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1. Detection of a Geminate Photoproduct of Bovine Cytochrome c Oxidase by Time-Resolved Serial Femtosecond Crystallography

Author

Ishigami, Izumi, Carbajo, Sergio, Zatsepin, Nadia, Hikita, Masahide, Conrad, Chelsie E, Nelson, Garrett, Coe, Jesse, Basu, Shibom, Grant, Thomas, Seaberg, Matthew H, Sierra, Raymond G, Hunter, Mark S, Fromme, Petra, Fromme, Raimund, Rousseau, Denis L, and Yeh, Syun-Ru

Subjects
Inorganic Chemistry, Chemical Sciences, Acquired Cognitive Impairment, Brain Disorders, Cattle, Animals, Electron Transport Complex IV, Oxidation-Reduction, Copper, Ligands, Oxygen, Crystallography, X-Ray, Iron, Water, General Chemistry, Chemical sciences, Engineering
Abstract

Cytochrome c oxidase (CcO) is a large membrane-bound hemeprotein that catalyzes the reduction of dioxygen to water. Unlike classical dioxygen binding hemeproteins with a heme b group in their active sites, CcO has a unique binuclear center (BNC) composed of a copper atom (CuB) and a heme a3 iron, where O2 binds and is reduced to water. CO is a versatile O2 surrogate in ligand binding and escape reactions. Previous time-resolved spectroscopic studies of the CO complexes of bovine CcO (bCcO) revealed that photolyzing CO from the heme a3 iron leads to a metastable intermediate (CuB-CO), where CO is bound to CuB, before it escapes out of the BNC. Here, with a pump-probe based time-resolved serial femtosecond X-ray crystallography, we detected a geminate photoproduct of the bCcO-CO complex, where CO is dissociated from the heme a3 iron and moved to a temporary binding site midway between the CuB and the heme a3 iron, while the locations of the two metal centers and the conformation of Helix-X, housing the proximal histidine ligand of the heme a3 iron, remain in the CO complex state. This new structure, combined with other reported structures of bCcO, allows for a clearer definition of the ligand dissociation trajectory as well as the associated protein dynamics.

Published
2023

2. 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

3. Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser

Author

Yun, Ji-Hye, Li, Xuanxuan, Yue, Jianing, Park, Jae-Hyun, Jin, Zeyu, Li, Chufeng, Hu, Hao, Shi, Yingchen, Pandey, Suraj, Carbajo, Sergio, Boutet, Sébastien, Hunter, Mark S, Liang, Mengning, Sierra, Raymond G, Lane, Thomas J, Zhou, Liang, Weierstall, Uwe, Zatsepin, Nadia A, Ohki, Mio, Tame, Jeremy RH, Park, Sam-Yong, Spence, John CH, Zhang, Wenkai, Schmidt, Marius, Lee, Weontae, and Liu, Haiguang

Subjects
Chemical Sciences, Physical Chemistry, Eye Disease and Disorders of Vision, Neurosciences, Cations, Monovalent, Chloride Channels, Chlorides, Crystallography, Electromagnetic Radiation, Lasers, Molecular Dynamics Simulation, Nocardioides, Protein Conformation, alpha-Helical, Protein Structure, Tertiary, Recombinant Proteins, Retinaldehyde, Rhodopsins, Microbial, Water, time-resolved crystallography, light-driven chloride-pumping rhodopsin, X-ray free-electron laser, serial femtosecond crystallography
Abstract

Chloride ion-pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl- into cells. How the ClR initiates the transport is elusive. Here, we show the dynamics of ion transport observed with time-resolved serial femtosecond (fs) crystallography using the Linac Coherent Light Source. X-ray pulses captured structural changes in ClR upon flash illumination with a 550 nm fs-pumping laser. High-resolution structures for five time points (dark to 100 ps after flashing) reveal complex and coordinated dynamics comprising retinal isomerization, water molecule rearrangement, and conformational changes of various residues. Combining data from time-resolved spectroscopy experiments and molecular dynamics simulations, this study reveals that the chloride ion close to the Schiff base undergoes a dissociation-diffusion process upon light-triggered retinal isomerization.

Published
2021

4. 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

5. 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

6. Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography

Author

Olmos, Jose L, Pandey, Suraj, Martin-Garcia, Jose M, Calvey, George, Katz, Andrea, Knoska, Juraj, Kupitz, Christopher, Hunter, Mark S, Liang, Mengning, Oberthuer, Dominik, Yefanov, Oleksandr, Wiedorn, Max, Heyman, Michael, Holl, Mark, Pande, Kanupriya, Barty, Anton, Miller, Mitchell D, Stern, Stephan, Roy-Chowdhury, Shatabdi, Coe, Jesse, Nagaratnam, Nirupa, Zook, James, Verburgt, Jacob, Norwood, Tyler, Poudyal, Ishwor, Xu, David, Koglin, Jason, Seaberg, Matthew H, Zhao, Yun, Bajt, Saša, Grant, Thomas, Mariani, Valerio, Nelson, Garrett, Subramanian, Ganesh, Bae, Euiyoung, Fromme, Raimund, Fung, Russell, Schwander, Peter, Frank, Matthias, White, Thomas A, Weierstall, Uwe, Zatsepin, Nadia, Spence, John, Fromme, Petra, Chapman, Henry N, Pollack, Lois, Tremblay, Lee, Ourmazd, Abbas, Phillips, George N, and Schmidt, Marius

Subjects
Biochemistry and Cell Biology, Biological Sciences, Rare Diseases, Infectious Diseases, Good Health and Well Being, Anti-Bacterial Agents, Bacterial Proteins, Biocatalysis, Ceftriaxone, Cephalosporin Resistance, Crystallography, X-Ray, Kinetics, Lasers, Models, Molecular, Mycobacterium tuberculosis, Time Factors, beta-Lactamases, Developmental Biology
Abstract

BackgroundEver since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases.ResultsHere, we demonstrate a general method for capturing enzyme catalysis "in action" by mix-and-inject serial crystallography (MISC). Specifically, we follow the catalytic reaction of the Mycobacterium tuberculosis β-lactamase with the third-generation antibiotic ceftriaxone by time-resolved serial femtosecond crystallography. The results reveal, in near atomic detail, antibiotic cleavage and inactivation from 30 ms to 2 s.ConclusionsMISC is a versatile and generally applicable method to investigate reactions of biological macromolecules, some of which are of immense biological significance and might be, in addition, important targets for structure-based drug design. With megahertz X-ray pulse rates expected at the Linac Coherent Light Source II and the European X-ray free-electron laser, multiple, finely spaced time delays can be collected rapidly, allowing a comprehensive description of biomolecular reactions in terms of structure and kinetics from the same set of X-ray data.

Published
2018

7. Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals

Author

Casadei, Cecilia M, Tsai, Ching-Ju, Barty, Anton, Hunter, Mark S, Zatsepin, Nadia A, Padeste, Celestino, Capitani, Guido, Benner, W Henry, Boutet, Sébastien, Hau-Riege, Stefan P, Kupitz, Christopher, Messerschmidt, Marc, Ogren, John I, Pardini, Tom, Rothschild, Kenneth J, Sala, Leonardo, Segelke, Brent, Williams, Garth J, Evans, James E, Li, Xiao-Dan, Coleman, Matthew, Pedrini, Bill, and Frank, Matthias

Subjects
Inorganic Chemistry, Chemical Sciences, Physical Sciences, Bioengineering, serial crystallography, free-electron lasers, membrane proteins, two-dimensional crystals, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Condensed Matter Physics, Physical Chemistry (incl. Structural), Physical chemistry, Condensed matter physics
Abstract

Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 Å. The results show that two-dimensional serial crystallography at X-ray FELs is a suitable method to study membrane proteins to near-atomic length scales at ambient temperature. The method presented here can be extended to pump-probe studies of optically triggered structural changes on submillisecond timescales in two-dimensional crystals, which allow functionally relevant large-scale motions that may be quenched in three-dimensional crystals.

Published
2018

8. Structural enzymology using X-ray free electron lasers

Author

Kupitz, Christopher, Olmos, Jose L, Holl, Mark, Tremblay, Lee, Pande, Kanupriya, Pandey, Suraj, Oberthür, Dominik, Hunter, Mark, Liang, Mengning, Aquila, Andrew, Tenboer, Jason, Calvey, George, Katz, Andrea, Chen, Yujie, Wiedorn, Max O, Knoska, Juraj, Meents, Alke, Majriani, Valerio, Norwood, Tyler, Poudyal, Ishwor, Grant, Thomas, Miller, Mitchell D, Xu, Weijun, Tolstikova, Aleksandra, Morgan, Andrew, Metz, Markus, Martin-Garcia, Jose M, Zook, James D, Roy-Chowdhury, Shatabdi, Coe, Jesse, Nagaratnam, Nirupa, Meza, Domingo, Fromme, Raimund, Basu, Shibom, Frank, Matthias, White, Thomas, Barty, Anton, Bajt, Sasa, Yefanov, Oleksandr, Chapman, Henry N, Zatsepin, Nadia, Nelson, Garrett, Weierstall, Uwe, Spence, John, Schwander, Peter, Pollack, Lois, Fromme, Petra, Ourmazd, Abbas, Phillips, George N, and Schmidt, Marius

Subjects
Inorganic Chemistry, Chemical Sciences, Physical Sciences, Infectious Diseases, Good Health and Well Being, Physical chemistry, Condensed matter physics, Particle and high energy physics
Abstract

Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic resolution, (ii) time resolution ranging from microseconds to seconds, and (iii) convenient reaction initiation. It outruns radiation damage by using femtosecond X-ray pulses allowing damage and chemistry to be separated. Here, we demonstrate that MISC is feasible at an X-ray free electron laser by studying the reaction of M. tuberculosis ß-lactamase microcrystals with ceftriaxone antibiotic solution. Electron density maps of the apo-ß-lactamase and of the ceftriaxone bound form were obtained at 2.8 Å and 2.4 Å resolution, respectively. These results pave the way to study cyclic and non-cyclic reactions and represent a new field of time-resolved structural dynamics for numerous substrate-triggered biological reactions.

Published
2017

9. Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

Author

Pande, Kanupriya, Hutchison, Christopher DM, Groenhof, Gerrit, Aquila, Andy, Robinson, Josef S, Tenboer, Jason, Basu, Shibom, Boutet, Sébastien, DePonte, Daniel P, Liang, Mengning, White, Thomas A, Zatsepin, Nadia A, Yefanov, Oleksandr, Morozov, Dmitry, Oberthuer, Dominik, Gati, Cornelius, Subramanian, Ganesh, James, Daniel, Zhao, Yun, Koralek, Jake, Brayshaw, Jennifer, Kupitz, Christopher, Conrad, Chelsie, Roy-Chowdhury, Shatabdi, Coe, Jesse D, Metz, Markus, Xavier, Paulraj Lourdu, Grant, Thomas D, Koglin, Jason E, Ketawala, Gihan, Fromme, Raimund, Šrajer, Vukica, Henning, Robert, Spence, John CH, Ourmazd, Abbas, Schwander, Peter, Weierstall, Uwe, Frank, Matthias, Fromme, Petra, Barty, Anton, Chapman, Henry N, Moffat, Keith, van Thor, Jasper J, and Schmidt, Marius

Subjects
Biological Sciences, Chemical Sciences, Theoretical and Computational Chemistry, Bacterial Proteins, Crystallography, Isomerism, Light, Photochemical Processes, Photons, Photoreceptors, Microbial, Protein Conformation, Time Factors, General Science & Technology
Abstract

A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.

Published
2016

10. Snapshot of an oxygen intermediate in the catalytic reaction of cytochrome c oxidase

Author

Ishigami, Izumi, Lewis-Ballester, Ariel, Echelmeier, Austin, Brehm, Gerrit, Zatsepin, Nadia A., Grant, Thomas D., Coe, Jesse D., Lisova, Stella, Nelson, Garrett, Zhang, Shangji, Dobson, Zachary F., Boutet, Sébastien, Sierra, Raymond G., Batyuk, Alexander, Fromme, Petra, Fromme, Raimund, Spence, John C. H., Ros, Alexandra, Yeh, Syun-Ru, and Rousseau, Denis L.

Published
2019

11. MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography

Author

Clabbers, Max T. B., Holmes, Susannah, Muusse, Timothy W., Vajjhala, Parimala R., Thygesen, Sara J., Malde, Alpeshkumar K., Hunter, Dominic J. B., Croll, Tristan I., Flueckiger, Leonie, Nanson, Jeffrey D., Rahaman, Md. Habibur, Aquila, Andrew, Hunter, Mark S., Liang, Mengning, Yoon, Chun Hong, Zhao, Jingjing, Zatsepin, Nadia A., Abbey, Brian, Sierecki, Emma, Gambin, Yann, Stacey, Katryn J., Darmanin, Connie, Kobe, Bostjan, Xu, Hongyi, and Ve, Thomas

Published
2021
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12. Synchronous RNA conformational changes trigger ordered phase transitions in crystals

Author

Ramakrishnan, Saminathan, Stagno, Jason R., Conrad, Chelsie E., Ding, Jienyu, Yu, Ping, Bhandari, Yuba R., Lee, Yun-Tzai, Pauly, Gary, Yefanov, Oleksandr, Wiedorn, Max O., Knoska, Juraj, Oberthür, Dominik, White, Thomas A., Barty, Anton, Mariani, Valerio, Li, Chufeng, Brehm, Wolfgang, Heinz, William F., Magidson, Valentin, Lockett, Stephen, Hunter, Mark S., Boutet, Sébastien, Zatsepin, Nadia A., Zuo, Xiaobing, Grant, Thomas D., Pandey, Suraj, Schmidt, Marius, Spence, John C. H., Chapman, Henry N., and Wang, Yun-Xing

Published
2021
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13. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

Author

Kang, Yanyong, Zhou, X Edward, Gao, Xiang, He, Yuanzheng, Liu, Wei, Ishchenko, Andrii, Barty, Anton, White, Thomas A, Yefanov, Oleksandr, Han, Gye Won, Xu, Qingping, de Waal, Parker W, Ke, Jiyuan, Tan, MH Eileen, Zhang, Chenghai, Moeller, Arne, West, Graham M, Pascal, Bruce D, Van Eps, Ned, Caro, Lydia N, Vishnivetskiy, Sergey A, Lee, Regina J, Suino-Powell, Kelly M, Gu, Xin, Pal, Kuntal, Ma, Jinming, Zhi, Xiaoyong, Boutet, Sébastien, Williams, Garth J, Messerschmidt, Marc, Gati, Cornelius, Zatsepin, Nadia A, Wang, Dingjie, James, Daniel, Basu, Shibom, Roy-Chowdhury, Shatabdi, Conrad, Chelsie E, Coe, Jesse, Liu, Haiguang, Lisova, Stella, Kupitz, Christopher, Grotjohann, Ingo, Fromme, Raimund, Jiang, Yi, Tan, Minjia, Yang, Huaiyu, Li, Jun, Wang, Meitian, Zheng, Zhong, Li, Dianfan, Howe, Nicole, Zhao, Yingming, Standfuss, Jörg, Diederichs, Kay, Dong, Yuhui, Potter, Clinton S, Carragher, Bridget, Caffrey, Martin, Jiang, Hualiang, Chapman, Henry N, Spence, John CH, Fromme, Petra, Weierstall, Uwe, Ernst, Oliver P, Katritch, Vsevolod, Gurevich, Vsevolod V, Griffin, Patrick R, Hubbell, Wayne L, Stevens, Raymond C, Cherezov, Vadim, Melcher, Karsten, and Xu, H Eric

Subjects
1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Arrestin, Binding Sites, Crystallography, X-Ray, Disulfides, Humans, Lasers, Mice, Models, Molecular, Multiprotein Complexes, Protein Binding, Reproducibility of Results, Rhodopsin, Signal Transduction, X-Rays, General Science & Technology
Abstract

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ∼20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.

Published
2015

14. Toxicity of Eosinophil MBP Is Repressed by Intracellular Crystallization and Promoted by Extracellular Aggregation

Author

Soragni, Alice, Yousefi, Shida, Stoeckle, Christina, Soriaga, Angela B, Sawaya, Michael R, Kozlowski, Evelyne, Schmid, Inès, Radonjic-Hoesli, Susanne, Boutet, Sebastien, Williams, Garth J, Messerschmidt, Marc, Seibert, M Marvin, Cascio, Duilio, Zatsepin, Nadia A, Burghammer, Manfred, Riekel, Christian, Colletier, Jacques-Philippe, Riek, Roland, Eisenberg, David S, and Simon, Hans-Uwe

Subjects
Biochemistry and Cell Biology, Biological Sciences, Neurodegenerative, Brain Disorders, Neurosciences, Inflammatory and immune system, Animals, Cell Death, Cell Line, Cell Membrane, Cellulitis, DNA-Binding Proteins, Dermatitis, Atopic, Eosinophilia, Eosinophils, Epithelial Cells, Escherichia coli, Host-Pathogen Interactions, Humans, Immunity, Innate, Mice, Inbred C57BL, Nanoparticles, Secretory Vesicles, Skin, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Eosinophils are white blood cells that function in innate immunity and participate in the pathogenesis of various inflammatory and neoplastic disorders. Their secretory granules contain four cytotoxic proteins, including the eosinophil major basic protein (MBP-1). How MBP-1 toxicity is controlled within the eosinophil itself and activated upon extracellular release is unknown. Here we show how intragranular MBP-1 nanocrystals restrain toxicity, enabling its safe storage, and characterize them with an X-ray-free electron laser. Following eosinophil activation, MBP-1 toxicity is triggered by granule acidification, followed by extracellular aggregation, which mediates the damage to pathogens and host cells. Larger non-toxic amyloid plaques are also present in tissues of eosinophilic patients in a feedback mechanism that likely limits tissue damage under pathological conditions of MBP-1 oversecretion. Our results suggest that MBP-1 aggregation is important for innate immunity and immunopathology mediated by eosinophils and clarify how its polymorphic self-association pathways regulate toxicity intra- and extracellularly.

Published
2015

15. XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity

Author

Johansson, Linda C., Stauch, Benjamin, McCorvy, John D., Han, Gye Won, Patel, Nilkanth, Huang, Xi-Ping, Batyuk, Alexander, Gati, Cornelius, Slocum, Samuel T., Li, Chufeng, Grandner, Jessica M., Hao, Shuming, Olsen, Reid H. J., Tribo, Alexandra R., Zaare, Sahba, Zhu, Lan, Zatsepin, Nadia A., Weierstall, Uwe, Yous, Saïd, Stevens, Raymond C., Liu, Wei, Roth, Bryan L., Katritch, Vsevolod, and Cherezov, Vadim

Published
2019
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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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18. 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

19. 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

20. Detection of a geminate photoproduct of bovine cytochrome c oxidase by time-resolved serial femtosecond crystallography

Author

Ishigami, Izumi, primary, Carbajo, Sergio, additional, Zatsepin, Nadia, additional, Hikita, Masahide, additional, Conrad, Chelsie E., additional, Nelson, Garrett, additional, Coe, Jesse, additional, Basu, Shibom, additional, Grant, Thomas, additional, Seaberg, Matthew H., additional, Sierra, Raymond G., additional, Hunter, Mark S., additional, Fromme, Petra, additional, Fromme, Raimund, additional, Rousseau, Denis L., additional, and Yeh, Syun-Ru, additional

Published
2023
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21. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

Author

Tenboer, Jason, Basu, Shibom, Zatsepin, Nadia, Pande, Kanupriya, Milathianaki, Despina, Frank, Matthias, Hunter, Mark, Boutet, Sébastien, Williams, Garth J., Koglin, Jason E., Oberthuer, Dominik, Heymann, Michael, Kupitz, Christopher, Conrad, Chelsie, Coe, Jesse, Roy-Chowdhury, Shatabdi, Weierstall, Uwe, James, Daniel, Wang, Dingjie, Grant, Thomas, Barty, Anton, Yefanov, Oleksandr, Scales, Jennifer, Gati, Cornelius, Seuring, Carolin, Srajer, Vukica, Henning, Robert, Schwander, Peter, Fromme, Raimund, Ourmazd, Abbas, Moffat, Keith, Van Thor, Jasper J., Spence, John C. H., Fromme, Petra, Chapman, Henry N., and Schmidt, Marius

Published
2014

23. 7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source

Author

Pedrini, Bill, Tsai, Ching-Ju, Capitani, Guido, Padeste, Celestino, Hunter, Mark S., Zatsepin, Nadia A., Barty, Anton, Benner, W. Henry, Boutet, Sébastien, Feld, Geoffrey K., Hau-Riege, Stefan P., Kirian, Richard A., Kupitz, Christopher, Messerschmitt, Marc, Ogren, John I., Pardini, Tommaso, Segelke, Brent, Williams, Garth J., Spence, John C. H., Abela, Rafael, Coleman, Matthew, Evans, James E., Schertler, Gebhard F. X., Frank, Matthias, and Li, Xiao-Dan

Published
2014

24. Serial Femtosecond Crystallography of G Protein-Coupled Receptors

Author

Liu, Wei, Wacker, Daniel, Gati, Cornelius, Han, Gye Won, James, Daniel, Wang, Dingjie, Nelson, Garrett, Weierstall, Uwe, Katritch, Vsevolod, Barty, Anton, Zatsepin, Nadia A., Li, Dianfan, Messerschmidt, Marc, Boutet, Sébastien, Williams, Garth J., Koglin, Jason E., Seibert, M. Marvin, Wang, Chong, Shah, Syed T. A., Basu, Shibom, Fromme, Raimund, Kupitz, Christopher, Rendek, Kimberley N., Grotjohann, Ingo, Fromme, Petra, Kirian, Richard A., Beyerlein, Kenneth R., White, Thomas A., Chapman, Henry N., Caffrey, Martin, Spence, John C. H., Stevens, Raymond C., and Cherezov, Vadim

Published
2013
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25. 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 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, 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, 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

Published
2018
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26. Detection of a Geminate Photoproduct of Bovine Cytochrome cOxidase by Time-Resolved Serial Femtosecond Crystallography

Author

Ishigami, Izumi, Carbajo, Sergio, Zatsepin, Nadia, Hikita, Masahide, Conrad, Chelsie E., Nelson, Garrett, Coe, Jesse, Basu, Shibom, Grant, Thomas, Seaberg, Matthew H., Sierra, Raymond G., Hunter, Mark S., Fromme, Petra, Fromme, Raimund, Rousseau, Denis L., and Yeh, Syun-Ru

Abstract

Cytochrome coxidase (CcO) is a large membrane-bound hemeprotein that catalyzes the reduction of dioxygen to water. Unlike classical dioxygen binding hemeproteins with a heme bgroup in their active sites, CcO has a unique binuclear center (BNC) composed of a copper atom (CuB) and a heme a3iron, where O2binds and is reduced to water. CO is a versatile O2surrogate in ligand binding and escape reactions. Previous time-resolved spectroscopic studies of the CO complexes of bovine CcO (bCcO) revealed that photolyzing CO from the heme a3iron leads to a metastable intermediate (CuB-CO), where CO is bound to CuB, before it escapes out of the BNC. Here, with a pump-probe based time-resolved serial femtosecond X-ray crystallography, we detected a geminate photoproduct of the bCcO–CO complex, where CO is dissociated from the heme a3iron and moved to a temporary binding site midway between the CuBand the heme a3iron, while the locations of the two metal centers and the conformation of Helix-X, housing the proximal histidine ligand of the heme a3iron, remain in the CO complex state. This new structure, combined with other reported structures of bCcO, allows for a clearer definition of the ligand dissociation trajectory as well as the associated protein dynamics.

Published
2023
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28. Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser

Author

Redecke, Lars, Nass, Karol, Deponte, Daniel P., White, Thomas A., Rehders, Dirk, Barty, Anton, Stellato, Francesco, Liang, Mengning, Barends, Thomas R.M., Boutet, Sébastien, Williams, Garth J., Messerschmidt, Marc, Seibert, M. Marvin, Aquila, Andrew, Arnlund, David, Bajt, Sasa, Barth, Torsten, Bogan, Michael J., Caleman, Carl, Chao, Tzu-Chiao, Doak, R. Bruce, Fleckenstein, Holger, Frank, Matthias, Fromme, Raimund, Galli, Lorenzo, Grotjohann, Ingo, Hunter, Mark S., Johansson, Linda C., Kassemeyer, Stephan, Katona, Gergely, Kirian, Richard A., Koopmann, Rudolf, Kupitz, Chris, Lomb, Lukas, Martin, Andrew V., Mogk, Stefan, Neutze, Richard, Shoeman, Robert L., Steinbrener, Jan, Timneanu, Nicusor, Wang, Dingjie, Weierstall, Uwe, Zatsepin, Nadia A., Spence, John C. H., Fromme, Petra, Schlichting, Ilme, Duszenko, Michael, Betzel, Christian, and Chapman, Henry N.

Published
2013
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29. High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

Author

Boutet, Sébastien, Lomb, Lukas, Williams, Garth J., Barends, Thomas R. M., Aquila, Andrew, Doak, R. Bruce, Weierstall, Uwe, DePonte, Daniel P., Steinbrener, Jan, Shoeman, Robert L., Messerschmidt, Marc, Barty, Anton, White, Thomas A., Kassemeyer, Stephan, Kirian, Richard A., Seibert, M. Marvin, Montanez, Paul A., Kenney, Chris, Herbst, Ryan, Hart, Philip, Pines, Jack, Haller, Gunther, Gruner, Sol M., Philipp, Hugh T., Tate, Mark W., Hromalik, Marianne, Koerner, Lucas J., van Bakel, Niels, Morse, John, Ghonsalves, Wilfred, Arnlund, David, Bogan, Michael J., Caleman, Carl, Fromme, Raimund, Hampton, Christina Y., Hunter, Mark S., Johansson, Linda C., Katona, Gergely, Kupitz, Christopher, Liang, Mengning, Martin, Andrew V., Nass, Karol, Redecke, Lars, Stellato, Francesco, Timneanu, Nicusor, Wang, Dingjie, Zatsepin, Nadia A., Schafer, Donald, Defever, James, Neutze, Richard, Fromme, Petra, Spence, John C. H., Chapman, Henry N., and Schlichting, Ilme

Published
2012
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30. 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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31. Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser

Author

Kupitz, Christopher, Basu, Shibom, Grotjohann, Ingo, Fromme, Raimund, Zatsepin, Nadia A., Rendek, Kimberly N., and Hunter, Mark S.

Subjects
Crystallography -- Research, Free electron lasers -- Research, Photosystem II -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Femtosecond X-ray pulses were used to obtain diffraction data on photosystem II, revealing conformational changes as the complex transitions from the dark S.sub.1 state to the double-pumped S.sub.3 state; the time-resolved serial femtosecond crystallography technique enables structural determination of protein conformations that are highly prone to traditional radiation damage. An X-ray snapshot of photosystem II structure It has recently been shown that extremely short and intense radiation pulses from X-ray free-electron lasers can be used to obtain diffraction data on nanometre- to micrometre-sized protein crystals before the crystal suffers radiation damage. The hope is that this 'serial femtosecond crystallography' (SFX) approach will produce structures of proteins and protein complexes that do not yield well-ordered macroscopic crystals. These authors collected time-resolved SFX data on small crystals of photosystem II of photosynthesis during its transition from the 'dark' S1 state to the double-excited S3 state. At present the resolution of this technique is moderate, but it is sufficient to reveal significant conformational changes at the Mn.sub.4CaO.sub.5 cluster at the heart of the oxygen evolving complex and at the electron acceptor site. Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere.sup.1. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S.sub.0 to S.sub.4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed.sup.2 technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S.sub.1 state and after double laser excitation (putative S.sub.3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn.sub.4CaO.sub.5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn.sub.3CaO.sub.x cubane in the S.sub.2 to S.sub.3 transition, as predicted by spectroscopic and computational studies.sup.3,4. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules., Author(s): Christopher Kupitz [sup.1] , Shibom Basu [sup.1] , Ingo Grotjohann [sup.1] , Raimund Fromme [sup.1] , Nadia A. Zatsepin [sup.2] , Kimberly N. Rendek [sup.1] , Mark S. Hunter [...]

Published
2014
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32. PROTEIN STRUCTURE: Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

Author

Pande, Kanupriya, Hutchison, Christopher D. M., Groenhof, Gerrit, Aquila, Andy, Robinson, Josef S., Tenboer, Jason, Basu, Shibom, Boutet, Sébastien, DePonte, Daniel P., Liang, Mengning, White, Thomas A., Zatsepin, Nadia A., Yefanov, Oleksandr, Morozov, Dmitry, Oberthuer, Dominik, Gati, Cornelius, Subramanian, Ganesh, James, Daniel, Zhao, Yun, Koralek, Jake, Brayshaw, Jennifer, Kupitz, Christopher, Conrad, Chelsie, Roy-Chowdhury, Shatabdi, Coe, Jesse D., Metz, Markus, Xavier, Paulraj Lourdu, Grant, Thomas D., Koglin, Jason E., Ketawala, Gihan, Fromme, Raimund, Šrajer, Vukica, Henning, Robert, Spence, John C. H., Ourmazd, Abbas, Schwander, Peter, Weierstall, Uwe, Frank, Matthias, Fromme, Petra, Barty, Anton, Chapman, Henry N., Moffat, Keith, van Thor, Jasper J., and Schmidt, Marius

Published
2016
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33. STRUCTURAL BIOLOGY: Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

Author

Tenboer, Jason, Basu, Shibom, Zatsepin, Nadia, Pande, Kanupriya, Milathianaki, Despina, Frank, Matthias, Hunter, Mark, Boutet, Sébastien, Williams, Garth J., Koglin, Jason E., Oberthuer, Dominik, Heymann, Michael, Kupitz, Christopher, Conrad, Chelsie, Coe, Jesse, Roy-Chowdhury, Shatabdi, Weierstall, Uwe, James, Daniel, Wang, Dingjie, Grant, Thomas, Barty, Anton, Yefanov, Oleksandr, Scales, Jennifer, Gati, Cornelius, Seuring, Carolin, Srajer, Vukica, Henning, Robert, Schwander, Peter, Fromme, Raimund, Ourmazd, Abbas, Moffat, Keith, Van Thor, Jasper J., Spence, John C. H., Fromme, Petra, Chapman, Henry N., and Schmidt, Marius

Published
2014
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34. MyD88 TIR domain higher-order assembly interactions revealed by serial femtosecond crystallography

Author

Holmes, Susannah, primary, Clabbers, Max T. B., additional, Muusse, Timothy W., additional, Vajjhala, Parimala R., additional, Thygesen, Sara J., additional, Malde, Alpeshkumar K., additional, Hunter, Dominic J. B., additional, Croll, Tristan I., additional, Flueckiger, Leonie, additional, Nanson, Jeffrey D., additional, Rahaman, Md. Habibur, additional, Aquila, Andrew, additional, Hunter, Mark S., additional, Liang, Mengning, additional, Yoon, Chun Hong, additional, Zhao, Jingjing, additional, Zatsepin, Nadia A., additional, Abbey, Brian, additional, Sierecki, Emma, additional, Gambin, Yann, additional, Stacey, Katryn J., additional, Darmanin, Connie, additional, Kobe, Bostjan, additional, Xu, Hongyi, additional, and Ve, Thomas, additional

Published
2021
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35. MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography

Author

Clabbers, Max T. B., primary, Holmes, Susannah, additional, Muusse, Timothy W., additional, Vajjhala, Parimala, additional, Thygesen, Sara J., additional, Malde, Alpeshkumar K., additional, Hunter, Dominic J. B., additional, Croll, Tristan I., additional, Flueckiger, Leonie, additional, Nanson, Jeffrey D., additional, Rahaman, M. Habibur, additional, Aquila, Andrew, additional, Hunter, Mark S., additional, Liang, Mengning, additional, Yoon, Chun Hong, additional, Zhao, Jingjing, additional, Zatsepin, Nadia A., additional, Abbey, Brian, additional, Sierecki, Emma, additional, Gambin, Yann, additional, Stacey, Katryn J., additional, Darmanin, Connie, additional, Kobe, Bostjan, additional, Xu, Hongyi, additional, and Ve, Thomas, additional

Published
2021
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36. Ultrafast Membrane Protein Dynamics Revealed by X-Ray Scattering with a Femtosecond Free-Electron Laser

Author

Grant, Thomas D., primary, Perera, Suchithranga M.D.C., additional, Salas-Estrada, Leslie A., additional, Struts, Andrey V., additional, Chawla, Udeep, additional, Fried, Steven D.E., additional, Weerasinghe, Nipuna, additional, Karpos, Kostantinos, additional, Meza, Domingo, additional, Zatsepin, Nadia A., additional, Grossfield, Alan, additional, Mendez, Derek, additional, Fromme, Petra, additional, Kirian, Richard A., additional, and Brown, Michael F., additional

Published
2021
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37. 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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38. XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia

Author

Zook, James, primary, Shekhar, Mrinal, additional, Hansen, Debra, additional, Conrad, Chelsie, additional, Grant, Thomas, additional, Gupta, Chitrak, additional, White, Thomas, additional, Barty, Anton, additional, Basu, Shibom, additional, Zhao, Yun, additional, Zatsepin, Nadia, additional, Ishchenko, Andrii, additional, Batyuk, Alex, additional, Gati, Cornelius, additional, Li, Chufeng, additional, Galli, Lorenzo, additional, Coe, Jesse, additional, Hunter, Mark, additional, Liang, Meng, additional, Weierstall, Uwe, additional, Nelson, Garret, additional, James, Daniel, additional, Stauch, Benjamin, additional, Craciunescu, Felicia, additional, Thifault, Darren, additional, Liu, Wei, additional, Cherezov, Vadim, additional, Singharoy, Abhishek, additional, and Fromme, Petra, additional

Published
2020
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39. 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

40. Additional file 1: of Enzyme intermediates captured 'on the fly' by mix-and-inject serial crystallography

Author

Olmos, Jose, Pandey, Suraj, Martin-Garcia, Jose, Calvey, George, Katz, Andrea, Knoska, Juraj, Kupitz, Christopher, Hunter, Mark, Mengning Liang, Oberthuer, Dominik, Yefanov, Oleksandr, Wiedorn, Max, Heyman, Michael, Holl, Mark, Kanupriya Pande, Barty, Anton, Miller, Mitchell, Stern, Stephan, Shatabdi Roy-Chowdhury, Coe, Jesse, Nirupa Nagaratnam, Zook, James, Verburgt, Jacob, Norwood, Tyler, Ishwor Poudyal, Xu, David, Koglin, Jason, Seaberg, Matthew, Zhao, Yun, Saša Bajt, Grant, Thomas, Mariani, Valerio, Nelson, Garrett, Subramanian, Ganesh, Euiyoung Bae, Fromme, Raimund, Fung, Russell, Schwander, Peter, Frank, Matthias, White, Thomas, Weierstall, Uwe, Zatsepin, Nadia, Spence, John, Fromme, Petra, Chapman, Henry, Pollack, Lois, Tremblay, Lee, Ourmazd, Abbas, Phillips, George, and Schmidt, Marius

Abstract

Figure S1. Schematics of the short-time-point mixing injector. Figure S2. Selected views of the CEF binding site in the BlaC shard crystals including simulated annealing omit maps. Figure S3. Structural details, and simulated annealing omit maps, shard crystal form, subunit B (stereo representation, from 30 ms to 2 s). Figure S4. Structural details and simulated annealing omit maps, shard crystal form, subunit D (stereo representation, from 30 ms to 2 s). Figure S5. Structural details, and simulated annealing omit maps, needle crystal form (stereo representation, from 30 ms to 2 s). Figure S6. Backside view of the catalytic cleft of BlaC in the shard crystal form, structural details and simulated annealing omit maps (stereo representation, selected time points). Figure S7. 2mFo-DFc electron density in the catalytic clefts of BlaC in the shard crystal form (stereo representation, from 30 ms to 2 s). Figure S8. 2mFo-DFc electron density and structural details in the catalytic clefts of BlaC in the needle crystal form (stereo representation from 30 ms to 2 s). Figure S9. Details in the catalytic cleft of subunit B in the shard crystal form at 500 ms including the stacked CEF, 2FoFc maps, and simulated annealing omit maps (stereo representation). Figure S10. The catalytic cleft of BlaC, further details, including a difference map between the 500 ms and 100 ms time points. Figure S11. Crystal packing in shards and needles. Figure S12. Dynamic light scattering results. Table S1. B-factors for CEF species observed in the shard crystals at different time delays. (PDF 1646 kb)

Published
2018
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41. ASU Compact XFEL

Author

Graves, William, Chen, Joe, Fromme, Petra, Holl, Mark, Hong, Kyung-Han, Kirian, Richard, Limborg-Deprey, Cecile, Malin, Lucas, Moncton, David, Nanni, Emilio, Schmidt, Kevin, Spence, John, Underhill, Matthew, Weierstall, Uwe, Zatsepin, Nadia, and Zhang, Chenou

Subjects
010308 nuclear & particles physics, Seeded FELs, 0103 physical sciences, Physics::Accelerator Physics, 010306 general physics, 01 natural sciences, Accelerator Physics
Abstract

ASU is pursuing a concept for a compact x-ray FEL (CXFEL) that uses nanopatterning of the electron beam via electron diffraction and emittance exchange to enable fully coherent x-ray output from electron beams with an energy of a few tens of MeV. This low energy is enabled by nanobunching and use of a short-pulse laser field as an undulator, resulting in an XFEL with 10 m total length and modest cost. The method of electron bunching is deterministic and flexible, rather than dependent on SASE amplification, so that the x-ray output is coherent in time and frequency. The phase of the x-ray pulse can be controlled and manipulated with this method so that new opportunities for ultrafast x-ray science are enabled using e.g. attosecond pulses, very narrow linewidths, or extremely precise timing among multiple pulses with different colors. These properties may be transferred to large XFELs through seeding with the CXFEL beam. Construction of the CXFEL accelerator and laboratory are underway, along with initial experiments to demonstrate nanopatterning via electron diffraction. An overview of the methods, project, and new science enabled are presented., Proceedings of the 38th Int. Free Electron Laser Conf., FEL2017, Santa Fe, NM, USA

Published
2018
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43. Toward G protein-coupled receptor structure-based drug design using X-ray lasers

Author

Ishchenko, Andrii, primary, Stauch, Benjamin, additional, Han, Gye Won, additional, Batyuk, Alexander, additional, Shiriaeva, Anna, additional, Li, Chufeng, additional, Zatsepin, Nadia, additional, Weierstall, Uwe, additional, Liu, Wei, additional, Nango, Eriko, additional, Nakane, Takanori, additional, Tanaka, Rie, additional, Tono, Kensuke, additional, Joti, Yasumasa, additional, Iwata, So, additional, Moraes, Isabel, additional, Gati, Cornelius, additional, and Cherezov, Vadim, additional

Published
2019
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45. 3D printed droplet generation devices for serial femtosecond crystallography enabled by surface coating

Author

Echelmeier, Austin, primary, Kim, Daihyun, additional, Cruz Villarreal, Jorvani, additional, Coe, Jesse, additional, Quintana, Sebastian, additional, Brehm, Gerrit, additional, Egatz-Gomez, Ana, additional, Nazari, Reza, additional, Sierra, Raymond G., additional, Koglin, Jason E., additional, Batyuk, Alexander, additional, Hunter, Mark S., additional, Boutet, Sébastien, additional, Zatsepin, Nadia, additional, Kirian, Richard A., additional, Grant, Thomas D., additional, Fromme, Petra, additional, and Ros, Alexandra, additional

Published
2019
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47. Structure and dynamics of chloride ion pumping rhodopsin revealed by time-resolved SFX and atomic molecular dynamics simulations

Author

Liu, Haiguang, primary, Yun, Ji-Hye, additional, Li, Xuanxuan, additional, Park, Jae-Hyun, additional, Jin, Zeyu, additional, Shi, Yingchen, additional, Li, Chufeng, additional, Hu, Hao, additional, Wang, Yang, additional, Pandey, Suraj, additional, Carbajo, Sergio, additional, Zatsepin, Nadia, additional, Weierstall, Uwe, additional, Hunter, Mark, additional, Liang, Meng, additional, Lane, T. J., additional, Yoon, Chun Hong, additional, Sierra, Raymond, additional, Schmidt, Marius, additional, and Lee, Weontae, additional

Published
2019
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48. High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source

Author

Martin-Garcia, Jose M., primary, Zhu, Lan, additional, Mendez, Derek, additional, Lee, Ming-Yue, additional, Chun, Eugene, additional, Li, Chufeng, additional, Hu, Hao, additional, Subramanian, Ganesh, additional, Kissick, David, additional, Ogata, Craig, additional, Henning, Robert, additional, Ishchenko, Andrii, additional, Dobson, Zachary, additional, Zhang, Shangji, additional, Weierstall, Uwe, additional, Spence, John C. H., additional, Fromme, Petra, additional, Zatsepin, Nadia A., additional, Fischetti, Robert F., additional, Cherezov, Vadim, additional, and Liu, Wei, additional

Published
2019
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49. Structure Determination of Active Full Length Human Taspase1: Towards Novel Anti-Cancer Therapeutics

Author

Garcia, Jose M., primary, Nagaratnam, Nirupa, additional, Jernigan, Rebecca, additional, Ketawala, Gihan, additional, Delker, Silvia, additional, Edwards, Thomas, additional, Mendez, Derek, additional, Li, Chufeng, additional, Zatsepin, Nadia, additional, Fromme, Raimund, additional, Tong, Liang, additional, Schneider, Joel, additional, Hsieh, James, additional, Flint, Andrew, additional, and Fromme, Petra, additional

Published
2019
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50. Study of Ultra-Fast Rhodopsin Activation Dynamics with Molecular Dynamics Simulations

Author

Salas, Letty, primary, Mendez, Derek, additional, Meza-Aguilar, José Domingo, additional, Perera, Suchithranga M.D.C., additional, Singharoy, Abhishek, additional, Struts, Andrey V., additional, Zatsepin, Nadia A., additional, Kirian, Richard A., additional, Grant, Thomas D., additional, Fromme, Petra, additional, Brown, Michael F., additional, and Grossfield, Alan, additional

Published
2019
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