043-7536], Hermoso, Juan A. [0000-0002-1862-8950], Batyuk, Alexander [0000-0002-9393-2880], Fromme, Raimund [0000-0003-4835-1080], Kirian, Richard A. [0000-0001-7197-3086], Martín-García, José M. [0000-0002-4558-3858], Ros, Alexandra [0000-0001-7709-8331], Doppler, Diandra, Sonker, Mukul, Egatz-Gomez, Ana, Grieco, Alice, Zaare, Sahba, Jernigan, Rebecca, Meza-Aguilar, Jose Domingo, Rabbani, Mohammad T., Manna, Abhik, Alvarez, Roberto C., Karpos, Konstantinos, Cruz Villarreal, Jorvani, Nelson, Garrett, Yang, Jay-How, Carrion, Jackson, Morin, Katherine, Ketawala, Gihan K, Pey, Angel L., Ruiz-Fresneda, Miguel A., Pacheco-Garcia, Juan Luis, Hermoso, Juan A., Nazari, Reza, Sierra, Raymond, Hunter, Mark S., Batyuk, Alexander, Kupitz, Christopher J., Sublett, Robert E., Lisova, Stella, Mariani, Valerio, Boutet, Sébastien, Fromme, Raimund, Grant, Thomas D., Botha, Sabine, Fromme, Petra, Kirian, Richard A., Martín-García, José M., Ros, Alexandra, National Science Foundation (US), National Institutes of Health (US), Department of Energy (US), Max Planck Institute for Medical Research, Comunidad de Madrid, Ministerio de Ciencia, Innovación y Universidades (España), Junta de Andalucía, Doppler, Diandra [0000-0002-3586-3936], Sonker, Mukul [0000-0001-5816-8410], Egatz-Gomez, Ana [0000-0002-6080-943X], Manna, Abhik [0000-0001-8681-6702], Cruz Villarreal, Jorvani [0000-0002-6762-7348], Pey, Angel L. [0000-0001-7706-3243], Ruiz-Fresneda, Miguel A. [0000-0001-6349-6566], Pacheco-Garcia, Juan Luis [0000-0001-6043-7536], Hermoso, Juan A. [0000-0002-1862-8950], Batyuk, Alexander [0000-0002-9393-2880], Fromme, Raimund [0000-0003-4835-1080], Kirian, Richard A. [0000-0001-7197-3086], Martín-García, José M. [0000-0002-4558-3858], Ros, Alexandra [0000-0001-7709-8331], Doppler, Diandra, Sonker, Mukul, Egatz-Gomez, Ana, Grieco, Alice, Zaare, Sahba, Jernigan, Rebecca, Meza-Aguilar, Jose Domingo, Rabbani, Mohammad T., Manna, Abhik, Alvarez, Roberto C., Karpos, Konstantinos, Cruz Villarreal, Jorvani, Nelson, Garrett, Yang, Jay-How, Carrion, Jackson, Morin, Katherine, Ketawala, Gihan K, Pey, Angel L., Ruiz-Fresneda, Miguel A., Pacheco-Garcia, Juan Luis, Hermoso, Juan A., Nazari, Reza, Sierra, Raymond, Hunter, Mark S., Batyuk, Alexander, Kupitz, Christopher J., Sublett, Robert E., Lisova, Stella, Mariani, Valerio, Boutet, Sébastien, Fromme, Raimund, Grant, Thomas D., Botha, Sabine, Fromme, Petra, Kirian, Richard A., Martín-García, José M., and Ros, Alexandra

Abstract

Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.

Published
2023

19. Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme

Author

Doppler, Diandra, primary, Sonker, Mukul, additional, Egatz-Gomez, Ana, additional, Grieco, Alice, additional, Zaare, Sahba, additional, Jernigan, Rebecca, additional, Meza-Aguilar, Jose Domingo, additional, Rabbani, Mohammad T., additional, Manna, Abhik, additional, Alvarez, Roberto C., additional, Karpos, Konstantinos, additional, Cruz Villarreal, Jorvani, additional, Nelson, Garrett, additional, Yang, Jay-How, additional, Carrion, Jackson, additional, Morin, Katherine, additional, Ketawala, Gihan K., additional, Pey, Angel L., additional, Ruiz-Fresneda, Miguel Angel, additional, Pacheco-Garcia, Juan Luis, additional, Hermoso, Juan A., additional, Nazari, Reza, additional, Sierra, Raymond, additional, Hunter, Mark S., additional, Batyuk, Alexander, additional, Kupitz, Christopher J., additional, Sublett, Robert E., additional, Lisova, Stella, additional, Mariani, Valerio, additional, Boutet, Sébastien, additional, Fromme, Raimund, additional, Grant, Thomas D., additional, Botha, Sabine, additional, Fromme, Petra, additional, Kirian, Richard A., additional, Martin-Garcia, Jose Manuel, additional, and Ros, Alexandra, additional

Published
2023
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20. Electrically stimulated droplet injector for reduced sample consumption in serial crystallography

Author

Sonker, Mukul, primary, Doppler, Diandra, additional, Egatz-Gomez, Ana, additional, Zaare, Sahba, additional, Rabbani, Mohammad T., additional, Manna, Abhik, additional, Cruz Villarreal, Jorvani, additional, Nelson, Garrett, additional, Ketawala, Gihan K., additional, Karpos, Konstantinos, additional, Alvarez, Roberto C., additional, Nazari, Reza, additional, Thifault, Darren, additional, Jernigan, Rebecca, additional, Oberthür, Dominik, additional, Han, Huijong, additional, Sierra, Raymond, additional, Hunter, Mark S., additional, Batyuk, Alexander, additional, Kupitz, Christopher J., additional, Sublett, Robert E., additional, Poitevin, Frederic, additional, Lisova, Stella, additional, Mariani, Valerio, additional, Tolstikova, Alexandra, additional, Boutet, Sebastien, additional, Messerschmidt, Marc, additional, Meza-Aguilar, J. Domingo, additional, Fromme, Raimund, additional, Martin-Garcia, Jose M., additional, Botha, Sabine, additional, Fromme, Petra, additional, Grant, Thomas D., additional, Kirian, Richard A., additional, and Ros, Alexandra, additional

Published
2022
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21. Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation

Author

Barends, Thomas R. M., Foucar, Lutz, Ardevol, Albert, Nass, Karol, Aquila, Andrew, Botha, Sabine, Doak, R. Bruce, Falahati, Konstantin, Hartmann, Elisabeth, Hilpert, Mario, Heinz, Marcel, Hoffmann, Matthias C., Köfinger, Jürgen, Koglin, Jason E., Kovacsova, Gabriela, Liang, Mengning, Milathianaki, Despina, Lemke, Henrik T., Reinstein, Jochen, Roome, Christopher M., Shoeman, Robert L., Williams, Garth J., Burghardt, Irene, Hummer, Gerhard, Boutet, Sébastien, and Schlichting, Ilme

Published
2015

22. Serial macromolecular crystallography at ALBA Synchrotron Light Source. Erratum

Author

Martin-Garcia, Jose M., primary, Botha, Sabine, additional, Hu, Hao, additional, Jernigan, Rebecca, additional, Castellví, Albert, additional, Lisova, Stella, additional, Gil, Fernando, additional, Calisto, Barbara, additional, Crespo, Isidro, additional, Roy-Chowdhury, Shatabdi, additional, Grieco, Alice, additional, Ketawala, Gihan, additional, Weierstall, Uwe, additional, Spence, John, additional, Fromme, Petra, additional, Zatsepin, Nadia, additional, Boer, Dirk Roeland, additional, and Carpena, Xavi, additional

Published
2022
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23. Serial macromolecular crystallography at ALBA Synchrotron Light Source. Erratum

Author

Castellví, Albert [0000-0002-1814-1210], Crespo, Isidro [0000-0001-7698-1720], Zatsepin, Nadia [0000-0003-1757-0205], Martín-García, José M., Botha, Sabine, Hu, Hao, Jernigan, Rebecca, Castellví, Albert, Lisova, Stella, Gil, Fernando, Calisto, Barbara, Crespo, Isidro, Roy-Chowdhury, Shatabdi, Grieco, Alice, Ketawala, Gihan, Weierstall, Uwe, Spence, John, Fromme, Petra, Zatsepin, Nadia, Boer, Dirk Roeland, Carpena, Xavi, Castellví, Albert [0000-0002-1814-1210], Crespo, Isidro [0000-0001-7698-1720], Zatsepin, Nadia [0000-0003-1757-0205], Martín-García, José M., Botha, Sabine, Hu, Hao, Jernigan, Rebecca, Castellví, Albert, Lisova, Stella, Gil, Fernando, Calisto, Barbara, Crespo, Isidro, Roy-Chowdhury, Shatabdi, Grieco, Alice, Ketawala, Gihan, Weierstall, Uwe, Spence, John, Fromme, Petra, Zatsepin, Nadia, Boer, Dirk Roeland, and Carpena, Xavi

Abstract

A revised version of Table 2 of Martin-Garcia et al. [J. Synchrotron Rad. (2022). 29, 896-907] is provided.

Published
2022

24. Electrically stimulated droplet injector for reduced sample consumption in serial crystallography

Author

National Science Foundation (US), National Institutes of Health (US), Department of Energy (US), Max Planck Institute for Medical Research, Sonker, Mukul, Doppler, Diandra, Egatz-Gomez, Ana, Zaare, Sahba, Rabbani, Mohammad T., Manna, Abhik, Cruz Villarreal, Jorvani, Nelson, Garrett, Ketawala, Gihan K., Karpos, Konstantinos, Alvarez, Roberto C., Nazari, Reza, Thifault, Darren, Jernigan, Rebecca, Oberthür, Dominik, Han, Huijong, Sierra, Raymond, Hunter, Mark S., Batyuk, Alexander, Kupitz, Christopher J., Sublett, Robert E., Poitevin, Frederic, Lisova, Stella, Mariani, Valerio, Tolstikova, Alexandra, Boutet, Sebastien, Messerschmidt, Marc, Meza-Aguilar, J Domingo, Fromme, Raimund, Martín-García, Jose Manuel, Botha, Sabine, Fromme, Petra, Grant, Thomas D., Kirian, Richard A., Ros, Alexandra, National Science Foundation (US), National Institutes of Health (US), Department of Energy (US), Max Planck Institute for Medical Research, Sonker, Mukul, Doppler, Diandra, Egatz-Gomez, Ana, Zaare, Sahba, Rabbani, Mohammad T., Manna, Abhik, Cruz Villarreal, Jorvani, Nelson, Garrett, Ketawala, Gihan K., Karpos, Konstantinos, Alvarez, Roberto C., Nazari, Reza, Thifault, Darren, Jernigan, Rebecca, Oberthür, Dominik, Han, Huijong, Sierra, Raymond, Hunter, Mark S., Batyuk, Alexander, Kupitz, Christopher J., Sublett, Robert E., Poitevin, Frederic, Lisova, Stella, Mariani, Valerio, Tolstikova, Alexandra, Boutet, Sebastien, Messerschmidt, Marc, Meza-Aguilar, J Domingo, Fromme, Raimund, Martín-García, Jose Manuel, Botha, Sabine, Fromme, Petra, Grant, Thomas D., Kirian, Richard A., and Ros, Alexandra

Abstract

With advances in X-ray free-electron lasers (XFELs), serial femtosecond crystallography (SFX) has enabled the static and dynamic structure determination for challenging proteins such as membrane protein complexes. In SFX with XFELs, the crystals are typically destroyed after interacting with a single XFEL pulse. Therefore, thousands of new crystals must be sequentially introduced into the X-ray beam to collect full data sets. Because of the serial nature of any SFX experiment, up to 99% of the sample delivered to the X-ray beam during its "off-time" between X-ray pulses is wasted due to the intrinsic pulsed nature of all current XFELs. To solve this major problem of large and often limiting sample consumption, we report on improvements of a revolutionary sample-saving method that is compatible with all current XFELs. We previously reported 3D-printed injection devices coupled with gas dynamic virtual nozzles (GDVNs) capable of generating samples containing droplets segmented by an immiscible oil phase for jetting crystal-laden droplets into the path of an XFEL. Here, we have further improved the device design by including metal electrodes inducing electrowetting effects for improved control over droplet generation frequency to stimulate the droplet release to matching the XFEL repetition rate by employing an electrical feedback mechanism. We report the improvements in this electrically triggered segmented flow approach for sample conservation in comparison with a continuous GDVN injection using the microcrystals of lysozyme and 3-deoxy-D-manno-octulosonate 8-phosphate synthase and report the segmented flow approach for sample injection applied at the Macromolecular Femtosecond Crystallography instrument at the Linear Coherent Light Source for the first time.

Published
2022

25. Protocol for structure determination of SARS-CoV-2 main protease at near-physiological-temperature by serial femtosecond crystallography

Author

Ertem, Fatma Betül; Güven, Ömür; Büyükdağ, Cengizhan; Göçenler, Oktay; Ayan, Esra; Yüksel, Büşra; Gül, Mehmet; Usta, Gözde; Çakılkaya, Barış; Johnson, J. Austin; Demirci, Hasan; Dağ, Çağdaş; Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Dao, E. Han; Su, Zhen; Poitevin, Frederic; Yoon, Chun Hong; Kupitz, Christopher; Hayes, Brandon; Liang, Mengning; Hunter, Mark S.; Batyuk, Alexander; Sierra, Raymond G.; Ketawala, Gihan; Botha, Sabine, Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID), Graduate School of Sciences and Engineering; College of Sciences, Department of Molecular Biology and Genetics, Ertem, Fatma Betül; Güven, Ömür; Büyükdağ, Cengizhan; Göçenler, Oktay; Ayan, Esra; Yüksel, Büşra; Gül, Mehmet; Usta, Gözde; Çakılkaya, Barış; Johnson, J. Austin; Demirci, Hasan; Dağ, Çağdaş; Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Dao, E. Han; Su, Zhen; Poitevin, Frederic; Yoon, Chun Hong; Kupitz, Christopher; Hayes, Brandon; Liang, Mengning; Hunter, Mark S.; Batyuk, Alexander; Sierra, Raymond G.; Ketawala, Gihan; Botha, Sabine, Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID), Graduate School of Sciences and Engineering; College of Sciences, and Department of Molecular Biology and Genetics

Abstract

The SARS-CoV-2 main protease of (Mpro) is an important target for SARS-CoV-2 related drug repurposing and development studies. Here, we describe the steps for structural characterization of SARS-CoV-2 Mpro, starting from plasmid preparation and protein purification. We detail the steps for crystallization using the sitting drop, microbatch (under oil) approach. Finally, we cover data collection and structure determination using serial femtosecond crystallography., National Science Foundation (NSF) Science and Technology Centers; BioXFEL; National Institutes of Health (NIH); National Institute of General Medical Sciences (NIGMS); Scientific and Technological Research Council of Turkey (TÜBİTAK); 2232 International Fellowship for Outstanding Researchers Program of TÜBİTAK; 2244 Industrial PhD Program of TÜBİTAK; 1001 TÜBİTAK Supporting Scientific and Technological Research Projects Program; Linac Coherent Light Source (LCLS); Stanford Synchrotron Light Source (SSRL); SLAC National Accelerator Laboratory; U.S. Department of Energy, Office of Science, Basic Energy Sciences

Published
2022

26. Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature

Author

Dağ, Çağdaş; Ayan, Esra; Yüksel, Büşra; Destan, Ebru; Ertem, Fatma Betül; Yıldırım, Günseli; Eren, Meryem; Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Yefanov, Oleksandr M.; Barty, Anton; Tolstikova, Alexandra; Ketawala, Gihan K.; Botha, Sabine; Dao, E. Han; Hayes, Brandon; Liang, Mengning; Seaberg, Matthew H.; Hunter, Mark S.; Batyuk, Alexander; Mariani, Valerio; Su, Zhen; Poitevin, Frederic; Yoon, Chun Hong; Kupitz, Christopher; Cohen, Aina; Doukov, Tzanko; Sierra, Raymond G., Graduate School of Sciences and Engineering; College of Engineering, Department of Molecular Biology and Genetics, Dağ, Çağdaş; Ayan, Esra; Yüksel, Büşra; Destan, Ebru; Ertem, Fatma Betül; Yıldırım, Günseli; Eren, Meryem; Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Yefanov, Oleksandr M.; Barty, Anton; Tolstikova, Alexandra; Ketawala, Gihan K.; Botha, Sabine; Dao, E. Han; Hayes, Brandon; Liang, Mengning; Seaberg, Matthew H.; Hunter, Mark S.; Batyuk, Alexander; Mariani, Valerio; Su, Zhen; Poitevin, Frederic; Yoon, Chun Hong; Kupitz, Christopher; Cohen, Aina; Doukov, Tzanko; Sierra, Raymond G., Graduate School of Sciences and Engineering; College of Engineering, and Department of Molecular Biology and Genetics

Abstract

Ayan et al. report two structures of the protein streptavidin - one at ambient temperature determined using serial femtosecond crystallography and a second one determined at cryogenic temperature. These results provide insights into the structural dynamics of apo streptavidin and reveal a cooperative allostery between monomers for binding to biotin, and the findings are supported by GNM analysis. Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 angstrom resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 angstrom resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature., National Science Foundation (NSF) Science and Technology Centers; 2232 International Fellowship for Outstanding Researchers Program; 1001 Scientific and Technological Research Projects Funding Program; Scientific and Technological Research Council of Turkey (TÜBİTAK); U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences (OBES); National Institutes of Health, National Institute of General Medical Sciences (NIGMS)

Published
2022

27. Protocol for structure determination of SARS-CoV-2 main protease at near-physiological-temperature by serial femtosecond crystallography

Author

Ertem, Fatma Betul, primary, Guven, Omur, additional, Buyukdag, Cengizhan, additional, Gocenler, Oktay, additional, Ayan, Esra, additional, Yuksel, Busra, additional, Gul, Mehmet, additional, Usta, Gozde, additional, Cakılkaya, Barıs, additional, Johnson, J. Austin, additional, Dao, E. Han, additional, Su, Zhen, additional, Poitevin, Frederic, additional, Yoon, Chun Hong, additional, Kupitz, Christopher, additional, Hayes, Brandon, additional, Liang, Mengning, additional, Hunter, Mark S., additional, Batyuk, Alexander, additional, Sierra, Raymond G., additional, Ketawala, Gihan, additional, Botha, Sabine, additional, Dağ, Çağdaş, additional, and DeMirci, Hasan, additional

Published
2022
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29. Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography

Author

Guven, Omur, primary, Gul, Mehmet, additional, Ayan, Esra, additional, Johnson, J Austin, additional, Cakilkaya, Baris, additional, Usta, Gozde, additional, Ertem, Fatma Betul, additional, Tokay, Nurettin, additional, Yuksel, Busra, additional, Gocenler, Oktay, additional, Buyukdag, Cengizhan, additional, Botha, Sabine, additional, Ketawala, Gihan, additional, Su, Zhen, additional, Hayes, Brandon, additional, Poitevin, Frederic, additional, Batyuk, Alexander, additional, Yoon, Chun Hong, additional, Kupitz, Christopher, additional, Durdagi, Serdar, additional, Sierra, Raymond G., additional, and DeMirci, Hasan, additional

Published
2021
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30. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

Author

Durdagi, Serdar, primary, Dağ, Çağdaş, additional, Dogan, Berna, additional, Yigin, Merve, additional, Avsar, Timucin, additional, Buyukdag, Cengizhan, additional, Erol, Ismail, additional, Ertem, Fatma Betul, additional, Calis, Seyma, additional, Yildirim, Gunseli, additional, Orhan, Muge D., additional, Guven, Omur, additional, Aksoydan, Busecan, additional, Destan, Ebru, additional, Sahin, Kader, additional, Besler, Sabri O., additional, Oktay, Lalehan, additional, Shafiei, Alaleh, additional, Tolu, Ilayda, additional, Ayan, Esra, additional, Yuksel, Busra, additional, Peksen, Ayse B., additional, Gocenler, Oktay, additional, Yucel, Ali D., additional, Can, Ozgur, additional, Ozabrahamyan, Serena, additional, Olkan, Alpsu, additional, Erdemoglu, Ece, additional, Aksit, Fulya, additional, Tanisali, Gokhan, additional, Yefanov, Oleksandr M., additional, Barty, Anton, additional, Tolstikova, Alexandra, additional, Ketawala, Gihan K., additional, Botha, Sabine, additional, Dao, E. Han, additional, Hayes, Brandon, additional, Liang, Mengning, additional, Seaberg, Matthew H., additional, Hunter, Mark S., additional, Batyuk, Alex, additional, Mariani, Valerio, additional, Su, Zhen, additional, Poitevin, Frederic, additional, Yoon, Chun Hong, additional, Kupitz, Christopher, additional, Sierra, Raymond G., additional, Snell, Edward H., additional, and DeMirci, Hasan, additional

Published
2021
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31. De novo protein crystal structure determination from X-ray free-electron laser data

Author

Barends, Thomas R.M., Foucar, Lutz, Botha, Sabine, Doak, R. Bruce, Shoeman, Robert L., Nass, Karol, Koglin, Jason E., Williams, Garth J., Boutet, Sebastien, Messerschmidt, Marc, and Schlichting, Ilme

Subjects
Proteins -- Structure, X-rays -- Diffraction, Crystals -- Structure, X-ray crystallography -- Methods, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The determination of protein crystal structures is hampered by the need for macroscopic crystals. X-ray free-electron lasers (FELs) provide extremely intense pulses of femtosecond duration, which allow data collection from [...]

Published
2014
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32. Cooperative Allostery and Structural Dynamics of Streptavidin at Cryogenic- and Ambient-temperature

Author

Ayan, Esra, primary, Yuksel, Busra, additional, Destan, Ebru, additional, Ertem, Fatma Betul, additional, Yildirim, Gunseli, additional, Eren, Meryem, additional, Yefanov, Oleksandr M., additional, Barty, Anton, additional, Tolstikova, Alexandra, additional, Ketawala, Gihan K., additional, Botha, Sabine, additional, Dao, E. Han, additional, Hayes, Brandon, additional, Liang, Mengning, additional, Seaberg, Matthew H., additional, Hunter, Mark S., additional, Batyuk, Alex, additional, Mariani, Valerio, additional, Su, Zhen, additional, Poitevin, Frederic, additional, Yoon, Chun Hong, additional, Kupitz, Christopher, additional, Cohen, Aina, additional, Doukov, Tzanko, additional, Sierra, Raymond G., additional, Dağ, Çağdaş, additional, and DeMirci, Hasan, additional

Published
2021
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33. PROTEIN DYNAMICS: Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation

Author

Barends, Thomas R. M., Foucar, Lutz, Ardevol, Albert, Nass, Karol, Aquila, Andrew, Botha, Sabine, Doak, Bruce R., Falahati, Konstantin, Hartmann, Elisabeth, Hilpert, Mario, Heinz, Marcel, Hoffmann, Matthias C., Köfinger, Jürgen, Koglin, Jason E., Kovacsova, Gabriela, Liang, Mengning, Milathianaki, Despina, Lemke, Henrik T., Reinstein, Jochen, Roome, Christopher M., Shoeman, Robert L., Williams, Garth J., Burghardt, Irene, Hummer, Gerhard, Boutet, Sébastien, and Schlichting, Ilme

Published
2015
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34. Case study of high-throughput drug screening and remote data collection for SARS-CoV-2 main protease by using serial femtosecond X-ray crystallography

Author

Güven, Ömür; Gül, Mehmet; Ayan, Esra; Johnson, Jerome Austin; Çakılkaya, Barış; Usta, Gözde Karakadıoğlu; Ertem, Fatma Betül; Tokay, Nurettin; Yüksel, Büşra; Göcenler, Oktay; Büyükdağ, Cengizhan; Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Botha, Sabine; Ketawala, Gihan; Su, Zhen; Hayes, Brandon; Poitevin, Frederic; Batyuk, Alexander; Yoon, Chun Hong; Kupitz, Christopher; Durdağı, Serdar; Sierra, Raymond G., Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID), Graduate School of Sciences and Engineering; College of Sciences, Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering, Güven, Ömür; Gül, Mehmet; Ayan, Esra; Johnson, Jerome Austin; Çakılkaya, Barış; Usta, Gözde Karakadıoğlu; Ertem, Fatma Betül; Tokay, Nurettin; Yüksel, Büşra; Göcenler, Oktay; Büyükdağ, Cengizhan; Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Botha, Sabine; Ketawala, Gihan; Su, Zhen; Hayes, Brandon; Poitevin, Frederic; Batyuk, Alexander; Yoon, Chun Hong; Kupitz, Christopher; Durdağı, Serdar; Sierra, Raymond G., Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID), Graduate School of Sciences and Engineering; College of Sciences, and Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering

Abstract

Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part of this research has been drug repurposing; therefore, confirmation of in silico drug screening studies have been carried out for this purpose. Here we demonstrated the possibility of screening a variety of drugs efficiently by leveraging a high data collection rate of 120 images/second with the new low-noise, high dynamic range ePix10k2M Pixel Array Detector installed at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS). The X-ray Free-Electron Laser (XFEL) is used for remote high-throughput data collection for drug repurposing of the main protease (Mpro) of SARS-CoV-2 at ambient temperature with mitigated X-ray radiation damage. We obtained multiple structures soaked with nine drug candidate molecules in two crystal forms. Although our drug binding attempts failed, we successfully established a high-throughput Serial Femtosecond X-ray crystallographic (SFX) data collection protocol., National Science Foundation (NSF) Science and Technology Centers Grant; Biology with X-ray Lasers (BioXFEL); Scientific and Technological Research Council of Turkey (TÜBİTAK); 2232 International Fellowship for Outstanding Researchers Program; 2244 Industrial PhD Fellowship Program; 1001 Scientific and Technological Research Projects Funding Program

Published
2021

35. Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing

Author

Durdagi, Serdar, primary, Dag, Cagdas, additional, Dogan, Berna, additional, Yigin, Merve, additional, Avsar, Timucin, additional, Buyukdag, Cengizhan, additional, Erol, Ismail, additional, Ertem, Betul, additional, Calis, Seyma, additional, Yildirim, Gunseli, additional, Orhan, Muge D., additional, Guven, Omur, additional, Aksoydan, Busecan, additional, Destan, Ebru, additional, Sahin, Kader, additional, Besler, Sabri O., additional, Oktay, Lalehan, additional, Shafiei, Alaleh, additional, Tolu, Ilayda, additional, Ayan, Esra, additional, Yuksel, Busra, additional, Peksen, Ayse B., additional, Gocenler, Oktay, additional, Yucel, Ali D., additional, Can, Ozgur, additional, Ozabrahamyan, Serena, additional, Olkan, Alpsu, additional, Erdemoglu, Ece, additional, Aksit, Fulya, additional, Tanisali, Gokhan, additional, Yefanov, Oleksandr M., additional, Barty, Anton, additional, Tolstikova, Alexandra, additional, Ketawala, Gihan K., additional, Botha, Sabine, additional, Dao, E. Han, additional, Hayes, Brandon, additional, Liang, Mengning, additional, Seaberg, Matthew H., additional, Hunter, Mark S., additional, Batyuk, Alex, additional, Mariani, Valerio, additional, Su, Zhen, additional, Poitevin, Frederic, additional, Yoon, Chun Hong, additional, Kupitz, Christopher, additional, Sierra, Raymond G., additional, Snell, Edward, additional, and DeMirci, Hasan, additional

Published
2020
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36. Enhanced X-ray diffraction of in vivo-grown μNS crystals by viscous jets at XFELs

Author

Nagaratnam, Nirupa, primary, Tang, Yanyang, additional, Botha, Sabine, additional, Saul, Justin, additional, Li, Chufeng, additional, Hu, Hao, additional, Zaare, Sahba, additional, Hunter, Mark, additional, Lowry, David, additional, Weierstall, Uwe, additional, Zatsepin, Nadia, additional, Spence, John C. H., additional, Qiu, Ji, additional, LaBaer, Joshua, additional, Fromme, Petra, additional, and Martin-Garcia, Jose M., additional

Published
2020
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37. Membrane protein megahertz crystallography at the European XFEL

Author

Gisriel, Christopher, Coe, Jesse, Letrun, Romain, Yefanov, Oleksandr, Luna-Chavez, Cesar, Stander, Natasha E., Lisova, Stella, Mariani, Valerio, Kuhn, Manuela, Aplin, Steven, Grant, Thomas D., Dörner, Katerina Henrike, Sato, Tokushi, Echelmeier, Austin, Cruz Villarreal, Jorvani, Hunter, Mark S., Wiedorn, Max Oliver, Knoška, Juraj, Mazalova, Victoria, Roy-Chowdhury, Shatabdi, Yang, Jay How, Jones, Alex, Bean, Richard, Bielecki, Johan, Kim, Yoonhee, Mills, Grant, Weinhausen, Britta, Meza, Jose D., Al-Qudami, Nasser, Bajt, Saša, Brehm, Gerrit, Botha, Sabine, Boukhelef, Djelloul, Brockhauser, Sandor, Bruce, Barry D., Coleman, Matthew A., Danilevski, Cyril, Discianno, Erin, Dobson, Zachary, Fangohr, Hans, Martin-Garcia, Jose Manuel, Gevorkov, Yaroslav, Hauf, Steffen, Hosseinizadeh, Ahmad, Januschek, F., Ketawala, Gihan K., Kupitz, Christopher, Maia, Luis, Manetti, Maurizio, Messerschmidt, Marc, Michelat, Thomas, Mondal, Jyotirmoy, Ourmazd, Abbas, Previtali, Gianpietro, Sarrou, Iosifina, Schön, Silvan, Schwander, Peter, Shelby, Megan L., Silenzi, Alessandro, Sztuk-Dambietz, Jolanta, Szuba, Janusz, Turcato, Monica, White, Thomas A., Wrona, Krzysztof, Xu, Chen, Abdellatif, Mohamed H., Zook, James D., Spence, John C. H., Chapman, Henry N., Barty, Anton, Kirian, Richard A., Frank, Matthias, Ros, Alexandra, Schmidt, Marius, Fromme, Raimund, Mancuso, Adrian P., Fromme, Petra, Zatsepin, Nadia, Gisriel, Christopher, Coe, Jesse, Letrun, Romain, Yefanov, Oleksandr, Luna-Chavez, Cesar, Stander, Natasha E., Lisova, Stella, Mariani, Valerio, Kuhn, Manuela, Aplin, Steven, Grant, Thomas D., Dörner, Katerina Henrike, Sato, Tokushi, Echelmeier, Austin, Cruz Villarreal, Jorvani, Hunter, Mark S., Wiedorn, Max Oliver, Knoška, Juraj, Mazalova, Victoria, Roy-Chowdhury, Shatabdi, Yang, Jay How, Jones, Alex, Bean, Richard, Bielecki, Johan, Kim, Yoonhee, Mills, Grant, Weinhausen, Britta, Meza, Jose D., Al-Qudami, Nasser, Bajt, Saša, Brehm, Gerrit, Botha, Sabine, Boukhelef, Djelloul, Brockhauser, Sandor, Bruce, Barry D., Coleman, Matthew A., Danilevski, Cyril, Discianno, Erin, Dobson, Zachary, Fangohr, Hans, Martin-Garcia, Jose Manuel, Gevorkov, Yaroslav, Hauf, Steffen, Hosseinizadeh, Ahmad, Januschek, F., Ketawala, Gihan K., Kupitz, Christopher, Maia, Luis, Manetti, Maurizio, Messerschmidt, Marc, Michelat, Thomas, Mondal, Jyotirmoy, Ourmazd, Abbas, Previtali, Gianpietro, Sarrou, Iosifina, Schön, Silvan, Schwander, Peter, Shelby, Megan L., Silenzi, Alessandro, Sztuk-Dambietz, Jolanta, Szuba, Janusz, Turcato, Monica, White, Thomas A., Wrona, Krzysztof, Xu, Chen, Abdellatif, Mohamed H., Zook, James D., Spence, John C. H., Chapman, Henry N., Barty, Anton, Kirian, Richard A., Frank, Matthias, Ros, Alexandra, Schmidt, Marius, Fromme, Raimund, Mancuso, Adrian P., Fromme, Petra, and Zatsepin, Nadia

Abstract

The world’s first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs.

Published
2019

38. Megahertz serial crystallography

Author

Wiedorn, Max Oliver, Oberthür, Dominik, Bean, Richard, Schubert, Robin, Werner, Nadine, Abbey, Brian, Aepfelbacher, Martin, Adriano, Luigi, Allahgholi, Aschkan, Al-Qudami, Nasser, Andreasson, Jakob, Shelby, Megan L., Shoemann, Robert L., Sikorski, Marcin, Silenzi, Alessandro, Stan, Claudiu A., Shi, Xintian, Stern, Stephan, Sztuk-Dambietz, Jolanta, Szuba, Janusz, Tolstikova, Aleksandra, Aplin, Steven, Trebbin, Martin, Trunk, Ulrich, Vagovic, Patrik, Ve, Thomas, Weinhausen, Britta, White, Thomas A., Wrona, Krzysztof, Xu, Chen, Yefanov, Oleksandr, Zatsepin, Nadia, Awel, Salah, Zhang, Jiaguo, Perbandt, Markus, Mancuso, Adrian P., Betzel, Christian, Chapman, Henry N., Banty, Anton, Ayyer, Kartik, Bajt, Saša, Barák, Imrich, Bari, Sadia, Bielecki, Johan, Botha, Sabine, Boukhelef, Djelloul, Brehm, Wolfgang, Brockhauser, Sandor, Cheviakov, Igor, Coleman, Matthew A., Cruz-Mazo, Francisco, Danilevski, Cyril, Darmanin, Connie, Doak, R. Bruce, Domaracky, Martin, Dörner, Katerina Henrike, Du, Yang, Fangohr, Hans, Fleckenstein, Holger, Frank, Matthias, Fromme, Petra, Gañán-Calvo, Alfonso M., Gevorkov, Yaroslav, Giewekemeyer, Klaus, Ginn, Helen Mary, Graafsma, Heinz, Graceffa, Rita, Greiffenberg, Dominic, Gumprecht, Lars, Göttlicher, Peter, Hajdu, János, Hauf, Steffen, Heymann, Michael, Holmes, Susannah, Horke, Daniel A., Hunter, Mark S., Imlau, Siegfried, Kaukher, Alexander, Kim, Yoonhee, Klyuev, Alexander, Knoška, Juraj, Kobe, Bostjan, Kuhn, Manuela, Kupitz, Christopher, Küpper, Jochen, Lahey-Rudolph, Janine Mia, Laurus, Torsten, Le Cong, Karoline, Letrun, Romain, Xavier, Paulrajpillai Lourdu, Maia, Luis, Maia, Filipe R. N. C., Mariani, Valerio, Messerschmidt, Marc, Metz, Markus, Mezza, Davide, Michelat, Thomas, Mills, Grant, Monteiro, Diana C.F., Morgan, Andrew J., Mühlig, Kerstin, Munke, Anna, Münnich, Astrid, Nette, Julia, Nugent, Keith A., Nuguid, Theresa, Orville, Allen M., Pandey, Suraj, Pena, Gisel, Vilanueva-Pérez, Pablo, Pöhlsen, Jennifer, Previtali, Gianpietro, Redecke, Lars, Riekehr, Winnie Maria, Rohde, Holger, Round, Adam R., Safenreiter, Tatiana, Sarrou, Iosifina, Sato, Tokushi, Schmidt, Marius, Schmitt, Bernd, Schönherr, Robert, Schulz, Joachim, Sellberg, Jonas Alexander, Seibert, M. Marvin, Seuring, Carolin, Wiedorn, Max Oliver, Oberthür, Dominik, Bean, Richard, Schubert, Robin, Werner, Nadine, Abbey, Brian, Aepfelbacher, Martin, Adriano, Luigi, Allahgholi, Aschkan, Al-Qudami, Nasser, Andreasson, Jakob, Shelby, Megan L., Shoemann, Robert L., Sikorski, Marcin, Silenzi, Alessandro, Stan, Claudiu A., Shi, Xintian, Stern, Stephan, Sztuk-Dambietz, Jolanta, Szuba, Janusz, Tolstikova, Aleksandra, Aplin, Steven, Trebbin, Martin, Trunk, Ulrich, Vagovic, Patrik, Ve, Thomas, Weinhausen, Britta, White, Thomas A., Wrona, Krzysztof, Xu, Chen, Yefanov, Oleksandr, Zatsepin, Nadia, Awel, Salah, Zhang, Jiaguo, Perbandt, Markus, Mancuso, Adrian P., Betzel, Christian, Chapman, Henry N., Banty, Anton, Ayyer, Kartik, Bajt, Saša, Barák, Imrich, Bari, Sadia, Bielecki, Johan, Botha, Sabine, Boukhelef, Djelloul, Brehm, Wolfgang, Brockhauser, Sandor, Cheviakov, Igor, Coleman, Matthew A., Cruz-Mazo, Francisco, Danilevski, Cyril, Darmanin, Connie, Doak, R. Bruce, Domaracky, Martin, Dörner, Katerina Henrike, Du, Yang, Fangohr, Hans, Fleckenstein, Holger, Frank, Matthias, Fromme, Petra, Gañán-Calvo, Alfonso M., Gevorkov, Yaroslav, Giewekemeyer, Klaus, Ginn, Helen Mary, Graafsma, Heinz, Graceffa, Rita, Greiffenberg, Dominic, Gumprecht, Lars, Göttlicher, Peter, Hajdu, János, Hauf, Steffen, Heymann, Michael, Holmes, Susannah, Horke, Daniel A., Hunter, Mark S., Imlau, Siegfried, Kaukher, Alexander, Kim, Yoonhee, Klyuev, Alexander, Knoška, Juraj, Kobe, Bostjan, Kuhn, Manuela, Kupitz, Christopher, Küpper, Jochen, Lahey-Rudolph, Janine Mia, Laurus, Torsten, Le Cong, Karoline, Letrun, Romain, Xavier, Paulrajpillai Lourdu, Maia, Luis, Maia, Filipe R. N. C., Mariani, Valerio, Messerschmidt, Marc, Metz, Markus, Mezza, Davide, Michelat, Thomas, Mills, Grant, Monteiro, Diana C.F., Morgan, Andrew J., Mühlig, Kerstin, Munke, Anna, Münnich, Astrid, Nette, Julia, Nugent, Keith A., Nuguid, Theresa, Orville, Allen M., Pandey, Suraj, Pena, Gisel, Vilanueva-Pérez, Pablo, Pöhlsen, Jennifer, Previtali, Gianpietro, Redecke, Lars, Riekehr, Winnie Maria, Rohde, Holger, Round, Adam R., Safenreiter, Tatiana, Sarrou, Iosifina, Sato, Tokushi, Schmidt, Marius, Schmitt, Bernd, Schönherr, Robert, Schulz, Joachim, Sellberg, Jonas Alexander, Seibert, M. Marvin, and Seuring, Carolin

Abstract

The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.

Published
2018

39. Megahertz serial crystallography

Author

Wiedorn, Max O., Oberthuer, Dominik, Bean, Richard, Schubert, Robin, Werner, Nadine, Abbey, Brian, Aepfelbacher, Martin, Adriano, Luigi, Allahgholi, Aschkan, Al-Qudami, Nasser, Andreasson, Jakob, Aplin, Steve, Awel, Salah, Ayyer, Kartik, Bajt, Sasa, Barak, Imrich, Bari, Sadia, Bielecki, Johan, Botha, Sabine, Boukhelef, Djelloul, Brehm, Wolfgang, Brockhauser, Sandor, Cheviakov, Igor, Coleman, Matthew A., Cruz-Mazo, Francisco, Danilevski, Cyril, Darmanin, Connie, Doak, R. Bruce, Domaracky, Martin, Doerner, Katerina, Du, Yang, Fangohr, Hans, Fleckenstein, Holger, Frank, Matthias, Fromme, Petra, Ganan-Calvo, Alfonso M., Gevorkov, Yaroslav, Giewekemeyer, Klaus, Ginn, Helen Mary, Graafsma, Heinz, Graceffa, Rita, Greiffenberg, Dominic, Gumprecht, Lars, Goettlicher, Peter, Hajdu, Janos, Hauf, Steffen, Heymann, Michael, Holmes, Susannah, Horke, Daniel A., Hunter, Mark S., Imlau, Siegfried, Kaukher, Alexander, Kim, Yoonhee, Klyuev, Alexander, Knoska, Juraj, Kobe, Bostjan, Kuhn, Manuela, Kupitz, Christopher, Kueper, Jochen, Lahey-Rudolph, Janine Mia, Laurus, Torsten, Le Cong, Karoline, Letrun, Romain, Xavier, P. Lourdu, Maia, Luis, Maia, Filipe R.N.C., Mariani, Valerio, Messerschmidt, Marc, Metz, Markus, Mezza, Davide, Michelat, Thomas, Mills, Grant, Monteiro, Diana C. F., Morgan, Andrew, Mühlig, Kerstin, Munke, Anna, Muennich, Astrid, Nette, Julia, Nugent, Keith A., Nuguid, Theresa, Orville, Allen M., Pandey, Suraj, Pena, Gisel, Villanueva-Perez, Pablo, Poehlsen, Jennifer, Previtali, Gianpietro, Redecke, Lars, Riekehr, Winnie Maria, Rohde, Holger, Round, Adam, Safenreiter, Tatiana, Sarrou, Iosifina, Sato, Tokushi, Schmidt, Marius, Schmitt, Bernd, Schoenherr, Robert, Schulz, Joachim, Sellberg, Jonas A., Seibert, M. Marvin, Seuring, Carolin, Shelby, Megan L., Shoeman, Robert L., Sikorski, Marcin, Silenzi, Alessandro, Stan, Claudiu A., Shi, Xintian, Stern, Stephan, Sztuk-Dambietz, Jola, Szuba, Janusz, Tolstikova, Aleksandra, Trebbin, Martin, Trunk, Ulrich, Vagovic, Patrik, Ve, Thomas, Weinhausen, Britta, White, Thomas A., Wrona, Krzysztof, Xu, Chen, Yefanov, Oleksandr, Zatsepin, Nadia, Zhang, Jiaguo, Perbandt, Markus, Mancuso, Adrian P., Betzel, Christian, Chapman, Henry, Barty, Anton, Wiedorn, Max O., Oberthuer, Dominik, Bean, Richard, Schubert, Robin, Werner, Nadine, Abbey, Brian, Aepfelbacher, Martin, Adriano, Luigi, Allahgholi, Aschkan, Al-Qudami, Nasser, Andreasson, Jakob, Aplin, Steve, Awel, Salah, Ayyer, Kartik, Bajt, Sasa, Barak, Imrich, Bari, Sadia, Bielecki, Johan, Botha, Sabine, Boukhelef, Djelloul, Brehm, Wolfgang, Brockhauser, Sandor, Cheviakov, Igor, Coleman, Matthew A., Cruz-Mazo, Francisco, Danilevski, Cyril, Darmanin, Connie, Doak, R. Bruce, Domaracky, Martin, Doerner, Katerina, Du, Yang, Fangohr, Hans, Fleckenstein, Holger, Frank, Matthias, Fromme, Petra, Ganan-Calvo, Alfonso M., Gevorkov, Yaroslav, Giewekemeyer, Klaus, Ginn, Helen Mary, Graafsma, Heinz, Graceffa, Rita, Greiffenberg, Dominic, Gumprecht, Lars, Goettlicher, Peter, Hajdu, Janos, Hauf, Steffen, Heymann, Michael, Holmes, Susannah, Horke, Daniel A., Hunter, Mark S., Imlau, Siegfried, Kaukher, Alexander, Kim, Yoonhee, Klyuev, Alexander, Knoska, Juraj, Kobe, Bostjan, Kuhn, Manuela, Kupitz, Christopher, Kueper, Jochen, Lahey-Rudolph, Janine Mia, Laurus, Torsten, Le Cong, Karoline, Letrun, Romain, Xavier, P. Lourdu, Maia, Luis, Maia, Filipe R.N.C., Mariani, Valerio, Messerschmidt, Marc, Metz, Markus, Mezza, Davide, Michelat, Thomas, Mills, Grant, Monteiro, Diana C. F., Morgan, Andrew, Mühlig, Kerstin, Munke, Anna, Muennich, Astrid, Nette, Julia, Nugent, Keith A., Nuguid, Theresa, Orville, Allen M., Pandey, Suraj, Pena, Gisel, Villanueva-Perez, Pablo, Poehlsen, Jennifer, Previtali, Gianpietro, Redecke, Lars, Riekehr, Winnie Maria, Rohde, Holger, Round, Adam, Safenreiter, Tatiana, Sarrou, Iosifina, Sato, Tokushi, Schmidt, Marius, Schmitt, Bernd, Schoenherr, Robert, Schulz, Joachim, Sellberg, Jonas A., Seibert, M. Marvin, Seuring, Carolin, Shelby, Megan L., Shoeman, Robert L., Sikorski, Marcin, Silenzi, Alessandro, Stan, Claudiu A., Shi, Xintian, Stern, Stephan, Sztuk-Dambietz, Jola, Szuba, Janusz, Tolstikova, Aleksandra, Trebbin, Martin, Trunk, Ulrich, Vagovic, Patrik, Ve, Thomas, Weinhausen, Britta, White, Thomas A., Wrona, Krzysztof, Xu, Chen, Yefanov, Oleksandr, Zatsepin, Nadia, Zhang, Jiaguo, Perbandt, Markus, Mancuso, Adrian P., Betzel, Christian, Chapman, Henry, and Barty, Anton

Abstract

The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a beta-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.

Published
2018
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40. Correction: Corrigendum: Diffraction data of core-shell nanoparticles from an X-ray free electron laser

Author

Li, Xuanxuan, primary, Chiu, Chun-Ya, additional, Wang, Hsiang-Ju, additional, Kassemeyer, Stephan, additional, Botha, Sabine, additional, Shoeman, Robert L, additional, Lawrence, Robert M, additional, Kupitz, Christopher, additional, Kirian, Richard, additional, James, Daniel, additional, Wang, Dingjie, additional, Nelson, Garrett, additional, Messerschmidt, Marc, additional, Boutet, Sébastien, additional, Williams, Garth J, additional, Hartmann, Elisabeth, additional, Jafarpour, Aliakbar, additional, Foucar, Lutz M, additional, Barty, Anton, additional, Chapman, Henry, additional, Liang, Mengning, additional, Menzel, Andreas, additional, Wang, Fenglin, additional, Basu, Shibom, additional, Fromme, Raimund, additional, Doak, R.Bruce, additional, Fromme, Petra, additional, Weierstall, Uwe, additional, Huang, Michael H, additional, Spence, John C.H, additional, Schlichting, Ilme, additional, Hogue, Brenda G, additional, and Liu, Haiguang, additional

Published
2017
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41. Diffraction data of core-shell nanoparticles from an X-ray free electron laser

Author

Li, Xuanxuan, primary, Chiu, Chun-Ya, additional, Wang, Hsiang-Ju, additional, Kassemeyer, Stephan, additional, Botha, Sabine, additional, Shoeman, Robert L., additional, Lawrence, Robert M., additional, Kupitz, Christopher, additional, Kirian, Richard, additional, James, Daniel, additional, Wang, Dingjie, additional, Nelson, Garrett, additional, Messerschmidt, Marc, additional, Boutet, Sébastien, additional, Williams, Garth J., additional, Hartmann, Elisabeth, additional, Jafarpour, Aliakbar, additional, Foucar, Lutz M., additional, Barty, Anton, additional, Chapman, Henry, additional, Liang, Mengning, additional, Menzel, Andreas, additional, Wang, Fenglin, additional, Basu, Shibom, additional, Fromme, Raimund, additional, Doak, R. Bruce, additional, Fromme, Petra, additional, Weierstall, Uwe, additional, Huang, Michael H., additional, Spence, John C. H., additional, Schlichting, Ilme, additional, Hogue, Brenda G., additional, and Liu, Haiguang, additional

Published
2017
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42. Liquid explosions induced by X-ray laser pulses

Author

Stan, Claudiu A., primary, Milathianaki, Despina, additional, Laksmono, Hartawan, additional, Sierra, Raymond G., additional, McQueen, Trevor A., additional, Messerschmidt, Marc, additional, Williams, Garth J., additional, Koglin, Jason E., additional, Lane, Thomas J., additional, Hayes, Matt J., additional, Guillet, Serge A. H., additional, Liang, Mengning, additional, Aquila, Andrew L., additional, Willmott, Philip R., additional, Robinson, Joseph S., additional, Gumerlock, Karl L., additional, Botha, Sabine, additional, Nass, Karol, additional, Schlichting, Ilme, additional, Shoeman, Robert L., additional, Stone, Howard A., additional, and Boutet, Sébastien, additional

Published
2016
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43. Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data

Author

Nass, Karol, primary, Meinhart, Anton, additional, Barends, Thomas R. M., additional, Foucar, Lutz, additional, Gorel, Alexander, additional, Aquila, Andrew, additional, Botha, Sabine, additional, Doak, R. Bruce, additional, Koglin, Jason, additional, Liang, Mengning, additional, Shoeman, Robert L., additional, Williams, Garth, additional, Boutet, Sebastien, additional, and Schlichting, Ilme, additional

Published
2016
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44. Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams

Author

Nass, Karol, Foucar, Lutz, Barends, Thomas R. M., Hartmann, Elisabeth, Botha, Sabine, Shoeman, Robert L., Doak, R. Bruce, Alonso-Mori, Roberto, Aquila, Andrew, Bajt, Saša, Barty, Anton, Bean, Richard, Beyerlein, Kenneth R., Bublitz, Maike, Drachmann, Nikolaj, Gregersen, Jonas, Jönsson, H. Olof, Kabsch, Wolfgang, Kassemeyer, Stephan, Koglin, Jason E., Krumrey, Michael, Mattle, Daniel, Messerschmidt, Marc, Nissen, Poul, Reinhard, Linda, Sitsel, Oleg, Sokaras, Dimosthenis, Williams, Garth J., Hau-Riege, Stefan, Timneanu, Nicusor, Caleman, Carl, Chapman, Henry N., Boutet, Sébastien, Schlichting, Ilme, Nass, Karol, Foucar, Lutz, Barends, Thomas R. M., Hartmann, Elisabeth, Botha, Sabine, Shoeman, Robert L., Doak, R. Bruce, Alonso-Mori, Roberto, Aquila, Andrew, Bajt, Saša, Barty, Anton, Bean, Richard, Beyerlein, Kenneth R., Bublitz, Maike, Drachmann, Nikolaj, Gregersen, Jonas, Jönsson, H. Olof, Kabsch, Wolfgang, Kassemeyer, Stephan, Koglin, Jason E., Krumrey, Michael, Mattle, Daniel, Messerschmidt, Marc, Nissen, Poul, Reinhard, Linda, Sitsel, Oleg, Sokaras, Dimosthenis, Williams, Garth J., Hau-Riege, Stefan, Timneanu, Nicusor, Caleman, Carl, Chapman, Henry N., Boutet, Sébastien, and Schlichting, Ilme

Abstract

Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe–4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe–4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.

Published
2015
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45. Towards phasing using high X-ray intensity

Author

Galli, Lorenzo, Son, Sang-Kil, Barends, Thomas R. M., White, Thomas A., Barty, Anton, Botha, Sabine, Boutet, Sébastien, Caleman, Carl, Doak, R. Bruce, Nanao, Max H., Nass, Karol, Shoeman, Robert L., Timneanu, Nicusor, Santra, Robin, Schlichting, Ilme, Chapman, Henry N., Galli, Lorenzo, Son, Sang-Kil, Barends, Thomas R. M., White, Thomas A., Barty, Anton, Botha, Sabine, Boutet, Sébastien, Caleman, Carl, Doak, R. Bruce, Nanao, Max H., Nass, Karol, Shoeman, Robert L., Timneanu, Nicusor, Santra, Robin, Schlichting, Ilme, and Chapman, Henry N.

Abstract

X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential ‘bleaching’ of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. A pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.

Published
2015
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46. Towards phasing using high X-ray intensity

Author

Galli, Lorenzo, primary, Son, Sang-Kil, additional, Barends, Thomas R. M., additional, White, Thomas A., additional, Barty, Anton, additional, Botha, Sabine, additional, Boutet, Sébastien, additional, Caleman, Carl, additional, Doak, R. Bruce, additional, Nanao, Max H., additional, Nass, Karol, additional, Shoeman, Robert L., additional, Timneanu, Nicusor, additional, Santra, Robin, additional, Schlichting, Ilme, additional, and Chapman, Henry N., additional

Published
2015
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47. Effects of self-seeding and crystal post-selection on the quality of Monte Carlo-integrated SFX data

Author

Barends, Thomas, primary, White, Thomas A., additional, Barty, Anton, additional, Foucar, Lutz, additional, Messerschmidt, Marc, additional, Alonso-Mori, Roberto, additional, Botha, Sabine, additional, Chapman, Henry, additional, Doak, R. Bruce, additional, Galli, Lorenzo, additional, Gati, Cornelius, additional, Gutmann, Matthias, additional, Koglin, Jason, additional, Markvardsen, Anders, additional, Nass, Karol, additional, Oberthur, Dominik, additional, Shoeman, Robert L., additional, Schlichting, Ilme, additional, and Boutet, Sébastien, additional

Published
2015
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48. Characterization and use of the spent beam for serial operation of LCLS

Author

Boutet, Sébastien, primary, Foucar, Lutz, additional, Barends, Thomas R. M., additional, Botha, Sabine, additional, Doak, R. Bruce, additional, Koglin, Jason E., additional, Messerschmidt, Marc, additional, Nass, Karol, additional, Schlichting, Ilme, additional, Seibert, M. Marvin, additional, Shoeman, Robert L., additional, and Williams, Garth J., additional

Published
2015
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49. Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams

Author

Nass, Karol, primary, Foucar, Lutz, additional, Barends, Thomas R. M., additional, Hartmann, Elisabeth, additional, Botha, Sabine, additional, Shoeman, Robert L., additional, Doak, R. Bruce, additional, Alonso-Mori, Roberto, additional, Aquila, Andrew, additional, Bajt, Saša, additional, Barty, Anton, additional, Bean, Richard, additional, Beyerlein, Kenneth R., additional, Bublitz, Maike, additional, Drachmann, Nikolaj, additional, Gregersen, Jonas, additional, Jönsson, H. Olof, additional, Kabsch, Wolfgang, additional, Kassemeyer, Stephan, additional, Koglin, Jason E., additional, Krumrey, Michael, additional, Mattle, Daniel, additional, Messerschmidt, Marc, additional, Nissen, Poul, additional, Reinhard, Linda, additional, Sitsel, Oleg, additional, Sokaras, Dimosthenis, additional, Williams, Garth J., additional, Hau-Riege, Stefan, additional, Timneanu, Nicusor, additional, Caleman, Carl, additional, Chapman, Henry N., additional, Boutet, Sébastien, additional, and Schlichting, Ilme, additional

Published
2015
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50. Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams

Author

Botha, Sabine, primary, Nass, Karol, additional, Barends, Thomas R. M., additional, Kabsch, Wolfgang, additional, Latz, Beatrice, additional, Dworkowski, Florian, additional, Foucar, Lutz, additional, Panepucci, Ezequiel, additional, Wang, Meitian, additional, Shoeman, Robert L., additional, Schlichting, Ilme, additional, and Doak, R. Bruce, additional

Published
2015
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