Search

Your search keyword '"Kupitz, Christopher"' showing total 269 results
Start Over Author "Kupitz, Christopher"
269 results on '"Kupitz, Christopher"'

52. 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
Full Text
View/download PDF

54. Time-resolved serial femtosecond crystallography at the European XFEL

Author

Pandey, Suraj, primary, Bean, Richard, additional, Sato, Tokushi, additional, Poudyal, Ishwor, additional, Bielecki, Johan, additional, Cruz Villarreal, Jorvani, additional, Yefanov, Oleksandr, additional, Mariani, Valerio, additional, White, Thomas A., additional, Kupitz, Christopher, additional, Hunter, Mark, additional, Abdellatif, Mohamed H., additional, Bajt, Saša, additional, Bondar, Valerii, additional, Echelmeier, Austin, additional, Doppler, Diandra, additional, Emons, Moritz, additional, Frank, Matthias, additional, Fromme, Raimund, additional, Gevorkov, Yaroslav, additional, Giovanetti, Gabriele, additional, Jiang, Man, additional, Kim, Daihyun, additional, Kim, Yoonhee, additional, Kirkwood, Henry, additional, Klimovskaia, Anna, additional, Knoska, Juraj, additional, Koua, Faisal H. M., additional, Letrun, Romain, additional, Lisova, Stella, additional, Maia, Luis, additional, Mazalova, Victoria, additional, Meza, Domingo, additional, Michelat, Thomas, additional, Ourmazd, Abbas, additional, Palmer, Guido, additional, Ramilli, Marco, additional, Schubert, Robin, additional, Schwander, Peter, additional, Silenzi, Alessandro, additional, Sztuk-Dambietz, Jolanta, additional, Tolstikova, Alexandra, additional, Chapman, Henry N., additional, Ros, Alexandra, additional, Barty, Anton, additional, Fromme, Petra, additional, Mancuso, Adrian P., additional, and Schmidt, Marius, additional

Published
2019
Full Text
View/download PDF

55. 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

56. Time-resolved cryogenic electron tomography for the study of transient cellular processes

Author

Yoniles, Joseph, Summers, Jacob A., Zielinski, Kara A., Antolini, Cali, Panjalingam, Mayura, Lisova, Stella, Moss, Frank R., Di Perna, Maximus Aldo, Kupitz, Christopher, Hunter, Mark S., Pollack, Lois, Wakatsuki, Soichi, and Dahlberg, Peter D.

Abstract

Cryogenic electron tomography (cryo-ET) is the highest resolution imaging technique applicable to the life sciences, enabling subnanometer visualization of specimens preserved in their near native states. The rapid plunge freezing process used to prepare samples lends itself to time-resolved studies, which researchers have pursued for in vitro samples for decades. Here, we focus on developing a freezing apparatus for time-resolved studies in situ. The device mixes cellular samples with solution-phase stimulants before spraying them directly onto an electron microscopy grid that is transiting into cryogenic liquid ethane. By varying the flow rates of cell and stimulant solutions within the device, we can control the reaction time from tens of milliseconds to over a second before freezing. In a proof-of-principle demonstration, the freezing method is applied to a model bacterium, Caulobacter crescentus,mixed with an acidic buffer. Through cryo-ET we resolved structural changes throughout the cell, including surface-layer protein dissolution, outer membrane deformation, and cytosolic rearrangement, all within 1.5 s of reaction time. This new approach, Time-Resolved cryo-ET (TR-cryo-ET), enhances the capabilities of cryo-ET by incorporating a subsecond temporal axis and enables the visualization of induced structural changes at the molecular, organelle, or cellular level.

Published
2024
Full Text
View/download PDF

57. 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
Full Text
View/download PDF

58. High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures

Author

Sanchez, Juan C., primary, Carrillo, Melissa, additional, Pandey, Suraj, additional, Noda, Moraima, additional, Aldama, Luis, additional, Feliz, Denisse, additional, Claesson, Elin, additional, Wahlgren, Weixiao Yuan, additional, Tracy, Gregory, additional, Duong, Phu, additional, Nugent, Angela C., additional, Field, Andrew, additional, Šrajer, Vukica, additional, Kupitz, Christopher, additional, Iwata, So, additional, Nango, Eriko, additional, Tanaka, Rie, additional, Tanaka, Tomoyuki, additional, Fangjia, Luo, additional, Tono, Kensuke, additional, Owada, Shigeki, additional, Westenhoff, Sebastian, additional, Schmidt, Marius, additional, and Stojković, Emina A., additional

Published
2019
Full Text
View/download PDF

59. X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis

Author

Jensen, Scott C., primary, Sullivan, Brendan, additional, Hartzler, Daniel A., additional, Aguilar, Jose Meza, additional, Awel, Salah, additional, Bajt, Saša, additional, Basu, Shibom, additional, Bean, Richard, additional, Chapman, Henry N., additional, Conrad, Chelsie, additional, Frank, Matthias, additional, Fromme, Raimund, additional, Martin-Garcia, Jose M., additional, Grant, Thomas D., additional, Heymann, Michael, additional, Hunter, Mark S., additional, Ketawala, Gihan, additional, Kirian, Richard A., additional, Knoska, Juraj, additional, Kupitz, Christopher, additional, Li, Xuanxuan, additional, Liang, Mengning, additional, Lisova, Stella, additional, Mariani, Valerio, additional, Mazalova, Victoria, additional, Messerschmidt, Marc, additional, Moran, Michael, additional, Nelson, Garrett, additional, Oberthür, Dominik, additional, Schaffer, Alex, additional, Sierra, Raymond G., additional, Vaughn, Natalie, additional, Weierstall, Uwe, additional, Wiedorn, Max O., additional, Xavier, P. Lourdu, additional, Yang, Jay-How, additional, Yefanov, Oleksandr, additional, Zatsepin, Nadia A., additional, Aquila, Andrew, additional, Fromme, Petra, additional, Boutet, Sébastien, additional, Seidler, Gerald T., additional, and Pushkar, Yulia, additional

Published
2018
Full Text
View/download PDF

60. 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

61. 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
Full Text
View/download PDF

62. Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome

Author

Woitowich, Nicole C., primary, Halavaty, Andrei S., additional, Waltz, Patricia, additional, Kupitz, Christopher, additional, Valera, Joseph, additional, Tracy, Gregory, additional, Gallagher, Kevin D., additional, Claesson, Elin, additional, Nakane, Takanori, additional, Pandey, Suraj, additional, Nelson, Garrett, additional, Tanaka, Rie, additional, Nango, Eriko, additional, Mizohata, Eiichi, additional, Owada, Shigeki, additional, Tono, Kensure, additional, Joti, Yasumasa, additional, Nugent, Angela C., additional, Patel, Hardik, additional, Mapara, Ayesha, additional, Hopkins, James, additional, Duong, Phu, additional, Bizhga, Dorina, additional, Kovaleva, Svetlana E., additional, St. Peter, Rachael, additional, Hernandez, Cynthia N., additional, Ozarowski, Wesley B., additional, Roy-Chowdhuri, Shatabdi, additional, Yang, Jay-How, additional, Edlund, Petra, additional, Takala, Heikki, additional, Ihalainen, Janne, additional, Brayshaw, Jennifer, additional, Norwood, Tyler, additional, Poudyal, Ishwor, additional, Fromme, Petra, additional, Spence, John C. H., additional, Moffat, Keith, additional, Westenhoff, Sebastian, additional, Schmidt, Marius, additional, and Stojković, Emina A., additional

Published
2018
Full Text
View/download PDF

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

Author

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

Published
2018
Full Text
View/download PDF

64. 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
Full Text
View/download PDF

65. Enzyme Intermediates Captured “on-the-fly” by Mix-and-Inject Serial Crystallography

Author

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

Published
2017
Full Text
View/download PDF

66. 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
Full Text
View/download PDF

67. Structural enzymology using X-ray free electron lasers

Author

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

Published
2016
Full Text
View/download PDF

68. X‑ray Emission Spectroscopy at X‑ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis.

Author

Jensen, Scott C., Sullivan, Brendan, Hartzler, Daniel A., Aguilar, Jose Meza, Awel, Salah, Bajt, Saša, Basu, Shibom, Bean, Richard, Chapman, Henry N., Conrad, Chelsie, Frank, Matthias, Fromme, Raimund, Martin-Garcia, Jose M., Grant, Thomas D., Heymann, Michael, Hunter, Mark S., Ketawala, Gihan, Kirian, Richard A., Knoska, Juraj, and Kupitz, Christopher

Published
2019
Full Text
View/download PDF

69. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

Author

University of Helsinki, Medicum, Edlund, Petra, Takala, Heikki, Claesson, Elin, Henry, Leocadie, Dods, Robert, Lehtivuori, Heli, Panman, Matthijs, Pande, Kanupriya, White, Thomas, Nakane, Takanori, Berntsson, Oskar, Gustavsson, Emil, Bath, Petra, Modi, Vaibhav, Roy-Chowdhury, Shatabdi, Zook, James, Berntsen, Peter, Pandey, Suraj, Poudyal, Ishwor, Tenboer, Jason, Kupitz, Christopher, Barty, Anton, Fromme, Petra, Koralek, Jake D., Tanaka, Tomoyuki, Spence, John, Liang, Mengning, Hunter, Mark S., Boutet, Sebastien, Nango, Eriko, Moffat, Keith, Groenhof, Gerrit, Ihalainen, Janne, Stojkovic, Emina A., Schmidt, Marius, Westenhoff, Sebastian, University of Helsinki, Medicum, Edlund, Petra, Takala, Heikki, Claesson, Elin, Henry, Leocadie, Dods, Robert, Lehtivuori, Heli, Panman, Matthijs, Pande, Kanupriya, White, Thomas, Nakane, Takanori, Berntsson, Oskar, Gustavsson, Emil, Bath, Petra, Modi, Vaibhav, Roy-Chowdhury, Shatabdi, Zook, James, Berntsen, Peter, Pandey, Suraj, Poudyal, Ishwor, Tenboer, Jason, Kupitz, Christopher, Barty, Anton, Fromme, Petra, Koralek, Jake D., Tanaka, Tomoyuki, Spence, John, Liang, Mengning, Hunter, Mark S., Boutet, Sebastien, Nango, Eriko, Moffat, Keith, Groenhof, Gerrit, Ihalainen, Janne, Stojkovic, Emina A., Schmidt, Marius, and Westenhoff, Sebastian

Abstract

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 angstrom resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 angstrom resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.

Published
2016

73. Ternary structure reveals mechanism of a membrane diacylglycerol kinase

Author

Li, Dianfan, primary, Stansfeld, Phillip J., additional, Sansom, Mark S. P., additional, Keogh, Aaron, additional, Vogeley, Lutz, additional, Howe, Nicole, additional, Lyons, Joseph A., additional, Aragao, David, additional, Fromme, Petra, additional, Fromme, Raimund, additional, Basu, Shibom, additional, Grotjohann, Ingo, additional, Kupitz, Christopher, additional, Rendek, Kimberley, additional, Weierstall, Uwe, additional, Zatsepin, Nadia A., additional, Cherezov, Vadim, additional, Liu, Wei, additional, Bandaru, Sateesh, additional, English, Niall J., additional, Gati, Cornelius, additional, Barty, Anton, additional, Yefanov, Oleksandr, additional, Chapman, Henry N., additional, Diederichs, Kay, additional, Messerschmidt, Marc, additional, Boutet, Sébastien, additional, Williams, Garth J., additional, Marvin Seibert, M., additional, and Caffrey, Martin, additional

Published
2015
Full Text
View/download PDF

74. Improving resolution in serial crystallography

Author

Ayyer, Kartik, primary, Yefanov, Oleksandr M., additional, Oberthuer, Dominik, additional, Chowdhury, Shatabdi, additional, Galli, Lorenzo, additional, Mariani, Valerio, additional, Basu, Shibom, additional, Coe, Jesse, additional, Conrad, Chelsie E., additional, Fromme, Raimund, additional, Doerner, Katerina, additional, Frank, Matthias, additional, James, Daniel, additional, Kupitz, Christopher, additional, Metz, Markus, additional, Nelson, Garrett, additional, Paulraj, Xavier L., additional, Beyerlein, Kenneth, additional, Schmidt, Marius, additional, Sarrou, Iosifina, additional, Spence, John C. H., additional, Weierstall, Uwe, additional, White, Thomas A., additional, Yang, Jayhow, additional, Zatsepin, Nadia A., additional, Zhao, Yun, additional, Liang, Mengning, additional, Aquila, Andrew, additional, Hunter, Mark S., additional, Robinson, Joseph S., additional, Koglin, Jason E., additional, Boutet, Sébastien, additional, Fromme, Petra, additional, Barty, Anton, additional, and Chapman, Henry N., additional

Published
2015
Full Text
View/download PDF

75. A novel inert crystal delivery medium for serial femtosecond crystallography

Author

Conrad, Chelsie E., primary, Basu, Shibom, additional, James, Daniel, additional, Wang, Dingjie, additional, Schaffer, Alexander, additional, Roy-Chowdhury, Shatabdi, additional, Zatsepin, Nadia A., additional, Aquila, Andrew, additional, Coe, Jesse, additional, Gati, Cornelius, additional, Hunter, Mark S., additional, Koglin, Jason E., additional, Kupitz, Christopher, additional, Nelson, Garrett, additional, Subramanian, Ganesh, additional, White, Thomas A., additional, Zhao, Yun, additional, Zook, James, additional, Boutet, Sébastien, additional, Cherezov, Vadim, additional, Spence, John C. H., additional, Fromme, Raimund, additional, Weierstall, Uwe, additional, and Fromme, Petra, additional

Published
2015
Full Text
View/download PDF

76. Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser

Author

Arnlund, David, Johansson, Linda C, Wickstrand, Cecilia, Barty, Anton, Williams, Garth J, Malmerberg, Erik, Davidsson, Jan, Milathianaki, Despina, DePonte, Daniel P, Shoeman, Robert L, Wang, Dingjie, James, Daniel, Katona, Gergely, Westenhoff, Sebastian, White, Thomas A, Aquila, Andrew, Bari, Sadia, Berntsen, Peter, Bogan, Mike, van Driel, Tim Brandt, Doak, R Bruce, Kjær, Kasper Skov, Frank, Matthias, Fromme, Raimund, Grotjohann, Ingo, Henning, Robert, Hunter, Mark S, Kirian, Richard A, Kosheleva, Irina, Kupitz, Christopher, Liang, Mengning, Martin, Andrew V, Nielsen, Martin Meedom, Messerschmidt, Marc, Seibert, M Marvin, Sjöhamn, Jennie, Stellato, Francesco, Weierstall, Uwe, Zatsepin, Nadia A, Spence, John C H, Fromme, Petra, Schlichting, Ilme, Boutet, Sébastien, Groenhof, Gerrit, Chapman, Henry N, Neutze, Richard, Arnlund, David, Johansson, Linda C, Wickstrand, Cecilia, Barty, Anton, Williams, Garth J, Malmerberg, Erik, Davidsson, Jan, Milathianaki, Despina, DePonte, Daniel P, Shoeman, Robert L, Wang, Dingjie, James, Daniel, Katona, Gergely, Westenhoff, Sebastian, White, Thomas A, Aquila, Andrew, Bari, Sadia, Berntsen, Peter, Bogan, Mike, van Driel, Tim Brandt, Doak, R Bruce, Kjær, Kasper Skov, Frank, Matthias, Fromme, Raimund, Grotjohann, Ingo, Henning, Robert, Hunter, Mark S, Kirian, Richard A, Kosheleva, Irina, Kupitz, Christopher, Liang, Mengning, Martin, Andrew V, Nielsen, Martin Meedom, Messerschmidt, Marc, Seibert, M Marvin, Sjöhamn, Jennie, Stellato, Francesco, Weierstall, Uwe, Zatsepin, Nadia A, Spence, John C H, Fromme, Petra, Schlichting, Ilme, Boutet, Sébastien, Groenhof, Gerrit, Chapman, Henry N, and Neutze, Richard

Abstract

We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast global conformational change that arises within picoseconds and precedes the propagation of heat through the protein. This provides direct structural evidence for a 'protein quake': the hypothesis that proteins rapidly dissipate energy through quake-like structural motions.

Published
2014
Full Text
View/download PDF

77. Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography

Author

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

Abstract

Lipidic cubic phase (LCP) crystallization has proven successful for high-resolution structure determination of challenging membrane proteins. Here we present a technique for extruding gel-like LCP with embedded membrane protein microcrystals, providing a continuously renewed source of material for serial femtosecond crystallography. Data collected from sub-10-mu m-sized crystals produced with less than 0.5 mg of purified protein yield structural insights regarding cyclopamine binding to the Smoothened receptor.

Published
2014
Full Text
View/download PDF

78. Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-1

Author

Lee, Ho-Hsien, Cherni, Irene, Yu, HongQi, Fromme, Raimund, Doran, Jeffrey D., Grotjohann, Ingo, Mittman, Michele, Basu, Shibom, Deb, Arpan, Dörner, Katerina, Aquila, Andrew, Barty, Anton, Boutet, Sébastien, Chapman, Henry N., Doak, R. Bruce, Hunter, Mark S., James, Daniel, Kirian, Richard A., Kupitz, Christopher, Lawrence, Robert M., Liu, Haiguang, Nass, Karol, Schlichting, Ilme, Schmidt, Kevin E., Seibert, M. Marvin, Shoeman, Robert L., Spence, John C. H., Stellato, Francesco, Weierstall, Uwe, Williams, Garth J., Yoon, Chunhong, Wang, Dingjie, Zatsepin, Nadia A., Hogue, Brenda G., Matoba, Nobuyuki, Fromme, Petra, Mor, Tsafrir S., Lee, Ho-Hsien, Cherni, Irene, Yu, HongQi, Fromme, Raimund, Doran, Jeffrey D., Grotjohann, Ingo, Mittman, Michele, Basu, Shibom, Deb, Arpan, Dörner, Katerina, Aquila, Andrew, Barty, Anton, Boutet, Sébastien, Chapman, Henry N., Doak, R. Bruce, Hunter, Mark S., James, Daniel, Kirian, Richard A., Kupitz, Christopher, Lawrence, Robert M., Liu, Haiguang, Nass, Karol, Schlichting, Ilme, Schmidt, Kevin E., Seibert, M. Marvin, Shoeman, Robert L., Spence, John C. H., Stellato, Francesco, Weierstall, Uwe, Williams, Garth J., Yoon, Chunhong, Wang, Dingjie, Zatsepin, Nadia A., Hogue, Brenda G., Matoba, Nobuyuki, Fromme, Petra, and Mor, Tsafrir S.

Abstract

CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) andthe membrane-proximal region of gp41 (MPR), the transmembrane envelopeprotein ofHuman immunodeficiency virus 1(HIV-1), and has previously beenshown to induce the production of anti-HIV-1 antibodies with antiviralfunctions. To further improve the design of this candidate vaccine, X-raycrystallography experiments were performed to obtain structural informationabout this fusion protein. Several variants of CTB-MPR were designed,constructed and recombinantly expressed inEscherichia coli. The first variantcontained a flexible GPGP linker between CTB and MPR, and yielded crystalsthat diffracted to a resolution of 2.3 A ̊, but only the CTB region was detectedin the electron-density map. A second variant, in which the CTB was directlyattached to MPR, was shown to destabilize pentamer formation. A thirdconstruct containing a polyalanine linker between CTB and MPR proved tostabilize the pentameric form of the protein during purification. The purificationprocedure was shown to produce a homogeneously pure and monodispersesample for crystallization. Initial crystallization experiments led to pseudo-crystals which were ordered in only two dimensions and were disordered inthe third dimension. Nanocrystals obtained using the same precipitant showedpromising X-ray diffraction to 5 A ̊resolution in femtosecond nanocrystallo-graphy experiments at the Linac Coherent Light Source at the SLAC NationalAccelerator Laboratory. The results demonstrate the utility of femtosecondX-ray crystallography to enable structural analysis based on nano/microcrystalsof a protein for which no macroscopic crystals ordered in three dimensions havebeen observed before.

Published
2014
Full Text
View/download PDF

79. Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-1

Author

Lee, Ho-Hsien, primary, Cherni, Irene, additional, Yu, HongQi, additional, Fromme, Raimund, additional, Doran, Jeffrey D., additional, Grotjohann, Ingo, additional, Mittman, Michele, additional, Basu, Shibom, additional, Deb, Arpan, additional, Dörner, Katerina, additional, Aquila, Andrew, additional, Barty, Anton, additional, Boutet, Sébastien, additional, Chapman, Henry N., additional, Doak, R. Bruce, additional, Hunter, Mark S., additional, James, Daniel, additional, Kirian, Richard A., additional, Kupitz, Christopher, additional, Lawrence, Robert M., additional, Liu, Haiguang, additional, Nass, Karol, additional, Schlichting, Ilme, additional, Schmidt, Kevin E., additional, Seibert, M. Marvin, additional, Shoeman, Robert L., additional, Spence, John C. H., additional, Stellato, Francesco, additional, Weierstall, Uwe, additional, Williams, Garth J., additional, Yoon, Chunhong, additional, Wang, Dingjie, additional, Zatsepin, Nadia A., additional, Hogue, Brenda G., additional, Matoba, Nobuyuki, additional, Fromme, Petra, additional, and Mor, Tsafrir S., additional

Published
2014
Full Text
View/download PDF

80. Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser

Author

Arnlund, David, primary, Johansson, Linda C, additional, Wickstrand, Cecilia, additional, Barty, Anton, additional, Williams, Garth J, additional, Malmerberg, Erik, additional, Davidsson, Jan, additional, Milathianaki, Despina, additional, DePonte, Daniel P, additional, Shoeman, Robert L, additional, Wang, Dingjie, additional, James, Daniel, additional, Katona, Gergely, additional, Westenhoff, Sebastian, additional, White, Thomas A, additional, Aquila, Andrew, additional, Bari, Sadia, additional, Berntsen, Peter, additional, Bogan, Mike, additional, van Driel, Tim Brandt, additional, Doak, R Bruce, additional, Kjær, Kasper Skov, additional, Frank, Matthias, additional, Fromme, Raimund, additional, Grotjohann, Ingo, additional, Henning, Robert, additional, Hunter, Mark S, additional, Kirian, Richard A, additional, Kosheleva, Irina, additional, Kupitz, Christopher, additional, Liang, Mengning, additional, Martin, Andrew V, additional, Nielsen, Martin Meedom, additional, Messerschmidt, Marc, additional, Seibert, M Marvin, additional, Sjöhamn, Jennie, additional, Stellato, Francesco, additional, Weierstall, Uwe, additional, Zatsepin, Nadia A, additional, Spence, John C H, additional, Fromme, Petra, additional, Schlichting, Ilme, additional, Boutet, Sébastien, additional, Groenhof, Gerrit, additional, Chapman, Henry N, additional, and Neutze, Richard, additional

Published
2014
Full Text
View/download PDF

83. Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography

Author

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

Published
2014
Full Text
View/download PDF

84. Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography

Author

Johansson, Linda C., Arnlund, David, Katona, Gergely, White, Thomas A., Barty, Anton, DePonte, Daniel P., Shoeman, Robert L., Wickstrand, Cecilia, Sharma, Amit, Williams, Garth J., Aquila, Andrew, Bogan, Michael J., Caleman, Carl, Davidsson, Jan, Doak, R. Bruce, Frank, Matthias, Fromme, Raimund, Galli, Lorenzo, Grotjohann, Ingo, Hunter, Mark S., Kassemeyer, Stephan, Kirian, Richard A., Kupitz, Christopher, Liang, Mengning, Lomb, Lukas, Malmerberg, Erik, Martin, Andrew V., Messerschmidt, Marc, Nass, Karol, Redecke, Lars, Seibert, M. Marvin, Sjoehamn, Jennie, Steinbrener, Jan, Stellato, Francesco, Wang, Dingjie, Wahlgren, Weixaio Y., Weierstall, Uwe, Westenhoff, Sebastian, Zatsepin, Nadia A., Boutet, Sebastien, Spence, John C. H., Schlichting, Ilme, Chapman, Henry N., Fromme, Petra, Neutze, Richard, Johansson, Linda C., Arnlund, David, Katona, Gergely, White, Thomas A., Barty, Anton, DePonte, Daniel P., Shoeman, Robert L., Wickstrand, Cecilia, Sharma, Amit, Williams, Garth J., Aquila, Andrew, Bogan, Michael J., Caleman, Carl, Davidsson, Jan, Doak, R. Bruce, Frank, Matthias, Fromme, Raimund, Galli, Lorenzo, Grotjohann, Ingo, Hunter, Mark S., Kassemeyer, Stephan, Kirian, Richard A., Kupitz, Christopher, Liang, Mengning, Lomb, Lukas, Malmerberg, Erik, Martin, Andrew V., Messerschmidt, Marc, Nass, Karol, Redecke, Lars, Seibert, M. Marvin, Sjoehamn, Jennie, Steinbrener, Jan, Stellato, Francesco, Wang, Dingjie, Wahlgren, Weixaio Y., Weierstall, Uwe, Westenhoff, Sebastian, Zatsepin, Nadia A., Boutet, Sebastien, Spence, John C. H., Schlichting, Ilme, Chapman, Henry N., Fromme, Petra, and Neutze, Richard

Abstract

Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 angstrom resolution and determine its serial femtosecond crystallography structure to 3.5 angstrom resolution. Although every microcrystal is exposed to a dose of 33MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure.

Published
2013
Full Text
View/download PDF

85. Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography

Author

Johansson, Linda C., primary, Arnlund, David, additional, Katona, Gergely, additional, White, Thomas A., additional, Barty, Anton, additional, DePonte, Daniel P., additional, Shoeman, Robert L., additional, Wickstrand, Cecilia, additional, Sharma, Amit, additional, Williams, Garth J., additional, Aquila, Andrew, additional, Bogan, Michael J., additional, Caleman, Carl, additional, Davidsson, Jan, additional, Doak, R Bruce, additional, Frank, Matthias, additional, Fromme, Raimund, additional, Galli, Lorenzo, additional, Grotjohann, Ingo, additional, Hunter, Mark S., additional, Kassemeyer, Stephan, additional, Kirian, Richard A., additional, Kupitz, Christopher, additional, Liang, Mengning, additional, Lomb, Lukas, additional, Malmerberg, Erik, additional, Martin, Andrew V., additional, Messerschmidt, Marc, additional, Nass, Karol, additional, Redecke, Lars, additional, Seibert, M Marvin, additional, Sjöhamn, Jennie, additional, Steinbrener, Jan, additional, Stellato, Francesco, additional, Wang, Dingjie, additional, Wahlgren, Weixaio Y., additional, Weierstall, Uwe, additional, Westenhoff, Sebastian, additional, Zatsepin, Nadia A., additional, Boutet, Sébastien, additional, Spence, John C.H., additional, Schlichting, Ilme, additional, Chapman, Henry N., additional, Fromme, Petra, additional, and Neutze, Richard, additional

Published
2013
Full Text
View/download PDF

89. New Avenues for Structure Determination of Membrane Proteins

Author

Fromme, Petra, primary, Hunter, Mark, additional, Kupitz, Christopher, additional, Kirian, Richard, additional, Fromme, Raimund, additional, Barty, Anton, additional, Grotjohann, Ingo, additional, Simpson, Garth, additional, Frank, Mathias, additional, Dorner, Katherina, additional, White, Thomas, additional, Aquilla, Andrew, additional, Ilme, Schlichting, additional, Chapman, Henry, additional, and Spence, John H.C., additional

Published
2012
Full Text
View/download PDF

91. Megahertz serial crystallography

Author

Wiedorn, Max Oliver, Oberth��r, Dominik, Bean, Richard, Schubert, Robin, Werner, Nadine, Abbey, Brian, Aepfelbacher, Martin, Adriano, Luigi, Allahgholi, Aschkan, Al-Qudami, Nasser, Andreasson, Jakob, Horke, Daniel A., Hunter, Mark S., Imlau, Siegfried, Kaukher, Alexander, Kim, Yoonhee, Klyuev, Alexander, Kno��ka, Juraj, Kobe, Bostjan, Kuhn, Manuela, Kupitz, Christopher, M��hlig, Kerstin, K��pper, 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, Munke, Anna, Metz, Markus, Mezza, Davide, Michelat, Thomas, Mills, Grant, Monteiro, Diana C.F., Morgan, Andrew J., M��nnich, Astrid, Nette, Julia, Nugent, Keith A., Nuguid, Theresa, Orville, Allen M., Pandey, Suraj, Pena, Gisel, Villanueva-Perez, Pablo, Shelby, Megan L., P��hlsen, Jennifer, Previtali, Gianpietro, Redecke, Lars, Riekehr, Winnie Maria, Rohde, Holger, Round, Adam R., Safenreiter, Tatiana, Sarrou, Iosifina, Sato, Tokushi, Schmidt, Marius, Shoemann, Robert L., Schmitt, Bernd, Sch��nherr, Robert, Schulz, Joachim, Sellberg, Jonas Alexander, Seibert, M. Marvin, Seuring, Carolin, 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, Sa��a, Bar��k, 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, D��rner, Katerina Henrike, Du, Yang, Fangohr, Hans, Fleckenstein, Holger, Frank, Matthias, Fromme, Petra, Ga����n-Calvo, Alfonso M., Gevorkov, Yaroslav, Giewekemeyer, Klaus, Ginn, Helen Mary, Graafsma, Heinz, Graceffa, Rita, Greiffenberg, Dominic, Gumprecht, Lars, G��ttlicher, Peter, Hajdu, J��nos, Hauf, Steffen, Heymann, Michael, and Holmes, Susannah

Subjects
600: Technik, 3. Good health
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 ��-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.

92. 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-Gracia, Jose, 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
3. Good health
Abstract

Structural dynamics 4(4), 044003 (2017). doi:10.1063/1.4972069, 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 by AIP Publishing LLC, Melville, NY

93. Ternary structure reveals mechanism of a membrane diacylglycerol kinase

Author

Li, Dianfan, Stansfeld, Phillip J., Sansom, Mark S. P., Keogh, Aaron, Vogeley, Lutz, Howe, Nicole, Lyons, Joseph A., Aragao, David, Fromme, Petra, Fromme, Raimund, Basu, Shibom, Grotjohann, Ingo, Kupitz, Christopher, Rendek, Kimberley, Weierstall, Uwe, Zatsepin, Nadia A., Cherezov, Vadim, Liu, Wei, Bandaru, Sateesh, English, Niall J., Gati, Cornelius, Barty, Anton, Yefanov, Oleksandr, Chapman, Henry N., Diederichs, Kay, Messerschmidt, Marc, Boutet, Sébastien, Williams, Garth J., Marvin Seibert, M., and Caffrey, Martin

Subjects
3. Good health
Abstract

Nature Communications 6, 10140 (2015). doi:10.1038/ncomms10140, iacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution., Published by Nature Publishing Group, London

94. Megahertz serial crystallography

Author

Wiedorn, Max O., Oberthür, Dominik, Bean, Richard, Schubert, Robin, Werner, Nadine, Abbey, Brian, Aepfelbacher, Martin, Adriano, Luigi, Allah Gholi, 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, 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, Knoska, 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, 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, Betzel, Christian, Chapman, Henry, and Barty, Anton

Subjects
3. Good health
Abstract

Nature Communications 9(1), 4025 (2018). doi:doi.org/10.1038/s41467-018-06156-7, 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 by Nature Publishing Group, London

95. 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
3. Good health
Abstract

BMC biology 16(1), 59 (2018). doi:10.1186/s12915-018-0524-5, Published by Springer, Berlin

96. 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, 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, Dörner, Katerina, Du, Yang, Fangohr, Hans, Fleckenstein, Holger, Frank, Matthias, Fromme, Petra, Ganan-Calvo, Alfonso, Gevorkov, Yaroslav, Giewekemeyer, Klaus, Ginn, Helen, 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, Knoska, 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, Morgan, Andrew, Mühlig, Kerstin, Munke, Anna, Münnich, Astrid, Nette, Julia, Nugent, Keith, Nuguid, Theresa, Orville, Allen, 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, Seibert, M. Marvin, Seuring, Carolin, Shelby, Megan, Shoeman, Robert, Sikorski, Marcin, Silenzi, Alessandro, Stan, Claudiu, 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

Subjects
3. Good health
Abstract

Nature Communications 9(1), 4025 (2018). doi:10.1038/s41467-018-06156-7, 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 reli- able 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 by Nature Publishing Group, London

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

Author

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

Subjects
Models, Molecular, Science (General), General Immunology and Microbiology, SARS-CoV-2, General Neuroscience, fungi, Crystallography, X-Ray, General Biochemistry, Genetics and Molecular Biology, body regions, Q1-390, X-ray Crystallography, X-Ray laser, Crystallography, Serials, Structural Biology, Protein Biochemistry, Protocol, Protein expression and purification, Humans, skin and connective tissue diseases, Protein biochemistry, Structural biology, X-ray crystallography, Crystallization, Coronavirus 3C Proteases
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. For complete details on the use and execution of this protocol, please refer to Durdagi et al. (2021)., Graphical 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.

Published
2022

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

Author

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

Subjects
Biology, Multidisciplinary sciences, genetic structures, QH301-705.5, Nanocrystallography, Temperature, Medicine (miscellaneous), General Biochemistry, Genetics and Molecular Biology, Article, Streptavidin, ddc:570, Enzyme mechanisms, Biology (General), General Agricultural and Biological Sciences
Abstract

Communications biology 5(1), 73 (2022). doi:10.1038/s42003-021-02903-7, 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 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å 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., Published by Springer Nature, London

Published
2022

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

Author

Gunseli Yildirim, Alaleh Shafiei, Oleksandr Yefanov, Hasan DeMirci, Frédéric Poitevin, Timucin Avsar, Chun Hong Yoon, Muge Didem Orhan, Merve Yigin, Lalehan Oktay, Fulya Aksit, Çağdaş Dağ, Serdar Durdagi, Christopher Kupitz, Omur Guven, Valerio Mariani, Ece Erdemoglu, Ebru Destan, Edward H. Snell, Ismail Erol, Mark S. Hunter, Esra Ayan, Berna Dogan, Mengning Liang, Busecan Aksoydan, A. Batyuk, Ozgur Can, Cengizhan Buyukdag, Sabri O. Besler, Seyma Calis, Brandon Hayes, Matthew Seaberg, Serena Ozabrahamyan, Ilayda Tolu, Gihan K. Ketawala, Anton Barty, Raymond G. Sierra, Kader Sahin, Gokhan Tanisali, Oktay Gocenler, Ali D. Yucel, E. Han Dao, Alpsu Olkan, Ayse B. Peksen, Zhen Su, A. Tolstikova, Sabine Botha, Busra Yuksel, Fatma Betul Ertem, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Dağ, Çağdaş, Yığın, Merve, Büyükdağ, Cengizhan, Ertem, Fatma Betül, Yıldırım, Günseli, Destan, Ebru, Güven, Ömür, Ayan, Esra, Yüksel, Büşra, Pekşen, Ayşe Buket, Göçenler, Oktay, Yücel, Ali Doğa, Can, Özgür, Ozabrahamyan, Serena, Shafiei, Alaleh, Akşit, Fulya, Tanısalı, Gökhan, Besler, Sabri Özkan, Durdağı, Serdar, Doğan, Berna, Avşar, Timuçin, Erol, İsmail, Çalış, Şeyma, Orhan, Müge D., Aksoydan, Busecan, Şahin, Kader, Oktay, Lalehan, Tolu, İlayda, Olkan, Alpsu, Erdemoğlu, Ece, Yefanov, Oleksandr M., Dao, E. Han, Hayes, Brandon, Liang, Mengning, Seaberg, Matthew H., Hunter, Mark S., Batyuk, Alex, Mariani, Valerio, Su, Zhen, Poitevin, Frederic, Yoon, Chun Hong, Kupitz, Christopher, Sierra, Raymond G., Snell, Edward H., Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID), College of Sciences, Graduate School of Sciences and Engineering, School of Nursing, Department of Molecular Biology and Genetics, Department of Chemical and Biological Engineering, and Department of Materials Science and Engineering

Subjects
Drug, Molecular model, Protein Conformation, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), media_common.quotation_subject, medicine.medical_treatment, ambient temperature, Molecular Conformation, Crystallography, X-Ray, Article, Structural Biology, Catalytic Domain, medicine, SFX, Computer Simulation, Molecular Biology, Coronavirus 3C Proteases, media_common, Principal Component Analysis, Protease, Biochemistry and molecular biology, Biophysics, Cell biology, biology, drug repurposing, Drug discovery, SARS-CoV-2, Drug Repositioning, Temperature, Active site, Small molecule, Recombinant Proteins, COVID-19 Drug Treatment, Molecular Docking Simulation, Drug repositioning, Crystallography, main protease, Drug Design, ddc:540, biology.protein, Dimerization, Ambient temperature, Drug repurposing, Main protease
Abstract

The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2., Graphical abstract, Durdağı et al. represent radiation damage-free high-resolution SARS-CoV-2 main protease SFX structures obtained at near-physiological temperature and performed MD simulation of apo-form proteins and three known main protease inhibitors. The structures reveal alternate conformation, while MD simulation indicates asymmetric behavior of the protein, which is invaluable information for immediate drug-repurposing studies.

Published
2021

Catalog

Books, media, physical & digital resources
See catalog results