Publications by BioXFEL Researchers Since Start of BioXFEL Grant

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Acknowledges BioXFEL NSF-STC
   
Authors: Cody Aplin, Shawn K. Milano, Kara A. Zielinski, Lois Pollack, Richard A. Cerione
Citation: Aplin, C., Milano, S. K., Zielinski, K. A., Pollack, L., & Cerione, R. A. (2022). Evolving Experimental Techniques for Structure-Based Drug Design. The Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.2c04344
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Anna Shiriaeva, Daejin Park, Gyudong Kim, Yoonji Lee, Xiyan Hou, Dnyandev B. Jarhad, Gibae Kim, Jinha Yu, Young Eum Hyun, Woomi Kim, Zhan-Guo Gao, Kenneth A. Jacobson, Gye Won Han, Raymond C. Stevens, Lak Shin Jeong, Sun Choi, Vadim Cherezov
Citation: Shiriaeva, A., Park, D., Kim, G., Lee, Y., Hou, X., Jarhad, D. B., Kim, G., Yu, J., Hyun, Y. E., Kim, W., Gao, Z.-G., Jacobson, K. A., Han, G. W., Stevens, R. C., Jeong, L. S., Choi, S., & Cherezov, V. (2022). GPCR Agonist-to-Antagonist Conversion: Enabling the Design of Nucleoside Functional Switches for the A2A Adenosine Receptor. Journal of Medicinal Chemistry. https://doi.org/10.1021/acs.jmedchem.2c00462
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Elizaveta Lyapina, Egor Marin, Anastasiia Gusach, Philipp Orekhov, Andrey Gerasimov, Aleksandra Luginina, Daniil Vakhrameev, Margarita Ergasheva, Margarita Kovaleva, Georgii Khusainov, Polina Khorn, Mikhail Shevtsov, Kirill Kovalev, Sergey Bukhdruker, Ivan Okhrimenko, Petr Popov, Hao Hu, Uwe Weierstall, Wei Liu, Yunje Cho, Ivan Gushchin, Andrey Rogachev, Gleb Bourenkov, Sehan Park, Gisu Park, Hyo Jung Hyun, Jaehyun Park, Valentin Gordeliy, Valentin Borshchevskiy, Alexey Mishin, Vadim Cherezov
Citation: Lyapina, E., Marin, E., Gusach, A., Orekhov, P., Gerasimov, A., Luginina, A., Vakhrameev, D., Ergasheva, M., Kovaleva, M., Khusainov, G., Khorn, P., Shevtsov, M., Kovalev, K., Bukhdruker, S., Okhrimenko, I., Popov, P., Hu, H., Weierstall, U., Liu, W., ... Cherezov, V. (2022). Structural basis for receptor selectivity and inverse agonism in S1P5 receptors. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-32447-1
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Nirupa Nagaratnam, Jose M. Martin-Garcia, Jay-How Yang, Matthew R. Goode, Gihan Ketawala, Felicia M. Craciunescu, James D. Zook, Manashi Sonowal, Dewight Williams, Thomas D. Grant, Raimund Fromme, Debra T. Hansen, Petra Fromme
Citation: Nagaratnam, N., Martin-Garcia, J. M., Yang, J.-H., Goode, M. R., Ketawala, G., Craciunescu, F. M., Zook, J. D., Sonowal, M., Williams, D., Grant, T. D., Fromme, R., Hansen, D. T., & Fromme, P. (2022). Structural and biophysical properties of FopA, a major outer membrane protein of Francisella tularensis. PLOS ONE, 17(8), e0267370. https://doi.org/10.1371/journal.pone.0267370
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Jeffrey Donatelli, John Spence
Citation: Donatelli, J., & Spence, J. (2022). Structure Determination from Multiple-Scattering Electron Crystallography. Microscopy and Microanalysis, 28(S1), 2766-2767. https://doi.org/10.1017/s1431927622010418
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Jayanath C. P. Koliyadu, Romain Letrun, Henry J. Kirkwood, Jia Liu, Man Jiang, Moritz Emons, Richard Bean, Valerio Bellucci, Johan Bielecki, Sarlota Birnsteinova, Raphael de Wijn, Thomas Dietze, Juncheng E, Jan Grünert, Daniel Kane, Chan Kim, Yoonhee Kim, Max Lederer, Bradley Manning, Grant Mills, Luis L. Morillo, Nadja Reimers, Dimitrios Rompotis, Adam Round, Marcin Sikorski, Cedric M. S. Takem, Patrik Vagovič, Sandhya Venkatesan, Jinxiong Wang, Ulrike Wegner, Adrian P. Mancuso, Tokushi Sato
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Galen J. Correy, Daniel W. Kneller, Gwyndalyn Phillips, Swati Pant, Silvia Russi, Aina E. Cohen, George Meigs, James M. Holton, Stefan Gahbauer, Michael C. Thompson, Alan Ashworth, Leighton Coates, Andrey Kovalevsky, Flora Meilleur, James S. Fraser
Citation: Correy, G. J., Kneller, D. W., Phillips, G., Pant, S., Russi, S., Cohen, A. E., Meigs, G., Holton, J. M., Gahbauer, S., Thompson, M. C., Ashworth, A., Coates, L., Kovalevsky, A., Meilleur, F., & Fraser, J. S. (2022). The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. Science Advances, 8(21). https://doi.org/10.1126/sciadv.abo5083
Type: Journal-article
Authors: Fiacre Kabayiza, Sarah B. Woodruff, William J. Bauer
Citation: Kabayiza, F., Woodruff, S. B., & Bauer, W. J. (2022). The Gamification of XFEL Education Using XFEL Crystal Blaster. Crystals, 12(5), 671. https://doi.org/10.3390/cryst12050671
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Gabriela Diaz‐Figueroa, Marc Messerschimdt, Jong Woo‐Kim, Tien Olson
Citation: Diaz‐Figueroa, G., Messerschimdt, M., Woo‐Kim, J., & Olson, T. (2022). From Alignment Laser to 3D Structures: Determining Structures of GPCRs in a Compact X‐ray Light Source. The FASEB Journal, 36(S1). Portico. https://doi.org/10.1096/fasebj.2022.36.s1.r3457
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Hasan DeMirci, Yashas Rao, Gabriele M. Stoffel, Bastian Vögeli, Kristina Schell, Aharon Gomez, Alexander Batyuk, Cornelius Gati, Raymond G. Sierra, Mark S. Hunter, E. Han Dao, Halil I. Ciftci, Brandon Hayes, Fredric Poitevin, Po-Nan Li, Manat Kaur, Kensuke Tono, David Adrian Saez, Samuel Deutsch, Yasuo Yoshikuni, Helmut Grubmüller, Tobias J. Erb, Esteban Vöhringer-Martinez, Soichi Wakatsuki
Citation: DeMirci, H., Rao, Y., Stoffel, G. M., Vögeli, B., Schell, K., Gomez, A., Batyuk, A., Gati, C., Sierra, R. G., Hunter, M. S., Dao, E. H., Ciftci, H. I., Hayes, B., Poitevin, F., Li, P.-N., Kaur, M., Tono, K., Saez, D. A., Deutsch, S., ... Wakatsuki, S. (2022). Intersubunit Coupling Enables Fast CO2-Fixation by Reductive Carboxylases. ACS Central Science. https://doi.org/10.1021/acscentsci.2c00057
Type: Journal-article
Authors: Tek Narsingh Malla, Marius Schmidt
Citation: Malla, T. N., & Schmidt, M. (2022). Transient state measurements on proteins by time-resolved crystallography. Current Opinion in Structural Biology, 74, 102376. https://doi.org/10.1016/j.sbi.2022.102376
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Salah Awel, Sebastian Lavin-Varela, Nils Roth, Daniel A. Horke, Andrei V. Rode, Richard A. Kirian, Jochen Küpper, Henry N. Chapman
Citation: Awel, S., Lavin-Varela, S., Roth, N., Horke, D. A., Rode, A. V., Kirian, R. A., Küpper, J., & Chapman, H. N. (2022). Optical Funnel to Guide and Focus Virus Particles for X-Ray Diffractive Imaging. Physical Review Applied, 17(4). https://doi.org/10.1103/physrevapplied.17.044044
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Jorvani Cruz Villarreal, Rory Kruithoff, Ana Egatz-Gomez, Paul D. Coleman, Robert Ros, Todd R. Sandrin, Alexandra Ros
Citation: Cruz Villarreal, J., Kruithoff, R., Egatz-Gomez, A., Coleman, P. D., Ros, R., Sandrin, T. R., & Ros, A. (2022). MIMAS: microfluidic platform in tandem with MALDI mass spectrometry for protein quantification from small cell ensembles. Analytical and Bioanalytical Chemistry, 414(13), 3945-3958. https://doi.org/10.1007/s00216-022-04038-y
Type: Journal-article
Authors: Jose M. Martin-Garcia, Sabine Botha, Hao Hu, Rebecca Jernigan, Albert Castellví, Stella Lisova, Fernando Gil, Barbara Calisto, Isidro Crespo, Shatabdi Roy-Chowdhury, Alice Grieco, Gihan Ketawala, Uwe Weierstall, John Spence, Petra Fromme, Nadia Zatsepin, Dirk Roeland Boer, Xavi Carpena
Citation: Martin-Garcia, J. M., Botha, S., Hu, H., Jernigan, R., Castellví, A., Lisova, S., Gil, F., Calisto, B., Crespo, I., Roy-Chowdhury, S., Grieco, A., Ketawala, G., Weierstall, U., Spence, J., Fromme, P., Zatsepin, N., Boer, D. R., & Carpena, X. (2022). Serial macromolecular crystallography at ALBA Synchrotron Light Source. Journal of Synchrotron Radiation, 29(3), 896-907. https://doi.org/10.1107/s1600577522002508
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: B. R. Mobley, K. E. Schmidt, J. P. J. Chen, R. A. Kirian
Citation: Mobley, B. R., Schmidt, K. E., Chen, J. P. J., & Kirian, R. A. (2022). A Metropolis Monte Carlo algorithm for merging single-particle diffraction intensities. Acta Crystallographica Section A Foundations and Advances, 78(3), 200-211. https://doi.org/10.1107/s2053273322001395
Type: Journal-article
Authors: Daniel J. Wells, Peter Berntsen, Eugeniu Balaur, Cameron M. Kewish, Patrick Adams, Andrew Aquila, Jack Binns, Sébastien Boutet, Hayden Broomhall, Carl Caleman, Andrew Christofferson, Charlotte E. Conn, Caroline Dahlqvist, Leonie Flueckiger, Francisco Gian Roque, Tamar L. Greaves, Majid Hejazian, Mark Hunter, Marjan Hadian Jazi, H. Olof Jönsson, Sachini Kadaoluwa Pathirannahalage, Richard A. Kirian, Alex Kozlov, Ruslan P. Kurta, Hugh Marman, Derek Mendez, Andrew Morgan, Keith Nugent, Dominik Oberthuer, Harry Quiney, Juliane Reinhardt, Saumitra Saha, Jonas A. Sellberg, Raymond Sierra, Max Wiedorn, Brian Abbey, Andrew V. Martin, Connie Darmanin
Citation: Wells, D. J., Berntsen, P., Balaur, E., Kewish, C. M., Adams, P., Aquila, A., Binns, J., Boutet, S., Broomhall, H., Caleman, C., Christofferson, A., Conn, C. E., Dahlqvist, C., Flueckiger, L., Gian Roque, F., Greaves, T. L., Hejazian, M., Hunter, M., Hadian Jazi, M., ... Darmanin, C. (2022). Observations of phase changes in monoolein during high viscous injection. Journal of Synchrotron Radiation, 29(3), 602-614. https://doi.org/10.1107/s1600577522001862
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Stephanie A Wankowicz, Saulo H de Oliveira, Daniel W Hogan, Henry van den Bedem, James S Fraser
Citation: Wankowicz, S. A., de Oliveira, S. H., Hogan, D. W., van den Bedem, H., & Fraser, J. S. (2022). Ligand binding remodels protein side-chain conformational heterogeneity. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.74114
Type: Journal-article
Authors: Jorvani Cruz Villarreal, Ana Egatz‐Gomez, Jiawei Liu, Robert Ros, George T. Noutsios, Todd R. Sandrin, Paul D. Coleman, Alexandra Ros
Citation: Villarreal, J. C., Egatz‐Gomez, A., Liu, J., Ros, R., Noutsios, G. T., Sandrin, T. R., Coleman, P. D., & Ros, A. (2021). Amyloid‐β analysis from brain cells using microfluidics and mass spectrometry. Alzheimer's & Dementia, 17(S3). Portico. https://doi.org/10.1002/alz.054274
Type: Journal-article
Authors: Ghoncheh Mashayekhi, John Vant, Abhigna Polavarapu, Abbas Ourmazd, Abhishek Singharoy
Citation: Mashayekhi, G., Vant, J., Polavarapu, A., Ourmazd, A., & Singharoy, A. (2022). Energy landscape of the SARS-CoV-2 reveals extensive conformational heterogeneity. Current Research in Structural Biology, 4, 68-77. https://doi.org/10.1016/j.crstbi.2022.02.001
Type: Journal-article
Authors: Cody Krivacic, Kale Kundert, Xingjie Pan, Roland A. Pache, Lin Liu, Shane O Conchúir, Jeliazko R. Jeliazkov, Jeffrey J. Gray, Michael C. Thompson, James S. Fraser, Tanja Kortemme
Citation: Krivacic, C., Kundert, K., Pan, X., Pache, R. A., Liu, L., O Conchúir, S., Jeliazkov, J. R., Gray, J. J., Thompson, M. C., Fraser, J. S., & Kortemme, T. (2022). Accurate positioning of functional residues with robotics-inspired computational protein design. Proceedings of the National Academy of Sciences, 119(11). https://doi.org/10.1073/pnas.2115480119
Type: Journal-article
Authors: Belgin Sever, Halilibrahim Ciftci, Hasan DeMirci, Hilal Sever, Firdevs Ocak, Burak Yulug, Hiroshi Tateishi, Takahisa Tateishi, Masami Otsuka, Mikako Fujita, Ayşe Nazlı Başak
Citation: Sever, B., Ciftci, H., DeMirci, H., Sever, H., Ocak, F., Yulug, B., Tateishi, H., Tateishi, T., Otsuka, M., Fujita, M., & Başak, A. N. (2022). Comprehensive Research on Past and Future Therapeutic Strategies Devoted to Treatment of Amyotrophic Lateral Sclerosis. International Journal of Molecular Sciences, 23(5), 2400. https://doi.org/10.3390/ijms23052400
Type: Journal-article
Authors: Kaitlyn Tsai, Vanja Stojković, D. John Lee, Iris D. Young, Teresa Szal, Dorota Klepacki, Nora Vázquez-Laslop, Alexander S. Mankin, James S. Fraser, Danica Galonić Fujimori
Citation: Tsai, K., Stojković, V., Lee, D. J., Young, I. D., Szal, T., Klepacki, D., Vázquez-Laslop, N., Mankin, A. S., Fraser, J. S., & Fujimori, D. G. (2022). Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics. Nature Structural & Molecular Biology, 29(2), 162-171. https://doi.org/10.1038/s41594-022-00723-9
Type: Journal-article
Authors: Iris D. Young, James S. Fraser
Citation: Young, I. D., & Fraser, J. S. (2022). Curiosity: a tool for exploring density features in crystallographic and cryoEM maps. Biophysical Journal, 121(3), 528a. https://doi.org/10.1016/j.bpj.2021.11.2781
Type: Journal-article
Authors: David Nedrud, Yungui He, Daniel Schmidt, James Fraser, Willow Coyote-Maestas
Citation: Nedrud, D., He, Y., Schmidt, D., Fraser, J., & Coyote-Maestas, W. (2022). Deconvoluting receptor trafficking, regulation, and function using massively parallel assays. Biophysical Journal, 121(3), 2a. https://doi.org/10.1016/j.bpj.2021.11.2700
Type: Journal-article
Authors: Matthew Hancock, Thomas-Otavio Peulen, Benjamin Webb, James S. Fraser, Paul D. Adams, Andrej Sali
Citation: Hancock, M., Peulen, T.-O., Webb, B., Fraser, J. S., Adams, P. D., & Sali, A. (2022). Integration of software tools for integrative modeling of biomolecular systems. Biophysical Journal, 121(3), 31a. https://doi.org/10.1016/j.bpj.2021.11.2555
Type: Journal-article
Authors: Alexis M. Kelley, Christian B. Macdonald, James Fraser
Citation: Kelley, A. M., Macdonald, C. B., & Fraser, J. (2022). Dismantling antibiotic resistance one variant at a time: in vitro and computational analysis of VatD. Biophysical Journal, 121(3), 48a. https://doi.org/10.1016/j.bpj.2021.11.2487
Type: Journal-article
Authors: C. Swathi K. Menon, Konstantinos Karpos, Thomas D. Grant, Andrey V. Struts, Steven D.E. Fried, Roberto C. Alvarez, Suchithranga M.D.C. Perera, Irina V. Kosheleva, Alan Grossfield, Petra Fromme, Richard A. Kirian, Michael F. Brown
Citation: Menon, C. S. K., Karpos, K., Grant, T. D., Struts, A. V., Fried, S. D. E., Alvarez, R. C., Perera, S. M. D. C., Kosheleva, I. V., Grossfield, A., Fromme, P., Kirian, R. A., & Brown, M. F. (2022). Time-resolved functional expansion of visual rhodopsin detected by x-ray scattering. Biophysical Journal, 121(3), 285a-286a. https://doi.org/10.1016/j.bpj.2021.11.1313
Type: Journal-article
Authors: Eric R. Greene, Erin Thompson, D. John Lee, Angelika Arada, Daphne Chen, James Fraser
Citation: Greene, E. R., Thompson, E., Lee, D. J., Arada, A., Chen, D., & Fraser, J. (2022). Connecting glutamine synthetase biophysics to the cellular environment. Biophysical Journal, 121(3), 348a. https://doi.org/10.1016/j.bpj.2021.11.1035
Type: Journal-article
Authors: Christian B. Macdonald, Alexis Kelley, Jenna Pellegrino, Willow Coyote-Maestas, James Fraser
Citation: Macdonald, C. B., Kelley, A., Pellegrino, J., Coyote-Maestas, W., & Fraser, J. (2022). Using deep mutational scanning to identify the determinants of antibiotic resistance. Biophysical Journal, 121(3), 422a. https://doi.org/10.1016/j.bpj.2021.11.665
Type: Journal-article
Authors: Matthew Hancock, Thomas-Otavio Peulen, Benjamin Webb, Billy Poon, James S Fraser, Paul Adams, Andrej Sali
Citation: Hancock, M., Peulen, T.-O., Webb, B., Poon, B., Fraser, J. S., Adams, P., & Sali, A. (2022). Integration of software tools for integrative modeling of biomolecular systems. Journal of Structural Biology, 214(1), 107841. https://doi.org/10.1016/j.jsb.2022.107841
Type: Journal-article
Authors: Surya V. S. R. K. Pulavarti, Jack B. Maguire, Shirley Yuen, Joseph S. Harrison, Jermel Griffin, Lakshmanane Premkumar, Edward A. Esposito, George I. Makhatadze, Angel E. Garcia, Thomas M. Weiss, Edward H. Snell, Brian Kuhlman, Thomas Szyperski
Citation: Pulavarti, S. V. S. R. K., Maguire, J. B., Yuen, S., Harrison, J. S., Griffin, J., Premkumar, L., Esposito, E. A., Makhatadze, G. I., Garcia, A. E., Weiss, T. M., Snell, E. H., Kuhlman, B., & Szyperski, T. (2022). From Protein Design to the Energy Landscape of a Cold Unfolding Protein. The Journal of Physical Chemistry B, 126(6), 1212-1231. https://doi.org/10.1021/acs.jpcb.1c10750
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Israel Rodríguez, Lauren Fernández-Vega, Andrea N. Maser-Figueroa, Branlee Sang, Patricia González-Pagán, Arthur D. Tinoco
Citation: Rodríguez, I., Fernández-Vega, L., Maser-Figueroa, A. N., Sang, B., González-Pagán, P., & Tinoco, A. D. (2022). Exploring Titanium(IV) Complexes as Potential Antimicrobial Compounds. Antibiotics, 11(2), 158. https://doi.org/10.3390/antibiotics11020158
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Dameli Assalauova, Young Yong Kim, Sergey Bobkov, Ruslan Khubbutdinov, Max Rose, Roberto Alvarez, Jakob Andreasson, Eugeniu Balaur, Alice Contreras, Hasan DeMirci, Luca Gelisio, Janos Hajdu, Mark S. Hunter, Ruslan P. Kurta, Haoyuan Li, Matthew McFadden, Reza Nazari, Peter Schwander, Anton Teslyuk, Peter Walter, P. Lourdu Xavier, Chun Hong Yoon, Sahba Zaare, Viacheslav A. Ilyin, Richard A. Kirian, Brenda G. Hogue, Andrew Aquila, Ivan A. Vartanyants
Citation: Assalauova, D., Kim, Y. Y., Bobkov, S., Khubbutdinov, R., Rose, M., Alvarez, R., Andreasson, J., Balaur, E., Contreras, A., DeMirci, H., Gelisio, L., Hajdu, J., Hunter, M. S., Kurta, R. P., Li, H., McFadden, M., Nazari, R., Schwander, P., Teslyuk, A., ... Vartanyants, I. A. (2022). An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. Corrigendum. IUCrJ, 9(2), 328-328. https://doi.org/10.1107/s2052252522000501
Type: Journal-article
Authors: 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
Citation: Ertem, F. B., Guven, O., Buyukdag, C., Gocenler, O., Ayan, E., Yuksel, B., Gul, M., Usta, G., Cakılkaya, B., Johnson, J. A., Dao, E. H., Su, Z., Poitevin, F., Yoon, C. H., Kupitz, C., Hayes, B., Liang, M., Hunter, M. S., Batyuk, A., ... DeMirci, H. (2022). Protocol for structure determination of SARS-CoV-2 main protease at near-physiological-temperature by serial femtosecond crystallography. STAR Protocols, 3(1), 101158. https://doi.org/10.1016/j.xpro.2022.101158
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Halilibrahim Ciftci, Belgin Sever, Firdevs Ocak, Nilüfer Bayrak, Mahmut Yıldız, Hatice Yıldırım, Hasan DeMirci, Hiroshi Tateishi, Masami Otsuka, Mikako Fujita, Amaç Fatih TuYuN
Citation: Ciftci, H., Sever, B., Ocak, F., Bayrak, N., Yıldız, M., Yıldırım, H., DeMirci, H., Tateishi, H., Otsuka, M., Fujita, M., & TuYuN, A. F. (2022). In Vitro and In Silico Study of Analogs of Plant Product Plastoquinone to Be Effective in Colorectal Cancer Treatment. Molecules, 27(3), 693. https://doi.org/10.3390/molecules27030693
Type: Journal-article
Authors: Roberto Ricardo-Gonzalez, Maya E. Kotas, Claire E. O'Leary, Iliana Tenvooren, Diana M. Marquez, Katelyn Singh, William Damsky, Andrew W. Schroeder, Jarish N. Cohen, Marlys Fassett, Jinwoo Lee, Scott G. Daniel, Kyle Bittinger, Roberto Efraín Díaz, James S. Fraser, Mark Ansel, Matthew Spitzer, Hong-Erh Liang, Richard M. Locksley
Citation: Ricardo-Gonzalez, R., Kotas, M. E., O'Leary, C. E., Tenvooren, I., Marquez, D. M., Singh, K., Damsky, W., Schroeder, A. W., Cohen, J. N., Fassett, M., Lee, J., Daniel, S. G., Bittinger, K., Díaz, R. E., Fraser, J. S., Ansel, M., Spitzer, M., Liang, H.-E., & Locksley, R. M. (2022). Innate Type 2 Immunity Controls Hair Follicle Commensalism by <i>Demodex</i> Mites. SSRN Electronic Journal. https://doi.org/10.2139/ssrn.4013912
Type: Journal-article
Authors: 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
Citation: Ayan, E., Yuksel, B., Destan, E., Ertem, F. B., Yildirim, G., Eren, M., Yefanov, O. M., Barty, A., Tolstikova, A., Ketawala, G. K., Botha, S., Dao, E. H., Hayes, B., Liang, M., Seaberg, M. H., Hunter, M. S., Batyuk, A., Mariani, V., Su, Z., ... DeMirci, H. (2022). Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature. Communications Biology, 5(1). https://doi.org/10.1038/s42003-021-02903-7
Type: Journal-article
Authors: Abbas Ourmazd, Keith Moffat, Eaton Edward Lattman
Citation: Ourmazd, A., Moffat, K., & Lattman, E. E. (2022). Structural biology is solved -- now what? Nature Methods, 19(1), 24-26. https://doi.org/10.1038/s41592-021-01357-3
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Kaitlyn Tsai, Vanja Stojković, Lianet Noda-Garcia, Iris D Young, Alexander G Myasnikov, Jordan Kleinman, Ali Palla, Stephen N Floor, Adam Frost, James S Fraser, Dan S Tawfik, Danica Galonić Fujimori
Citation: Tsai, K., Stojković, V., Noda-Garcia, L., Young, I. D., Myasnikov, A. G., Kleinman, J., Palla, A., Floor, S. N., Frost, A., Fraser, J. S., Tawfik, D. S., & Fujimori, D. G. (2022). Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.70017
Type: Journal-article
Authors: Yen-Lin Chen, Weiwei He, Serdal Kirmizialtin, Lois Pollack
Citation: Chen, Y.-L., He, W., Kirmizialtin, S., & Pollack, L. (2022). RNA Triplex Structures Revealed by WAXS-Driven MD Simulations. SSRN Electronic Journal. https://doi.org/10.2139/ssrn.4000889
Type: Journal-article
Authors: Jonathon G. Gray, George M. Giambaşu, David A. Case, Tyler Luchko
Citation: Gray, J. G., Giambaşu, G. M., Case, D. A., & Luchko, T. (2022). Integral equation models for solvent in macromolecular crystals. The Journal of Chemical Physics, 156(1), 014801. https://doi.org/10.1063/5.0070869
Type: Journal-article
Authors: Ricardo Ortiz, Domin Koh, Dai Hyun Kim, Mohammad Towshif Rabbani, Cesar Anguaya Velasquez, Mukul Sonker, Edgar A. Arriaga, Alexandra Ros
Citation: Ortiz, R., Koh, D., Kim, D. H., Rabbani, M. T., Anguaya Velasquez, C., Sonker, M., Arriaga, E. A., & Ros, A. (2022). Continuous organelle separation in an insulator‐based dielectrophoretic device. ELECTROPHORESIS, 43(12), 1283-1296. Portico. https://doi.org/10.1002/elps.202100326
Type: Journal-article
Authors: Vijay Jayaraman, D. John Lee, Nadav Elad, Shay Vimer, Michal Sharon, James S. Fraser, Dan S. Tawfik
Citation: Jayaraman, V., Lee, D. J., Elad, N., Vimer, S., Sharon, M., Fraser, J. S., & Tawfik, D. S. (2021). A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Nature Chemical Biology, 18(2), 161-170. https://doi.org/10.1038/s41589-021-00919-y
Type: Journal-article
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Citation: Guven, O., Gul, M., Ayan, E., Johnson, J. A., Cakilkaya, B., Usta, G., Ertem, F. B., Tokay, N., Yuksel, B., Gocenler, O., Buyukdag, C., Botha, S., Ketawala, G., Su, Z., Hayes, B., Poitevin, F., Batyuk, A., Yoon, C. H., Kupitz, C., ... DeMirci, H. (2021). Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography. Crystals, 11(12), 1579. https://doi.org/10.3390/cryst11121579
Type: Journal-article
Authors: Diandra Doppler, Mohammad T. Rabbani, Romain Letrun, Jorvani Cruz Villarreal, Dai Hyun Kim, Sahir Gandhi, Ana Egatz-Gomez, Mukul Sonker, Joe Chen, Faisal H. M. Koua, Jayhow Yang, Mohamed Youssef, Victoria Mazalova, Saša Bajt, Megan L. Shelby, Matt A. Coleman, Max O. Wiedorn, Juraj Knoska, Silvan Schön, Tokushi Sato, Mark S. Hunter, Ahmad Hosseinizadeh, Christopher Kuptiz, Reza Nazari, Roberto C. Alvarez, Konstantinos Karpos, Sahba Zaare, Zachary Dobson, Erin Discianno, Shangji Zhang, James D. Zook, Johan Bielecki, Raphael de Wijn, Adam R. Round, Patrik Vagovic, Marco Kloos, Mohammad Vakili, Gihan K. Ketawala, Natasha E. Stander, Tien L. Olson, Katherine Morin, Jyotirmory Mondal, Jonathan Nguyen, José Domingo Meza-Aguilar, Gerdenis Kodis, Sara Vaiana, Jose M. Martin-Garcia, Valerio Mariani, Peter Schwander, Marius Schmidt, Marc Messerschmidt, Abbas Ourmazd, Nadia Zatsepin, Uwe Weierstall, Barry D. Bruce, Adrian P. Mancuso, Thomas Grant, Anton Barty, Henry N. Chapman, Matthias Frank, Raimund Fromme, John C. H. Spence, Sabine Botha, Petra Fromme, Richard A. Kirian, Alexandra Ros
Citation: Doppler, D. et al., 2022. Co-flow injection for serial crystallography at X-ray free-electron lasers. Journal of Applied Crystallography, 55(1).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Abigael J. Kosgei, Mitchell D. Miller, Minakshi Bhardwaj, Weijun Xu, Jon S. Thorson, Steven G. Van Lanen, George N. Phillips
Citation: Kosgei, A.J. et al., 2022. The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina. Acta Crystallographica Section F Structural Biology Communications, 78(1), pp.1-7.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Liqiang Zhang, Jordan R Yaron, Lauren Schutz, Emily Aliskevich, Kyle Browder, Nicholas Saldevar, Isabela R Zanetti, Nora Elmadbouly, Honor Glenn, Yize Li, Karen Kibler, Brenda Hogue, Grant McFadden, Alexandra R Lucas
Citation: Zhang, L., Yaron, J. R., Schutz, L., Aliskevich, E., Browder, K., Saldevar, N., Zanetti, I. R., Elmadbouly, N., Glenn, H., Li, Y., Kibler, K., Hogue, B., McFadden, G., & Lucas, A. R. (2021). Abstract 13747: Targeting Urokinase-Type Plasminogen Activator (uPA) and the uPA Receptor, Reduces Vascular Inflammation and Lung Hemorrhage in Systemic Lupus and SARS CoV2 Infection in Mouse Models of Respiratory Distress Syndromes. Circulation, 144(Suppl_2). https://doi.org/10.1161/circ.144.suppl_2.13747
Type: Journal-article
Authors: Ebru Destan, Busra Yuksel, Bradley B. Tolar, Esra Ayan, Sam Deutsch, Yasuo Yoshikuni, Soichi Wakatsuki, Christopher A. Francis, Hasan DeMirci
Citation: Destan, E., Yuksel, B., Tolar, B. B., Ayan, E., Deutsch, S., Yoshikuni, Y., Wakatsuki, S., Francis, C. A., & DeMirci, H. (2021). Structural insights into bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-02180-8
Type: Journal-article
Authors: A. Hosseinizadeh, N. Breckwoldt, R. Fung, R. Sepehr, M. Schmidt, P. Schwander, R. Santra, A. Ourmazd
Citation: Hosseinizadeh, A. et al., 2021. Few-fs resolution of a photoactive protein traversing a conical intersection. Nature, 599(7886), pp.697-701.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Marius Schmidt
Citation: Schmidt, M., 2021. Macromolecular movies, storybooks written by nature. Biophysical Reviews.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Tanner J. Finney, Sanjai J. Parikh, Amir Berman, Darryl Y. Sasaki, Tonya L. Kuhl
Citation: Finney, T. J., Parikh, S. J., Berman, A., Sasaki, D. Y., & Kuhl, T. L. (2021). Characterizing and Tuning the Properties of Polydiacetylene Films for Sensing Applications. Langmuir, 37(44), 12940-12951. https://doi.org/10.1021/acs.langmuir.1c02004
Type: Journal-article
Authors: Serdar Durdagi, Timucin Avsar, Muge Didem Orhan, Muge Serhatli, Bertan Koray Balcioglu, Hasan Umit Ozturk, Alisan Kayabolen, Yuksel Cetin, Seyma Aydinlik, Tugba Bagci-Onder, Saban Tekin, Hasan Demirci, Mustafa Guzel, Atilla Akdemir, Seyma Calis, Lalehan Oktay, Ilayda Tolu, Yasar Enes Butun, Ece Erdemoglu, Alpsu Olkan, Nurettin Tokay, Şeyma Işık, Aysenur Ozcan, Elif Acar, Sehriban Buyukkilic, Yesim Yumak
Citation: Durdagi, S., Avsar, T., Orhan, M. D., Serhatli, M., Balcioglu, B. K., Ozturk, H. U., Kayabolen, A., Cetin, Y., Aydinlik, S., Bagci-Onder, T., Tekin, S., Demirci, H., Guzel, M., Akdemir, A., Calis, S., Oktay, L., Tolu, I., Butun, Y. E., Erdemoglu, E., ... Yumak, Y. (2022). The neutralization effect of montelukast on SARS-CoV-2 is shown by multiscale in silico simulations and combined in vitro studies. Molecular Therapy, 30(2), 963-974. https://doi.org/10.1016/j.ymthe.2021.10.014
Type: Journal-article
Authors: Yen-Lin Chen, Lois Pollack
Citation: Chen, Y.-L., & Pollack, L. (2021). Decoding hidden structural information in solution wide-angle X-ray scattering (WAXS): from ensemble modeling to machine learning. Acta Crystallographica Section A Foundations and Advances, 77(a1), a126-a126. https://doi.org/10.1107/s0108767321098731
Type: Journal-article
Authors: Weiwei He, Yen-Lin Chen, Serdal Kirmizialtin, Lois Pollack
Citation: He, W., Chen, Y.-L., Kirmizialtin, S., & Pollack, L. (2021). Visualization of biomolecular structures by WAXS and MD. Acta Crystallographica Section A Foundations and Advances, 77(a1), a124-a124. https://doi.org/10.1107/s0108767321098755
Type: Journal-article
Authors: Kara Zielinski, Lois Pollack
Citation: Zielinski, K., & Pollack, L. (2021). What it takes for a successful mix-and-inject serial crystallography experiment: from a sample preparation and sample delivery perspective. Acta Crystallographica Section A Foundations and Advances, 77(a1), a78-a78. https://doi.org/10.1107/s0108767321099219
Type: Journal-article
Authors: Michael Thompson, Alexander Wolff, Benjamin Barad, Wilson Nieves Vasquez, Nathaniel Brown, Hyun Sun Cho, Friedrich Schotte, Valentyn Stadnytskyi, Philip Anfinrud, James Fraser
Citation: Thompson, M., Wolff, A., Barad, B., Vasquez, W. N., Brown, N., Cho, H. S., Schotte, F., Stadnytskyi, V., Anfinrud, P., & Fraser, J. (2021). Turning up the heat on molecular machines with multi-temperature and temperature-jump X-ray scattering experiments. Acta Crystallographica Section A Foundations and Advances, 77(a1), a215-a215. https://doi.org/10.1107/s0108767321097841
Type: Journal-article
Authors: Sarah Bowman, Miranda Lynch, Angela Lauricella, Edward Snell
Citation: Bowman, S., Lynch, M., Lauricella, A., & Snell, E. (2021). Pushing the boundaries in crystallization screening: making automated user-accessible crystallization work. Acta Crystallographica Section A Foundations and Advances, 77(a1), a152-a152. https://doi.org/10.1107/s0108767321098470
Type: Journal-article
Authors: Edward Snell, Diana Monteiro, Sarah Bowman
Citation: Snell, E., Monteiro, D., & Bowman, S. (2021). The ideal crystal for structural biology. Acta Crystallographica Section A Foundations and Advances, 77(a1), a109-a109. https://doi.org/10.1107/s0108767321098901
Type: Journal-article
Authors: Suraj Pandey, George Calvey, Andrea M. Katz, Tek Narsingh Malla, Faisal H. M. Koua, Jose M. Martin-Garcia, Ishwor Poudyal, Jay-How Yang, Mohammad Vakili, Oleksandr Yefanov, Kara A. Zielinski, Sasa Bajt, Salah Awel, Katarina Doerner, Matthias Frank, Luca Gelisio, Rebecca Jernigan, Henry Kirkwood, Marco Kloos, Jayanath Koliyadu, Valerio Mariani, Mitchell D. Miller, Grant Mills, Garrett Nelson, Jose L. Olmos, Alireza Sadri, Tokushi Sato, Alexandra Tolstikova, Weijun Xu, Abbas Ourmazd, John C. H. Spence, Peter Schwander, Anton Barty, Henry N. Chapman, Petra Fromme, Adrian P. Mancuso, George N. Phillips, Richard Bean, Lois Pollack, Marius Schmidt
Citation: Pandey, S. et al., 2021. Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography. IUCrJ, 8(6).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Terra Sztain, Surl-Hee Ahn, Anthony T. Bogetti, Lorenzo Casalino, Jory A. Goldsmith, Evan Seitz, Ryan S. McCool, Fiona L. Kearns, Francisco Acosta-Reyes, Suvrajit Maji, Ghoncheh Mashayekhi, J. Andrew McCammon, Abbas Ourmazd, Joachim Frank, Jason S. McLellan, Lillian T. Chong, Rommie E. Amaro
Citation: Sztain, T. et al., 2021. A glycan gate controls opening of the SARS-CoV-2 spike protein. Nature Chemistry.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Serdar Durdagi, Çağdaş Dağ, Berna Dogan, Merve Yigin, Timucin Avsar, Cengizhan Buyukdag, Ismail Erol, Fatma Betul Ertem, Seyma Calis, Gunseli Yildirim, Muge D. Orhan, Omur Guven, Busecan Aksoydan, Ebru Destan, Kader Sahin, Sabri O. Besler, Lalehan Oktay, Alaleh Shafiei, Ilayda Tolu, Esra Ayan, Busra Yuksel, Ayse B. Peksen, Oktay Gocenler, Ali D. Yucel, Ozgur Can, Serena Ozabrahamyan, Alpsu Olkan, Ece Erdemoglu, Fulya Aksit, Gokhan Tanisali, 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, Alex Batyuk, Valerio Mariani, Zhen Su, Frederic Poitevin, Chun Hong Yoon, Christopher Kupitz, Raymond G. Sierra, Edward H. Snell, Hasan DeMirci
Citation: Durdagi, S. et al., 2021. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing. Structure.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: M. Sonker, B.G. Abdallah, A. Ros
Citation: Sonker, M., Abdallah, B.G. & Ros, A., 2021. Surface coatings for microfluidic biomedical devices. Microfluidic Devices for Biomedical Applications, pp.79-123.
Type: Book-chapter
Authors: Jonathan K. Williams, Baifan Wang, Andrew Sam, Cody L. Hoop, David A. Case, Jean Baum
Type: Journal-article
Authors: Timothy R. Stachowski, Mary E. Snell, Edward H. Snell
Citation: Stachowski, T.R., Snell, M.E. & Snell, E.H., 2021. A SAXS-based approach to rationally evaluate radical scavengers - toward eliminating radiation damage in solution and crystallographic studies. Journal of Synchrotron Radiation, 28(5).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Halilibrahim Ciftci, Hiroshi Tateishi, Kotaro Koiwai, Ryoko Koga, Kensaku Anraku, Kazuaki Monde, Çağdaş Dağ, Ebru Destan, Busra Yuksel, Esra Ayan, Gunseli Yildirim, Merve Yigin, F. Betul Ertem, Alaleh Shafiei, Omur Guven, Sabri O. Besler, Raymond G. Sierra, Chun Hong Yoon, Zhen Su, Mengling Liang, Burcin Acar, Turkan Haliloglu, Masami Otsuka, Fumiaki Yumoto, Mikako Fujita, Toshiya Senda, Hasan DeMirci
Citation: Ciftci, H. et al., 2021. Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein. Scientific Reports, 11(1).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Andrea Cellini, Weixiao Yuan Wahlgren, Léocadie Henry, Suraj Pandey, Swagatha Ghosh, Leticia Castillon, Elin Claesson, Heikki Takala, Joachim Kübel, Amke Nimmrich, Valentyna Kuznetsova, Eriko Nango, So Iwata, Shigeki Owada, Emina A. Stojković, Marius Schmidt, Janne A. Ihalainen, Sebastian Westenhoff
Citation: Cellini, A. et al., 2021. The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature. Acta Crystallographica Section D Structural Biology, 77(8), pp.1001-1009.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Gokhan Tanisali, Ahmet Sozak, Abdul Samet Bulut, Tolga Ziya Sander, Ozlem Dogan, Cagdas Dag, Mehmet Gönen, Fusun Can, Hasan Demirci, Onder Ergonul
Citation: Tanisali, G. et al., 2021. Effectiveness of different types of Masks in Aerosol Dispersion in SARS-CoV-2 Infection. International Journal of Infectious Diseases.
Type: Journal-article
Authors: Shuo Sui, Anne Mulichak, Raviraj Kulathila, Joshua McGee, Danny Filiatreault, Sarthak Saha, Aina Cohen, Jinhu Song, Holly Hung, Jonathan Selway, Christina Kirby, Om K. Shrestha, Wilhelm Weihofen, Michelle Fodor, Mei Xu, Rajiv Chopra, Sarah L. Perry
Citation: Sui, S. et al., 2021. A capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screening. Journal of Applied Crystallography, 54(4).
Type: Journal-article
Authors: Mikael H Elias, James S Fraser, Shina Caroline Lynn Kamerlin, Wayne M Patrick, Colin J Jackson
Citation: Elias, M.H. et al., 2021. Dan Salah Tawfik (1955‐2021)--A giant of protein evolution. EMBO reports.
Type: Journal-article
Authors: Paul Bogdan, Gustavo Caetano-Anollés, Anna Jolles, Hyunju Kim, James Morris, Cheryl A Murphy, Catherine Royer, Edward H Snell, Adam Steinbrenner, Nicholas Strausfeld
Citation: Bogdan, P., Caetano-Anollés, G., Jolles, A., Kim, H., Morris, J., Murphy, C. A., Royer, C., Snell, E. H., Steinbrenner, A., & Strausfeld, N. (2021). Biological Networks across Scales--The Theoretical and Empirical Foundations for Time-Varying Complex Networks that Connect Structure and Function across Levels of Biological Organization. Integrative and Comparative Biology, 61(6), 1991-2010. https://doi.org/10.1093/icb/icab069
Type: Journal-article
Authors: Kara Zielinski, Lois Pollack
Citation: Zielinski, K. & Pollack, L., 2020. Applications of microfluidic mixers for time-resolved SAXS and crystallography experiments. Acta Crystallographica Section A Foundations and Advances, 76(a1), pp.a33-a33.
Type: Journal-article
Authors: Tek Narsingh Malla, Suraj Pandey, Luis Aldama, Dennisse Feliz, Moraima Noda, Ishwor Poudyal, George N. Phillips, Emina A. Stojković, Marius Schmidt
Citation: Malla, T.N. et al., 2021. Vitamin C Binds to SARS Coronavirus-2 Main Protease Essential for Viral Replication.
Type: Posted-content
Authors: Weiwei He, Yen-Lin Chen, Lois Pollack, Serdal Kirmizialtin
Citation: He, W. et al., 2021. The structural plasticity of nucleic acid duplexes revealed by WAXS and MD. Science Advances, 7(17), p.eabf6106.
Type: Journal-article
Authors: Miranda L. Lynch, Edward H. Snell, Sarah E. J. Bowman
Citation: Lynch, M.L., Snell, E.H. & Bowman, S.E.J., 2021. Structural biology in the time of COVID-19: perspectives on methods and milestones. IUCrJ, 8(3), pp.335-341.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Edmond M. Linossi, Gabriella O. Estevam, Masaya Oshima, James S. Fraser, Eric A. Collisson, Natalia Jura
Citation: Linossi, E. M., Estevam, G. O., Oshima, M., Fraser, J. S., Collisson, E. A., & Jura, N. (2021). State of the structure address on MET receptor activation by HGF. Biochemical Society Transactions, 49(2), 645-661. https://doi.org/10.1042/bst20200394
Type: Journal-article
Authors: Willow Coyote-Maestas, James S Fraser
Citation: Coyote-Maestas, W., & Fraser, J. S. (2021). ORACLE reveals a bright future to fight bacteria. ELife, 10. CLOCKSS. https://doi.org/10.7554/elife.68277
Type: Journal-article
Authors: Marion Schuller, Galen J. Correy, Stefan Gahbauer, Daren Fearon, Taiasean Wu, Roberto Efraín Díaz, Iris D. Young, Luan Carvalho Martins, Dominique H. Smith, Ursula Schulze-Gahmen, Tristan W. Owens, Ishan Deshpande, Gregory E. Merz, Aye C. Thwin, Justin T. Biel, Jessica K. Peters, Michelle Moritz, Nadia Herrera, Huong T. Kratochvil, Anthony Aimon, James M. Bennett, Jose Brandao Neto, Aina E. Cohen, Alexandre Dias, Alice Douangamath, Louise Dunnett, Oleg Fedorov, Matteo P. Ferla, Martin R. Fuchs, Tyler J. Gorrie-Stone, James M. Holton, Michael G. Johnson, Tobias Krojer, George Meigs, Ailsa J. Powell, Johannes Gregor Matthias Rack, Victor L. Rangel, Silvia Russi, Rachael E. Skyner, Clyde A. Smith, Alexei S. Soares, Jennifer L. Wierman, Kang Zhu, Peter O’Brien, Natalia Jura, Alan Ashworth, John J. Irwin, Michael C. Thompson, Jason E. Gestwicki, Frank von Delft, Brian K. Shoichet, James S. Fraser, Ivan Ahel,
Citation: Schuller, M. et al., 2021. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Science Advances, 7(16), p.eabf8711.
Type: Journal-article
Authors: Alexander W Mauney, Uma M Muthurajan, Karolin Luger, Lois Pollack
Citation: Mauney, A.W. et al., 2021. Solution structure(s) of trinucleosomes from contrast variation SAXS. Nucleic Acids Research, 49(9), pp.5028-5037.
Type: Journal-article
Authors: E. H. Snell, J. R. Helliwell
Citation: Snell, E.H. & Helliwell, J.R., 2021. Microgravity as an environment for macromolecular crystallization - an outlook in the era of space stations and commercial space flight. Crystallography Reviews, pp.1-44.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Mian Yang, Jorvani Cruz Villarreal, Nethmi Ariyasinghe, Rory Kruithoff, Robert Ros, Alexandra Ros
Citation: Yang, M. et al., 2021. Quantitative Approach for Protein Analysis in Small Cell Ensembles by an Integrated Microfluidic Chip with MALDI Mass Spectrometry. Analytical Chemistry, 93(15), pp.6053-6061.
Type: Journal-article
Authors: Darya Marchany‐Rivera, Rafael A. Estremera‐Andújar, Carlos Nieves‐Marrero, Carlos R. Ruiz‐Martínez, William Bauer, Juan López‐Garriga
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Melissa Carrillo, Suraj Pandey, Juan Sanchez, Moraima Noda, Ishwor Poudyal, Luis Aldama, Tek Narsingh Malla, Elin Claesson, Weixiao Yuan Wahlgren, Denisse Feliz, Vukica Šrajer, Michał Maj, Leticia Castillon, So Iwata, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, Kensuke Tono, Shigeki Owada, Sebastian Westenhoff, Emina A. Stojković, Marius Schmidt
Citation: Carrillo, M. et al., 2021. High-resolution crystal structures of transient intermediates in the phytochrome photocycle. Structure.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Ji-Hye Yun, Xuanxuan Li, Jianing Yue, Jae-Hyun Park, Zeyu Jin, Chufeng Li, Hao Hu, Yingchen Shi, Suraj Pandey, Sergio Carbajo, Sébastien Boutet, Mark S. Hunter, Mengning Liang, Raymond G. Sierra, Thomas J. Lane, Liang Zhou, Uwe Weierstall, Nadia A. Zatsepin, Mio Ohki, Jeremy R. H. Tame, Sam-Yong Park, John C. H. Spence, Wenkai Zhang, Marius Schmidt, Weontae Lee, Haiguang Liu
Citation: Yun, J.-H. et al., 2021. Early-stage dynamics of chloride ion-pumping rhodopsin revealed by a femtosecond X-ray laser. Proceedings of the National Academy of Sciences, 118(13), p.e2020486118.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Saminathan Ramakrishnan, Jason R. Stagno, Chelsie E. Conrad, Jienyu Ding, Ping Yu, Yuba R. Bhandari, Yun-Tzai Lee, Gary Pauly, Oleksandr Yefanov, Max O. Wiedorn, Juraj Knoska, Dominik Oberthür, Thomas A. White, Anton Barty, Valerio Mariani, Chufeng Li, Wolfgang Brehm, William F. Heinz, Valentin Magidson, Stephen Lockett, Mark S. Hunter, Sébastien Boutet, Nadia A. Zatsepin, Xiaobing Zuo, Thomas D. Grant, Suraj Pandey, Marius Schmidt, John C. H. Spence, Henry N. Chapman, Yun-Xing Wang
Citation: Ramakrishnan, S. et al., 2021. Synchronous RNA conformational changes trigger ordered phase transitions in crystals. Nature Communications, 12(1).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Charles L. Brooks, David A. Case, Steve Plimpton, Benoît Roux, David van der Spoel, Emad Tajkhorshid
Citation: Brooks, C.L. et al., 2021. Classical molecular dynamics. The Journal of Chemical Physics, 154(10), p.100401.
Type: Journal-article
Authors: William J. Bauer, Sarah B. Woodruff
Citation: Bauer, W.J. & Woodruff, S.B., 2021. A science education model for large collaborative centers. Structural Dynamics, 8(2), p.020402.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Carlos Sanchez-Cano, Ramon A. Alvarez-Puebla, John M. Abendroth, Tobias Beck, Robert Blick, Yuan Cao, Frank Caruso, Indranath Chakraborty, Henry N. Chapman, Chunying Chen, Bruce E. Cohen, Andre L. C. Conceição, David P. Cormode, Daxiang Cui, Kenneth A. Dawson, Gerald Falkenberg, Chunhai Fan, Neus Feliu, Mingyuan Gao, Elisabetta Gargioni, Claus-C. Glüer, Florian Grüner, Moustapha Hassan, Yong Hu, Yalan Huang, Samuel Huber, Nils Huse, Yanan Kang, Ali Khademhosseini, Thomas F. Keller, Christian Körnig, Nicholas A. Kotov, Dorota Koziej, Xing-Jie Liang, Beibei Liu, Sijin Liu, Yang Liu, Ziyao Liu, Luis M. Liz-Marzán, Xiaowei Ma, Andres Machicote, Wolfgang Maison, Adrian P. Mancuso, Saad Megahed, Bert Nickel, Ferdinand Otto, Cristina Palencia, Sakura Pascarelli, Arwen Pearson, Oula Peñate-Medina, Bing Qi, Joachim Rädler, Joseph J. Richardson, Axel Rosenhahn, Kai Rothkamm, Michael Rübhausen, Milan K. Sanyal, Raymond E. Schaak, Heinz-Peter Schlemmer, Marius Schmidt, Oliver Schmutzler, Theo Schotten, Florian Schulz, A. K. Sood, Kathryn M. Spiers, Theresa Staufer, Dominik M. Stemer, Andreas Stierle, Xing Sun, Gohar Tsakanova, Paul S. Weiss, Horst Weller, Fabian Westermeier, Ming Xu, Huijie Yan, Yuan Zeng, Ying Zhao, Yuliang Zhao, Dingcheng Zhu, Ying Zhu, Wolfgang J. Parak
Citation: Sanchez-Cano, C. et al., 2021. X-ray-Based Techniques to Study the Nano-Bio Interface. ACS Nano, 15(3), pp.3754-3807.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Thomas D. Grant
Citation: Grant, T.D., 2021. Reply to: Limitations of the iterative electron density reconstruction algorithm from solution scattering data. Nature Methods, 18(3), pp.246-248.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Laura Lemel, Katarzyna Nieścierowicz, M. Dolores García-Fernández, Leonardo Darré, Thierry Durroux, Marta Busnelli, Mylène Pezet, Fabrice Rébeillé, Juliette Jouhet, Bernard Mouillac, Carmen Domene, Bice Chini, Vadim Cherezov, Christophe J. Moreau
Citation: Lemel, L. et al., 2021. The ligand-bound state of a G protein-coupled receptor stabilizes the interaction of functional cholesterol molecules. Journal of Lipid Research, 62, p.100059.
Type: Journal-article
Authors: J.P.J. Chen, K.E. Schmidt, J.C.H. Spence, R.A. Kirian
Citation: Chen, J.P.J. et al., 2021. A new solution to the curved Ewald sphere problem for 3D image reconstruction in electron microscopy. Ultramicroscopy, p.113234.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Halilibrahim Ciftci, Hiroshi Tateishi, Kotaro Koiwai, Ryoko Koga, Kensaku Anraku, Kazuaki Monde, Çağdaş Dağ, Ebru Destan, Busra Yuksel, Esra Ayan, Gunseli Yildirim, Merve Yigin, F. Betul Ertem, Alaleh Shafiei, Omur Guven, Sabri O. Besler, Raymond G. Sierra, Chun Hong Yoon, Zhen Su, Mengling Liang, Burcin Acar, Turkan Haliloglu, Masami Otsuka, Fumiaki Yumoto, Mikako Fujita, Toshiya Senda, Hasan DeMirci
Citation: Ciftci, H. et al., 2021. Structural insight into host plasma membrane association and assembly of HIV-1 Matrix protein.
Type: Posted-content
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Ethan T. Holleman, Erica Duguid, Lisa J. Keefe, Sarah E. J. Bowman
Citation: Holleman, E.T. et al., 2021. Polo: an open-source graphical user interface for crystallization screening. Journal of Applied Crystallography, 54(2), pp.673-679.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Qiuyun Guo, Jordan R. Yaron, John W. Wallen, Kyle F. Browder, Ryan Boyd, Tien L. Olson, Michelle Burgin, Peaches Ulrich, Emily Aliskevich, Lauren N. Schutz, Petra Fromme, Liqiang Zhang, Alexandra R. Lucas
Citation: Guo, Q. et al., 2021. PEGylated Serp-1 Markedly Reduces Pristane-Induced Experimental Diffuse Alveolar Hemorrhage, Altering uPAR Distribution, and Macrophage Invasion. Frontiers in Cardiovascular Medicine, 8.
Type: Journal-article
Authors: Eduardo R. Cruz-Chú, Ahmad Hosseinizadeh, Ghoncheh Mashayekhi, Russell Fung, Abbas Ourmazd, Peter Schwander
Citation: Cruz-Chú, E.R. et al., 2021. Selecting XFEL single-particle snapshots by geometric machine learning. Structural Dynamics, 8(1), p.014701.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Yen-Lin Chen, Weiwei He, Lois Pollack, Serdal Kirmizialtin
Citation: Chen, Y.-L. et al., 2021. Breaking the Boundary between Solution X-Ray Scattering and Molecular Dynamics Simulations of Structured Nucleic Acids. Biophysical Journal, 120(3), p.315a.
Type: Journal-article
Authors: Premila P. Samuel, David A. Case
Citation: Samuel, P.P. & Case, D.A., 2021. Molecular Dynamics Simulations Unravel the Mysteries of Hemoglobin Diseases. Biophysical Journal, 120(3), p.298a.
Type: Journal-article
Authors: P. Lourdu Xavier, Kartik Ayyer, Oleksandr Yefanov, Luca Gelisio, Johan Bielecki, Amit K. Samanta, Saša Bajt, Ruojie Sha, David A. Bushnell, Roger D. Kornberg, Yevheniy Ovcharenko, Jochen Kuepper, Michael Meyer, Nadrian C. Seeman, Henry N. Chapman
Citation: Xavier, P.L. et al., 2021. Femtosecond Single-Particle Diffractive Imaging of 3D DNA-Origami Molecular Scaffolds with XFEL Pulses. Biophysical Journal, 120(3), p.265a.
Type: Journal-article
Authors: Thomas D. Grant, Suchithranga M.D.C. Perera, Leslie A. Salas-Estrada, Andrey V. Struts, Udeep Chawla, Steven D.E. Fried, Nipuna Weerasinghe, Kostantinos Karpos, Domingo Meza, Nadia A. Zatsepin, Alan Grossfield, Derek Mendez, Petra Fromme, Richard A. Kirian, Michael F. Brown
Citation: Grant, T.D. et al., 2021. Ultrafast Membrane Protein Dynamics Revealed by X-Ray Scattering with a Femtosecond Free-Electron Laser. Biophysical Journal, 120(3), p.133a.
Type: Journal-article
Authors: C. Swathi K. Menon, Konstantinos Karpos, Thomas D. Grant, Andrey V. Struts, Steven D.E. Fried, Suchithranga M.D.C. Perera, Irina V. Kosheleva, Leslie Salas-Estrada, Alan Grossfield, Petra Fromme, Richard A. Kirian, Michael F. Brown
Citation: Menon, C.S.K. et al., 2021. Functional Expansion of G-Protein-Coupled Receptor Shown by Time-Resolved X-Ray Scattering. Biophysical Journal, 120(3), p.132a.
Type: Journal-article
Authors: Viktoriia Shaulskaia, Aleksandra Luginina, Polina Khorn, Anastasiia Gusach, Olga Sukhacheva, Ekaterina Smirnova, Valentin Borshchevskiy, Alexey Mishin, Vadim Cherezov
Citation: Shaulskaia, V. et al., 2021. Sodium Binding in Cysteinyl Leukotriene G Protein-Coupled Receptors. Biophysical Journal, 120(3), p.129a.
Type: Journal-article
Authors: Heqiao Zhang, Dong-Hua Chen, Rayees U.H. Mattoo, David A. Bushnell, Yannan Wang, Chao Yuan, Lin Wang, Chunnian Wang, Ralph E. Davis, Yan Nie, Roger D. Kornberg
Type: Journal-article
Authors: L.E. Malin, W.S. Graves, M. Holl, J.C.H. Spence, E.A. Nanni, R.K. Li, X. Shen, S. Weathersby
Citation: Malin, L.E. et al., 2021. Quantitative agreement between dynamical rocking curves in ultrafast electron diffraction for x-ray lasers. Ultramicroscopy, 223, p.113211.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Catherine L. Lawson, Andriy Kryshtafovych, Paul D. Adams, Pavel V. Afonine, Matthew L. Baker, Benjamin A. Barad, Paul Bond, Tom Burnley, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kevin Cowtan, Ken A. Dill, Frank DiMaio, Daniel P. Farrell, James S. Fraser, Mark A. Herzik, Soon Wen Hoh, Jie Hou, Li-Wei Hung, Maxim Igaev, Agnel P. Joseph, Daisuke Kihara, Dilip Kumar, Sumit Mittal, Bohdan Monastyrskyy, Mateusz Olek, Colin M. Palmer, Ardan Patwardhan, Alberto Perez, Jonas Pfab, Grigore D. Pintilie, Jane S. Richardson, Peter B. Rosenthal, Daipayan Sarkar, Luisa U. Schäfer, Michael F. Schmid, Gunnar F. Schröder, Mrinal Shekhar, Dong Si, Abishek Singharoy, Genki Terashi, Thomas C. Terwilliger, Andrea Vaiana, Liguo Wang, Zhe Wang, Stephanie A. Wankowicz, Christopher J. Williams, Martyn Winn, Tianqi Wu, Xiaodi Yu, Kaiming Zhang, Helen M. Berman, Wah Chiu
Citation: Lawson, C.L. et al., 2021. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Methods, 18(2), pp.156-164.
Type: Journal-article
Authors: Iosifina Sarrou, Christian G. Feiler, Sven Falke, Nolan Peard, Oleksandr Yefanov, Henry Chapman
Citation: Sarrou, I. et al., 2021. C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening. Acta Crystallographica Section D Structural Biology, 77(2), pp.224-236.
Type: Journal-article
Authors: Jonathan K. Williams, Baifan Wang, Andrew Sam, Cody L. Hoop, David A. Case, Jean Baum
Citation: Williams, J.K. et al., 2021. Molecular Dynamics Analysis of a Flexible Loop at the Binding Interface of the SARS-CoV-2 Spike Protein Receptor-Binding Domain.
Type: Posted-content
Authors: James Geiger, Rick Sexton, Zina Al-Sahouri, Ming-Yue Lee, Eugene Chun, Kaleeckal G. Harikumar, Laurence J. Miller, Oliver Beckstein, Wei Liu
Citation: Geiger, J. et al., 2021. Evidence that specific interactions play a role in the cholesterol sensitivity of G protein-coupled receptors. Biochimica et Biophysica Acta (BBA) - Biomembranes, p.183557.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Israel Rodríguez, Ritika Gautam, Arthur D. Tinoco
Citation: Rodríguez, I., Gautam, R. & Tinoco, A.D., 2020. Using X-ray Diffraction Techniques for Biomimetic Drug Development, Formulation, and Polymorphic Characterization. Biomimetics, 6(1), p.1.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Filip Yabukarski, Justin T. Biel, Margaux M. Pinney, Tzanko Doukov, Alexander S. Powers, James S. Fraser, Daniel Herschlag
Citation: Yabukarski, F. et al., 2020. Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles. Proceedings of the National Academy of Sciences, 117(52), pp.33204-33215.
Type: Journal-article
Authors: Hannes Braberg, Ignacia Echeverria, Stefan Bohn, Peter Cimermancic, Anthony Shiver, Richard Alexander, Jiewei Xu, Michael Shales, Raghuvar Dronamraju, Shuangying Jiang, Gajendradhar Dwivedi, Derek Bogdanoff, Kaitlin K. Chaung, Ruth Hüttenhain, Shuyi Wang, David Mavor, Riccardo Pellarin, Dina Schneidman, Joel S. Bader, James S. Fraser, John Morris, James E. Haber, Brian D. Strahl, Carol A. Gross, Junbiao Dai, Jef D. Boeke, Andrej Sali, Nevan J. Krogan
Citation: Braberg, H. et al., 2020. Genetic interaction mapping informs integrative structure determination of protein complexes. Science, 370(6522), p.eaaz4910.
Type: Journal-article
Authors: Ryan S. Edmonds, Tanner J. Finney, Michael R. Bull, Aude A. Watrelot, Tonya L. Kuhl
Citation: Edmonds, R.S. et al., 2021. Friction measurements of model saliva-wine solutions between polydimethylsiloxane surfaces. Food Hydrocolloids, 113, p.106522.
Type: Journal-article
Authors: Markus Metz, Romain D. Arnal, Wolfgang Brehm, Henry N. Chapman, Andrew J. Morgan, Rick P. Millane
Citation: Metz, M. et al., 2021. Macromolecular phasing using diffraction from multiple crystal forms. Acta Crystallographica Section A Foundations and Advances, 77(1), pp.19-35.
Type: Journal-article
Authors: Huijong Han, Ekaterina Round, Robin Schubert, Yasmin Gül, Jana Makroczyová, Domingo Meza, Philipp Heuser, Martin Aepfelbacher, Imrich Barák, Christian Betzel, Petra Fromme, Inari Kursula, Poul Nissen, Elena Tereschenko, Joachim Schulz, Charlotte Uetrecht, Jozef Ulicný, Matthias Wilmanns, Janos Hajdu, Victor S. Lamzin, Kristina Lorenzen
Citation: Han, H. et al., 2021. The XBI BioLab for life science experiments at the European XFEL. Journal of Applied Crystallography, 54(1), pp.7-21.
Type: Journal-article
Authors: Suraj Pandey, George Calvey, Andrea M. Katz, Tek Narsingh Malla, Faisal H. M. Koua, Jose M. Martin-Garcia, Ishwor Poudyal, Jay-How Yang, Mohammad Vakili, Oleksandr Yefanov, Kara A. Zielinski, Saša Bajt, Salah Awel, Katerina Dörner, Matthias Frank, Luca Gelisio, Rebecca Jernigan, Henry Kirkwood, Marco Kloos, Jayanath Koliyadu, Valerio Mariani, Mitchell D. Miller, Grant Mills, Garrett Nelson, Jose L. Olmos, Alireza Sadri, Tokushi Sato, Alexandra Tolstikova, Weijun Xu, Abbas Ourmazd, John H. C. Spence, Peter Schwander, Anton Barty, Henry N. Chapman, Petra Fromme, Adrian P. Mancuso, George N. Phillips, Richard Bean, Lois Pollack, Marius Schmidt
Citation: Pandey, S. et al., 2020. Direct Observation of the Mechanism of Antibiotic Resistance by Mix-and-Inject at the European XFEL.
Type: Posted-content
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Mohamed Abdellatif-Youssef, Martin Etter, Petra Fromme, Marco Salerno
Citation: Abdellatif-Youssef, M. et al., 2021. Extended properties of magnetic spins of zinc ferrite nanoparticles in the THz frequency range. Journal of Magnetism and Magnetic Materials, 525, p.167574.
Type: Journal-article
Authors: Kartik Ayyer, P. Lourdu Xavier, Johan Bielecki, Zhou Shen, Benedikt J. Daurer, Amit K. Samanta, Salah Awel, Richard Bean, Anton Barty, Martin Bergemann, Tomas Ekeberg, Armando D. Estillore, Hans Fangohr, Klaus Giewekemeyer, Mark S. Hunter, Mikhail Karnevskiy, Richard A. Kirian, Henry Kirkwood, Yoonhee Kim, Jayanath Koliyadu, Holger Lange, Romain Letrun, Jannik Lübke, Thomas Michelat, Andrew J. Morgan, Nils Roth, Tokushi Sato, Marcin Sikorski, Florian Schulz, John C. H. Spence, Patrik Vagovic, Tamme Wollweber, Lena Worbs, Oleksandr Yefanov, Yulong Zhuang, Filipe R. N. C. Maia, Daniel A. Horke, Jochen Küpper, N. Duane Loh, Adrian P. Mancuso, Henry N. Chapman
Citation: Ayyer, K. et al., 2020. 3D diffractive imaging of nanoparticle ensembles using an x-ray laser. Optica, 8(1), p.15.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Renee Otten, Ricardo A. P. Pádua, H. Adrian Bunzel, Vy Nguyen, Warintra Pitsawong, MacKenzie Patterson, Shuo Sui, Sarah L. Perry, Aina E. Cohen, Donald Hilvert, Dorothee Kern
Citation: Otten, R. et al., 2020. How directed evolution reshapes the energy landscape in an enzyme to boost catalysis. Science, p.eabd3623.
Type: Journal-article
Authors: Haoyuan Li, Reza Nazari, Brian Abbey, Roberto Alvarez, Andrew Aquila, Kartik Ayyer, Anton Barty, Peter Berntsen, Johan Bielecki, Alberto Pietrini, Maximilian Bucher, Gabriella Carini, Henry N. Chapman, Alice Contreras, Benedikt J. Daurer, Hasan DeMirci, Leonie Flűckiger, Matthias Frank, Janos Hajdu, Max F. Hantke, Brenda G. Hogue, Ahmad Hosseinizadeh, Mark S. Hunter, H. Olof Jönsson, Richard A. Kirian, Ruslan P. Kurta, Duane Loh, Filipe R. N. C. Maia, Adrian P. Mancuso, Andrew J. Morgan, Matthew McFadden, Kerstin Muehlig, Anna Munke, Hemanth Kumar Narayana Reddy, Carl Nettelblad, Abbas Ourmazd, Max Rose, Peter Schwander, M. Marvin Seibert, Jonas A. Sellberg, Raymond G. Sierra, Zhibin Sun, Martin Svenda, Ivan A. Vartanyants, Peter Walter, Daniel Westphal, Garth Williams, P. Lourdu Xavier, Chun Hong Yoon, Sahba Zaare
Citation: Li, H. et al., 2020. Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source. Scientific Data, 7(1).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Blake T. Riley, Stephanie A. Wankowicz, Saulo H. P. Oliveira, Gydo C. P. Zundert, Daniel W. Hogan, James S. Fraser, Daniel A. Keedy, Henry Bedem
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Timothy R. Stachowski, Mary E. Snell, Edward H. Snell
Citation: Stachowski, T.R., Snell, M.E. & Snell, E.H., 2020. SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique T. J. Boggon, ed. PLOS ONE, 15(11), p.e0239702.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: A. Hosseinizadeh, N. Breckwoldt, R. Fung, R. Sepehr, M. Schmidt, P. Schwander, R. Santra, A. Ourmazd
Citation: Hosseinizadeh, A. et al., 2020. Single-femtosecond atomic-resolution observation of a protein traversing a conical intersection.
Type: Posted-content
Authors: Suzette A. Pabit, Yen-Lin Chen, Emery T. Usher, Erik C. Cook, Lois Pollack, Scott A. Showalter
Citation: Pabit, S.A. et al., 2020. Elucidating the Role of Microprocessor Protein DGCR8 in Bending RNA Structures. Biophysical Journal, 119(12), pp.2524-2536.
Type: Journal-article
Authors: Tobias Krojer, James S Fraser, Frank von Delft
Citation: Krojer, T., Fraser, J.S. & von Delft, F., 2020. Discovery of allosteric binding sites by crystallographic fragment screening. Current Opinion in Structural Biology, 65, pp.209-216.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Christopher Gisriel, Petra Fromme, Jose M. Martin-Garcia
Citation: Gisriel, C., Fromme, P. & Martin-Garcia, J.M., 2020. Methods for Crystallization and Structural Determination of M-T7 Protein from Myxoma Virus. Viruses as Therapeutics, pp.125-162.
Type: Book-chapter
Authors: Shikai Jin, Mitchell D. Miller, Mingchen Chen, Nicholas P. Schafer, Xingcheng Lin, Xun Chen, George N. Phillips, Peter G. Wolynes
Citation: Jin, S. et al., 2020. Molecular-replacement phasing using predicted protein structures from AWSEM-Suite. IUCrJ, 7(6), pp.1168-1178.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Xingjie Pan, Michael C. Thompson, Yang Zhang, Lin Liu, James S. Fraser, Mark J. S. Kelly, Tanja Kortemme
Citation: Pan, X. et al., 2020. Expanding the space of protein geometries by computational design of de novo fold families. Science, 369(6507), pp.1132-1136.
Type: Journal-article
Authors: D Koulentianos, A E A Fouda, S H Southworth, J D Bozek, J Küpper, R Santra, N V Kryzhevoi, L S Cederbaum, C Bostedt, M Messerschmidt, N Berrah, L Fang, B Murphy, T Osipov, J P Cryan, J Glownia, S Ghimire, P J Ho, B Krässig, D Ray, Y Li, E P Kanter, L Young, G Doumy
Citation: Koulentianos, D. et al., 2020. High intensity x-ray interaction with a model bio-molecule system: double-core-hole states and fragmentation of formamide. Journal of Physics B: Atomic, Molecular and Optical Physics, 53(24), p.244005.
Type: Journal-article
Authors: Dameli Assalauova, Young Yong Kim, Sergey Bobkov, Ruslan Khubbutdinov, Max Rose, Roberto Alvarez, Jakob Andreasson, Eugeniu Balaur, Alice Contreras, Hasan DeMirci, Luca Gelisio, Janos Hajdu, Mark S. Hunter, Ruslan P. Kurta, Haoyuan Li, Matthew McFadden, Reza Nazari, Peter Schwander, Anton Teslyuk, Peter Walter, P. Lourdu Xavier, Chun Hong Yoon, Sahba Zaare, Viacheslav A. Ilyin, Richard A. Kirian, Brenda G. Hogue, Andrew Aquila, Ivan A. Vartanyants
Citation: Assalauova, D. et al., 2020. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. IUCrJ, 7(6), pp.1102-1113.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Ming-Yue Lee, James Geiger, Andrii Ishchenko, Gye Won Han, Anton Barty, Thomas A. White, Cornelius Gati, Alexander Batyuk, Mark S. Hunter, Andrew Aquila, Sébastien Boutet, Uwe Weierstall, Vadim Cherezov, Wei Liu
Citation: Lee, M.-Y. et al., 2020. Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase. IUCrJ, 7(6), pp.976-984.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Justin F. Lucas, Milton L. Chip Routt, Jonathan G. Eastman
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Megan L. Shelby, Deepshika Gilbile, Thomas D. Grant, William J. Bauer, Brent Segelke, Wei He, Angela C. Evans, Natalia Crespo, Pontus Fischer, Tim Pakendorf, Vincent Hennicke, Mark S. Hunter, Alex Batyuk, Miriam Barthelmess, Alke Meents, Tonya L. Kuhl, Matthias Frank, Matthew A. Coleman
Citation: Shelby, M.L. et al., 2020. Crystallization of ApoA1 and ApoE4 Nanolipoprotein Particles and Initial XFEL-Based Structural Studies. Crystals, 10(10), p.886.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Qi Li, Jenna Pellegrino, D. John Lee, Arthur A. Tran, Hector A. Chaires, Ruoxi Wang, Jesslyn E. Park, Kaijie Ji, David Chow, Na Zhang, Axel F. Brilot, Justin T. Biel, Gydo van Zundert, Kenneth Borrelli, Dean Shinabarger, Cindy Wolfe, Beverly Murray, Matthew P. Jacobson, Estelle Mühle, Olivier Chesneau, James S. Fraser, Ian B. Seiple
Citation: Li, Q. et al., 2020. Synthetic group A streptogramin antibiotics that overcome Vat resistance. Nature, 586(7827), pp.145-150.
Type: Journal-article
Authors: Aron Broom, Rojo V. Rakotoharisoa, Michael C. Thompson, Niayesh Zarifi, Erin Nguyen, Nurzhan Mukhametzhanov, Lin Liu, James S. Fraser, Roberto A. Chica
Citation: Broom, A. et al., 2020. Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico. Nature Communications, 11(1).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: T. Burian, J. Chalupský, V. Hájková, M. Toufarová, V. Vorlíček, S. Hau-Riege, J. Krzywinski, J.D. Bozek, C. Bostedt, A.T. Graf, U.F. Jastrow, S. Kreis, R.A. London, M. Messerschmidt, S. Moeller, R. Sobierajski, K. Tiedtke, M. de Grazia, T. Auguste, B. Carré, S. Guizard, H. Merdji, N. Medvedev, L. Juha
Citation: Burian, T. et al., 2020. Subthreshold Erosion of an Organic Polymer Induced by Multiple Shots of an X-Ray Free-Electron Laser. Physical Review Applied, 14(3).
Type: Journal-article
Authors: George D. Calvey, Andrea M. Katz, Kara A. Zielinski, Boris Dzikovski, Lois Pollack
Citation: Calvey, G.D. et al., 2020. Characterizing Enzyme Reactions in Microcrystals for Effective Mix-and-Inject Experiments using X-ray Free-Electron Lasers. Analytical Chemistry, 92(20), pp.13864-13870.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Ali Dashti, Ghoncheh Mashayekhi, Mrinal Shekhar, Danya Ben Hail, Salah Salah, Peter Schwander, Amedee des Georges, Abhishek Singharoy, Joachim Frank, Abbas Ourmazd
Citation: Dashti, A. et al., 2020. Retrieving functional pathways of biomolecules from single-particle snapshots. Nature Communications, 11(1).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Melissa Carrillo, Suraj Pandey, Juan Sanchez, Moraima Noda, Ishwor Poudyal, Luis Aldama, Tek Narsingh Malla, Elin Claesson, Weixiao Yuan Wahlgren, Denisse Feliz, Vukica Šrajer, Michal Maj, Leticia Castillon, So Iwata, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, Kensuke Tono, Shigeki Owada, Sebastian Westenhoff, Emina A. Stojković, Marius Schmidt
Citation: Carrillo, M. et al., 2020. High-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle.
Type: Posted-content
Authors: Austin Echelmeier, Jorvani Cruz Villarreal, Marc Messerschmidt, Daihyun Kim, Jesse D. Coe, Darren Thifault, Sabine Botha, Ana Egatz-Gomez, Sahir Gandhi, Gerrit Brehm, Chelsie E. Conrad, Debra T. Hansen, Caleb Madsen, Saša Bajt, J. Domingo Meza-Aguilar, Dominik Oberthür, Max O. Wiedorn, Holger Fleckenstein, Derek Mendez, Juraj Knoška, Jose M. Martin-Garcia, Hao Hu, Stella Lisova, Aschkan Allahgholi, Yaroslav Gevorkov, Kartik Ayyer, Steve Aplin, Helen Mary Ginn, Heinz Graafsma, Andrew J. Morgan, Dominic Greiffenberg, Alexander Klujev, Torsten Laurus, Jennifer Poehlsen, Ulrich Trunk, Davide Mezza, Bernd Schmidt, Manuela Kuhn, Raimund Fromme, Jolanta Sztuk-Dambietz, Natascha Raab, Steffen Hauf, Alessandro Silenzi, Thomas Michelat, Chen Xu, Cyril Danilevski, Andrea Parenti, Leonce Mekinda, Britta Weinhausen, Grant Mills, Patrik Vagovic, Yoonhee Kim, Henry Kirkwood, Richard Bean, Johan Bielecki, Stephan Stern, Klaus Giewekemeyer, Adam R. Round, Joachim Schulz, Katerina Dörner, Thomas D. Grant, Valerio Mariani, Anton Barty, Adrian P. Mancuso, Uwe Weierstall, John C. H. Spence, Henry N. Chapman, Nadia Zatsepin, Petra Fromme, Richard A. Kirian, Alexandra Ros
Citation: Echelmeier, A. et al., 2020. Segmented flow generator for serial crystallography at the European X-ray free electron laser. Nature Communications, 11(1).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Serdar Durdagi, Cagdas Dag, Berna Dogan, Merve Yigin, Timucin Avsar, Cengizhan Buyukdag, Ismail Erol, Betul Ertem, Seyma Calis, Gunseli Yildirim, Muge D. Orhan, Omur Guven, Busecan Aksoydan, Ebru Destan, Kader Sahin, Sabri O. Besler, Lalehan Oktay, Alaleh Shafiei, Ilayda Tolu, Esra Ayan, Busra Yuksel, Ayse B. Peksen, Oktay Gocenler, Ali D. Yucel, Ozgur Can, Serena Ozabrahamyan, Alpsu Olkan, Ece Erdemoglu, Fulya Aksit, Gokhan Tanisali, 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, Alex Batyuk, Valerio Mariani, Zhen Su, Frederic Poitevin, Chun Hong Yoon, Christopher Kupitz, Raymond G. Sierra, Edward Snell, Hasan DeMirci
Citation: Durdagi, S. et al., 2020. Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing.
Type: Posted-content
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Josué A. Benjamín-Rivera, Andrés E. Cardona-Rivera, Ángel L. Vázquez-Maldonado, Christian Y. Dones-Lassalle, Héctor L. Pabón-Colon, Héctor M. Rodríguez-Rivera, Israel Rodríguez, Jean C. González-Espiet, Jessika Pazol, Jobaniel D. Pérez-Ríos, José F. Catala-Torres, Marielie Carrasquillo Rivera, Michael G. De Jesus-Soto, Nicolle A. Cordero-Virella, Paola M. Cruz-Maldonado, Patricia González-Pagan, Raul Hernández-Ríos, Kavita Gaur, Sergio A. Loza-Rosas, Arthur D. Tinoco
Citation: Benjamín-Rivera, J.A. et al., 2020. Exploring Serum Transferrin Regulation of Nonferric Metal Therapeutic Function and Toxicity. Inorganics, 8(9), p.48.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Jonathan A. Clinger, Xiachang Wang, Wenlong Cai, Yanyan Zhu, Mitchell D. Miller, Chang‐Guo Zhan, Steven G. Van Lanen, Jon S. Thorson, George N. Phillips
Citation: Clinger, J.A. et al., 2020. The crystal structure ofAbsH3: A putative flavin adenine dinucleotide‐dependent reductase in the abyssomicin biosynthesis pathway. Proteins: Structure, Function, and Bioinformatics, 89(1), pp.132-137.
Type: Journal-article
Authors: Rafael Maldonado-Hernández, Orestes Quesada, José A. Lasalde-Dominicci
Citation: Maldonado-Hernández, R., Quesada, O. & Lasalde-Dominicci, J.A., 2020. Biophysical characterization dataset of native nicotinic acetylcholine receptor in lipid-like detergent complexes. Data in Brief, 32, p.106230.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Sarah A. H. Hulgan, Abhishek A. Jalan, I-Che Li, Douglas R. Walker, Mitchell D. Miller, Abigael J. Kosgei, Weijun Xu, George N. Phillips, Jeffrey D. Hartgerink
Citation: Hulgan, S.A.H. et al., 2020. Covalent Capture of Collagen Triple Helices Using Lysine-Aspartate and Lysine-Glutamate Pairs. Biomacromolecules, 21(9), pp.3772-3781.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: David P. Klebl, Molly S.C. Gravett, Dimitrios Kontziampasis, David J. Wright, Robin S. Bon, Diana C.F. Monteiro, Martin Trebbin, Frank Sobott, Howard D. White, Michele C. Darrow, Rebecca F. Thompson, Stephen P. Muench
Citation: Klebl, D.P. et al., 2020. Need for Speed: Examining Protein Behavior during CryoEM Grid Preparation at Different Timescales. Structure, 28(11), pp.1238-1248.e4.
Type: Journal-article
Authors: Yen-Lin Chen, Lois Pollack
Citation: Chen, Y.-L. & Pollack, L., 2020. Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering. IUCrJ, 7(5).
Type: Journal-article
Authors: Mohammad Vakili, Ramakrishna Vasireddi, Paul V. Gwozdz, Diana C. F. Monteiro, Michael Heymann, Robert H. Blick, Martin Trebbin
Citation: Vakili, M. et al., 2020. Microfluidic polyimide gas dynamic virtual nozzles for serial crystallography. Review of Scientific Instruments, 91(8), p.085108.
Type: Journal-article
Authors: Yanyang Tang, Justin Saul, Nirupa Nagaratnam, Jose M. Martin-Garcia, Petra Fromme, Ji Qiu, Joshua LaBaer
Citation: Tang, Y. et al., 2020. Construction of gateway-compatible baculovirus expression vectors for high-throughput protein expression and in vivo microcrystal screening. Scientific Reports, 10(1).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Jeffrey J. Donatelli, John C. H. Spence
Citation: Donatelli, J.J. & Spence, J.C.H., 2020. Inversion of Many-Beam Bragg Intensities for Phasing by Iterated Projections: Removal of Multiple Scattering Artifacts from Diffraction Data. Physical Review Letters, 125(6).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Lan Zhu, Guanhong Bu, Liang Jing, Dan Shi, Ming-Yue Lee, Tamir Gonen, Wei Liu, Brent L. Nannenga
Citation: Zhu, L. et al., 2020. Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED. Structure, 28(10), pp.1149-1159.e4.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Ghoncheh Mashayekhi, Ali Dashti, Peter Schwander, Abbas Ourmazd
Citation: Mashayekhi, G. et al., 2020. From Static Structures to Continuous Conformational Changes on the Energy Landscapes. Microscopy and Microanalysis, 26(S2), pp.1614-1615.
Type: Journal-article
Authors: Suraj Pandey, Ishwor Poudyal, Tek Narsingh Malla
Citation: Pandey, S., Poudyal, I. & Malla, T.N., 2020. Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers. Crystals, 10(7), p.628.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Andrew J. Morgan, Kevin T. Murray, Mauro Prasciolu, Holger Fleckenstein, Oleksandr Yefanov, Pablo Villanueva-Perez, Valerio Mariani, Martin Domaracky, Manuela Kuhn, Steve Aplin, Istvan Mohacsi, Marc Messerschmidt, Karolina Stachnik, Yang Du, Anja Burkhart, Alke Meents, Evgeny Nazaretski, Hanfei Yan, Xiaojing Huang, Yong S. Chu, Henry N. Chapman, Saša Bajt
Citation: Morgan, A.J. et al., 2020. Ptychographic X-ray speckle tracking with multi-layer Laue lens systems. Journal of Applied Crystallography, 53(4), pp.927-936.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Michael C. Thompson, Todd O. Yeates, Jose A. Rodriguez
Citation: Thompson, M.C., Yeates, T.O. & Rodriguez, J.A., 2020. Advances in methods for atomic resolution macromolecular structure determination. F1000Research, 9, p.667.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Reza Nazari, Sahba Zaare, Roberto C. Alvarez, Konstantinos Karpos, Trent Engelman, Caleb Madsen, Garrett Nelson, John C. H. Spence, Uwe Weierstall, Ronald J. Adrian, Richard A. Kirian
Citation: Nazari, R. et al., 2020. 3D printing of gas-dynamic virtual nozzles and optical characterization of high-speed microjets. Optics Express, 28(15), p.21749.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Y. Kim, A. Ourmazd
Citation: Kim, Y. & Ourmazd, A., 1990. Diffusion in multilayers, studied by quantitative chemical mapping at the atomic level. Proceedings, annual meeting, Electron Microscopy Society of America, 48(4), pp.354-355.
Type: Journal-article
Authors: Chris S. Thomas, Doug R. Braun, Jose Luis Olmos, Scott R. Rajski, George N. Phillips, David Andes, Tim S. Bugni
Citation: Thomas, C.S. et al., 2020. Pyridine-2,6-Dithiocarboxylic Acid and Its Metal Complexes: New Inhibitors of New Delhi Metallo β-Lactamase-1. Marine Drugs, 18(6), p.295.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Mohammad Towshif Rabbani, Mukul Sonker, Alexandra Ros
Citation: Rabbani, M.T., Sonker, M. & Ros, A., 2020. Carbon nanotube dielectrophoresis: Theory and applications. ELECTROPHORESIS.
Type: Journal-article
Authors: Nirupa Nagaratnam, Yanyang Tang, Sabine Botha, Justin Saul, Chufeng Li, Hao Hu, Sahba Zaare, Mark Hunter, David Lowry, Uwe Weierstall, Nadia Zatsepin, John C. H. Spence, Ji Qiu, Joshua LaBaer, Petra Fromme, Jose M. Martin-Garcia
Citation: Nagaratnam, N. et al., 2020. Enhanced X-ray diffraction of in vivo-grown μNS crystals by viscous jets at XFELs. Acta Crystallographica Section F Structural Biology Communications, 76(6), pp.278-289.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Egor Sobolev, Sergei Zolotarev, Klaus Giewekemeyer, Johan Bielecki, Kenta Okamoto, Hemanth K. N. Reddy, Jakob Andreasson, Kartik Ayyer, Imrich Barak, Sadia Bari, Anton Barty, Richard Bean, Sergey Bobkov, Henry N. Chapman, Grzegorz Chojnowski, Benedikt J. Daurer, Katerina Dörner, Tomas Ekeberg, Leonie Flückiger, Oxana Galzitskaya, Luca Gelisio, Steffen Hauf, Brenda G. Hogue, Daniel A. Horke, Ahmad Hosseinizadeh, Vyacheslav Ilyin, Chulho Jung, Chan Kim, Yoonhee Kim, Richard A. Kirian, Henry Kirkwood, Olena Kulyk, Jochen Küpper, Romain Letrun, N. Duane Loh, Kristina Lorenzen, Marc Messerschmidt, Kerstin Mühlig, Abbas Ourmazd, Natascha Raab, Andrei V. Rode, Max Rose, Adam Round, Takushi Sato, Robin Schubert, Peter Schwander, Jonas A. Sellberg, Marcin Sikorski, Alessandro Silenzi, Changyong Song, John C. H. Spence, Stephan Stern, Jolanta Sztuk-Dambietz, Anthon Teslyuk, Nicusor Timneanu, Martin Trebbin, Charlotte Uetrecht, Britta Weinhausen, Garth J. Williams, P. Lourdu Xavier, Chen Xu, Ivan A. Vartanyants, Victor S. Lamzin, Adrian Mancuso, Filipe R. N. C. Maia
Citation: Sobolev, E. et al., 2020. Megahertz single-particle imaging at the European XFEL. Communications Physics, 3(1).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Wei Wu, Ross A. Okimoto, Collin Michael Blakely, James Fraser, Trever G. Bivona
Citation: Wu, W. et al., 2020. Targeted DNA sequencing analysis to reveal genetic diversity and androgen-receptor alteration in advanced EGFR mutant lung adenocarcinoma. Journal of Clinical Oncology, 38(15_suppl), pp.9526-9526.
Type: Journal-article
Authors: Grant Mills, Richard Bean, Adrian P. Mancuso
Type: Journal-article
Authors: Mohammad T. Rabbani, Christoph F. Schmidt, Alexandra Ros
Citation: Rabbani, M.T., Schmidt, C.F. & Ros, A., 2020. Length-Selective Dielectrophoretic Manipulation of Single-Walled Carbon Nanotubes. Analytical Chemistry.
Type: Journal-article
Authors: Abbas Ourmazd
Citation: Ourmazd, A., 2020. Science in the age of machine learning. Nature Reviews Physics.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Ian J. Campbell, Jose Luis Olmos, Weijun Xu, Dimithree Kahanda, Joshua T Atkinson, Othneil Noble Sparks, Mitchell D. Miller, George N Phillips, George N. Bennett, Jonathan J. Silberg
Citation: Campbell, I.J. et al., 2020. Prochlorococcus phage ferredoxin: Structural characterization and electron transfer to cyanobacterial sulfite reductases. Journal of Biological Chemistry, p.jbc.RA120.013501.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Tokushi Sato, Romain Letrun, Henry J. Kirkwood, Jia Liu, Patrik Vagovič, Grant Mills, Yoonhee Kim, Cedric M. S. Takem, Marc Planas, Moritz Emons, Tomasz Jezynski, Guido Palmer, Max Lederer, Sebastian Schulz, Jost Mueller, Holger Schlarb, Alessandro Silenzi, Gabriele Giovanetti, Andrea Parenti, Martin Bergemann, Thomas Michelat, Janusz Szuba, Jan Grünert, Henry N. Chapman, Adrian P. Mancuso
Citation: Sato, T. et al., 2020. Femtosecond timing synchronization at megahertz repetition rates for an x-ray free-electron laser. Optica, 7(6), p.716.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Richard A. Kirian, Henry N. Chapman
Citation: Kirian, R.A. & Chapman, H.N., 2020. Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser Pulses. Synchrotron Light Sources and Free-Electron Lasers, pp.1337-1397.
Type: Book-chapter
Authors: LaRinda A. Holland, Emily A. Kaelin, Rabia Maqsood, Bereket Estifanos, Lily I. Wu, Arvind Varsani, Rolf U. Halden, Brenda G. Hogue, Matthew Scotch, Efrem S. Lim
Citation: Holland, L.A. et al., 2020. An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020) T. Gallagher, ed. Journal of Virology, 94(14).
Type: Journal-article
Authors: David E. Gordon, Gwendolyn M. Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Kris M. White, Matthew J. O’Meara, Veronica V. Rezelj, Jeffrey Z. Guo, Danielle L. Swaney, Tia A. Tummino, Ruth Hüttenhain, Robyn M. Kaake, Alicia L. Richards, Beril Tutuncuoglu, Helene Foussard, Jyoti Batra, Kelsey Haas, Maya Modak, Minkyu Kim, Paige Haas, Benjamin J. Polacco, Hannes Braberg, Jacqueline M. Fabius, Manon Eckhardt, Margaret Soucheray, Melanie J. Bennett, Merve Cakir, Michael J. McGregor, Qiongyu Li, Bjoern Meyer, Ferdinand Roesch, Thomas Vallet, Alice Mac Kain, Lisa Miorin, Elena Moreno, Zun Zar Chi Naing, Yuan Zhou, Shiming Peng, Ying Shi, Ziyang Zhang, Wenqi Shen, Ilsa T. Kirby, James E. Melnyk, John S. Chorba, Kevin Lou, Shizhong A. Dai, Inigo Barrio-Hernandez, Danish Memon, Claudia Hernandez-Armenta, Jiankun Lyu, Christopher J. P. Mathy, Tina Perica, Kala Bharath Pilla, Sai J. Ganesan, Daniel J. Saltzberg, Ramachandran Rakesh, Xi Liu, Sara B. Rosenthal, Lorenzo Calviello, Srivats Venkataramanan, Jose Liboy-Lugo, Yizhu Lin, Xi-Ping Huang, YongFeng Liu, Stephanie A. Wankowicz, Markus Bohn, Maliheh Safari, Fatima S. Ugur, Cassandra Koh, Nastaran Sadat Savar, Quang Dinh Tran, Djoshkun Shengjuler, Sabrina J. Fletcher, Michael C. O’Neal, Yiming Cai, Jason C. J. Chang, David J. Broadhurst, Saker Klippsten, Phillip P. Sharp, Nicole A. Wenzell, Duygu Kuzuoglu-Ozturk, Hao-Yuan Wang, Raphael Trenker, Janet M. Young, Devin A. Cavero, Joseph Hiatt, Theodore L. Roth, Ujjwal Rathore, Advait Subramanian, Julia Noack, Mathieu Hubert, Robert M. Stroud, Alan D. Frankel, Oren S. Rosenberg, Kliment A. Verba, David A. Agard, Melanie Ott, Michael Emerman, Natalia Jura, Mark von Zastrow, Eric Verdin, Alan Ashworth, Olivier Schwartz, Christophe d’Enfert, Shaeri Mukherjee, Matt Jacobson, Harmit S. Malik, Danica G. Fujimori, Trey Ideker, Charles S. Craik, Stephen N. Floor, James S. Fraser, John D. Gross, Andrej Sali, Bryan L. Roth, Davide Ruggero, Jack Taunton, Tanja Kortemme, Pedro Beltrao, Marco Vignuzzi, Adolfo García-Sastre, Kevan M. Shokat, Brian K. Shoichet, Nevan J. Krogan
Citation: Gordon, D.E. et al., 2020. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature, 583(7816), pp.459-468.
Type: Journal-article
Authors: LaRinda A. Holland, Emily A. Kaelin, Rabia Maqsood, Bereket Estifanos, Lily I. Wu, Arvind Varsani, Rolf U. Halden, Brenda G. Hogue, Matthew Scotch, Efrem S. Lim
Citation: Holland, L.A. et al., 2020. An 81 base-pair deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020).
Type: Posted-content
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: J. Candanedo, C. Caleman, N. Tîmneanu, O. Beckstein, J. C. H. Spence
Citation: Candanedo, J. et al., 2020. Dynamics of rare gas solids irradiated by electron beams. The Journal of Chemical Physics, 152(14), p.144303.
Type: Journal-article
Authors: Elin Claesson, Weixiao Yuan Wahlgren, Heikki Takala, Suraj Pandey, Leticia Castillon, Valentyna Kuznetsova, Léocadie Henry, Matthijs Panman, Melissa Carrillo, Joachim Kübel, Rahul Nanekar, Linnéa Isaksson, Amke Nimmrich, Andrea Cellini, Dmitry Morozov, Michał Maj, Moona Kurttila, Robert Bosman, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, So Iwata, Shigeki Owada, Keith Moffat, Gerrit Groenhof, Emina A. Stojković, Janne A. Ihalainen, Marius Schmidt, Sebastian Westenhoff
Citation: Claesson, E. et al., 2020. The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser. eLife, 9.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: David P. Klebl, Diana C. F. Monteiro, Dimitrios Kontziampasis, Florian Kopf, Frank Sobott, Howard D. White, Martin Trebbin, Stephen P. Muench
Citation: Klebl, D.P. et al., 2020. Sample deposition onto cryo-EM grids: from sprays to jets and back. Acta Crystallographica Section D Structural Biology, 76(4), pp.340-349.
Type: Journal-article
Authors: Suvrajit Maji, Hstau Liao, Ali Dashti, Ghoncheh Mashayekhi, Abbas Ourmazd, Joachim Frank
Citation: Maji, S. et al., 2020. Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding. Journal of Chemical Information and Modeling.
Type: Journal-article
Authors: Russell Fung, Jose Villar, Ali Dashti, Leila Cheikh Ismail, Eleonora Staines-Urias, Eric O. Ohuma, Laurent J. Salomon, Cesar G. Victora, Fernando C. Barros, Ann Lambert, Maria Carvalho, Yasmin A. Jaffer, Alison J. Noble, Michael G. Gravett, Manorama Purwar, Ruyan Pang, Enrico Bertino, Shama Munim, Aung Myat Min, Rose McGready, Shane A. Norris, Zulfiqar A Bhutta, Stephen H. Kennedy, Aris T. Papageorghiou, Abbas Ourmazd, International Fetal, Newborn Gro Group
Citation: Fung, R. et al., 2019. Using Machine Learning to Achieve Accurate Estimates of Fetal Gestational Age and Personalized Predictions of Fetal Growth. SSRN Electronic Journal.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: I. Poudyal, M. Schmidt, P. Schwander
Citation: Poudyal, I., Schmidt, M. & Schwander, P., 2020. Single-particle imaging by x-ray free-electron lasers--How many snapshots are needed? Structural Dynamics, 7(2), p.024102.
Type: Journal-article
Authors: James Zook, Mrinal Shekhar, Debra Hansen, Chelsie Conrad, Thomas Grant, Chitrak Gupta, Thomas White, Anton Barty, Shibom Basu, Yun Zhao, Nadia Zatsepin, Andrii Ishchenko, Alex Batyuk, Cornelius Gati, Chufeng Li, Lorenzo Galli, Jesse Coe, Mark Hunter, Meng Liang, Uwe Weierstall, Garret Nelson, Daniel James, Benjamin Stauch, Felicia Craciunescu, Darren Thifault, Wei Liu, Vadim Cherezov, Abhishek Singharoy, Petra Fromme
Citation: Zook, J. et al., 2020. XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia. Structure.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Darya Marchany-Rivera, Clyde A. Smith, Josiris D. Rodriguez-Perez, Juan López-Garriga
Citation: Marchany-Rivera, D. et al., 2020. Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility. Journal of Inorganic Biochemistry, 207, p.111055.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Nilkanth Patel, Xi Ping Huang, Jessica M Grandner, Linda C Johansson, Benjamin Stauch, John D McCorvy, Yongfeng Liu, Bryan Roth, Vsevolod Katritch
Citation: Patel, N. et al., 2020. Structure-based discovery of potent and selective melatonin receptor agonists. eLife, 9.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Alexander M. Wolff, Iris D. Young, Raymond G. Sierra, Aaron S. Brewster, Michael W. Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, Justin T. Biel, Sergio Carbajo, Aina E. Cohen, Saul Cortez, Ana Gonzalez, Tomoya Hino, Dohyun Im, Jake D. Koralek, Minoru Kubo, Tomas S. Lazarou, Takashi Nomura, Shigeki Owada, Avi J. Samelson, Tomoyuki Tanaka, Rie Tanaka, Erin M. Thompson, Henry van den Bedem, Rahel A. Woldeyes, Fumiaki Yumoto, Wei Zhao, Kensuke Tono, Sebastien Boutet, So Iwata, Tamir Gonen, Nicholas K. Sauter, James S. Fraser, Michael C. Thompson
Citation: Wolff, A.M. et al., 2020. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals. IUCrJ, 7(2), pp.306-323.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Tyler D. Huber, Jonathan A. Clinger, Yang Liu, Weijun Xu, Mitchell D. Miller, George N. Phillips, Jon S. Thorson
Citation: Huber, T.D. et al., 2020. Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes. ACS Chemical Biology, 15(3), pp.695-705.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: John C. H. Spence
Citation: Spence, J.C.H., 2020. Serial Crystallography: Preface. Crystals, 10(2), p.135.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Marius Schmidt
Citation: Schmidt, M., 2020. Reaction Initiation in Enzyme Crystals by Diffusion of Substrate. Crystals, 10(2), p.116.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Reed M. Stein, Hye Jin Kang, John D. McCorvy, Grant C. Glatfelter, Anthony J. Jones, Tao Che, Samuel Slocum, Xi-Ping Huang, Olena Savych, Yurii S. Moroz, Benjamin Stauch, Linda C. Johansson, Vadim Cherezov, Terry Kenakin, John J. Irwin, Brian K. Shoichet, Bryan L. Roth, Margarita L. Dubocovich
Citation: Stein, R.M. et al., 2020. Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. Nature.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Ian J. Campbell, Jose L. Olmos, Weijun Xu, Dimithree Kahanda, Joshua T. Atkinson, Othneil N. Sparks, Mitchell D. Miller, George N. Phillips, George N. Bennett, Jonathan J. Silberg
Citation: Campbell, I.J. et al., 2020. Prochlorococcusphage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases.
Type: Posted-content
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Yen-Lin Chen, Lois Pollack
Citation: Chen, Y.-L. & Pollack, L., 2020. Convolutional Neural Networks Bridge Molecular Models and Solution X-ray Scattering Experiments. Biophysical Journal, 118(3), p.301a.
Type: Poster
Authors: Leslie A. Salas-Estrada, Thomas D. Grant, Suchithranga M. Perera, Andrey V. Struts, Udeep Chawla, Xiaolin Xu, Steven D. Fried, Nipuna Weerasinghe, D. Mendez, R. Alvarez, K. Karpos, S. Lisova, S. Zaare, R. Nazari, N.A. Zatsepsin, Abhishek Singharoy, S. Boutet, S. Carbajo, M.S. Hunter, M. Liang, M.D. Seaberg, Raimund Fromme, Petra Fromme, Richard A. Kirian, Michael F. Brown, Alan Grossfield
Citation: Salas-Estrada, L.A. et al., 2020. Rhodopsin's Ultra-Fast Activation Dynamics in Bilayer and Micelle Environments. Biophysical Journal, 118(3), p.92a.
Type: Journal-article
Authors: Alex Plumridge, Lois Pollack
Citation: Plumridge, A. & Pollack, L., 2020. Discovering Design Principles to Re-Engineer Functional RNA Elements. Biophysical Journal, 118(3), p.70a.
Type: Poster
Authors: Derrick R. Lin, Suzette A. Pabit, Lois Pollack
Citation: Lin, D.R., Pabit, S.A. & Pollack, L., 2020. Probing Mg2+-Mediated RNA-RNA Interactions in the Presence of Metabolites. Biophysical Journal, 118(3), p.69a.
Type: Poster
Authors: Yen-Lin Chen, Lois Pollack
Citation: Chen, Y.-L. & Pollack, L., 2020. Quantitative Analysis of Salt-Induced RNA Duplex Variations by Wide-Angle X-ray Scattering (WAXS). Biophysical Journal, 118(3), p.68a.
Type: Poster
Authors: Alex Mauney, Lois Pollack
Citation: Mauney, A. & Pollack, L., 2020. DNA Sequence and Histone Core Composition Determine the Unwrapping Pathways in Nucleosomes. Biophysical Journal, 118(3), p.489a.
Type: Poster
Authors: Thomas D. Grant, Suchithranga M. Perera, Leslie A. Salas-Estrada, Andrey V. Struts, Udeep Chawla, Xiaolin Xu, Steven D. Fried, Nipuna Weerasinghe, D. Mendez, R. Alvarez, K. Karpos, S. Lisova, S. Zaare, R. Nazari, N.A. Zatsepsin, Abhishek Singharoy, S. Boutet, S. Carbajo, M.S. Hunter, M. Liang, M.D. Seaberg, Raimund Fromme, Petra Fromme, Alan Grossfield, Richard A. Kirian, Michael F. Brown
Citation: Grant, T.D. et al., 2020. Membrane Protein Dynamics Revealed by X-Ray Scattering with a Femtosecond Free-Electron Laser. Biophysical Journal, 118(3), p.365a.
Type: Journal-article
Authors: Suzette A. Pabit, Yen-Lin Chen, Grace A. Usher, Erik C. Cook, Lois Pollack, Scott A. Showalter
Citation: Pabit, S.A. et al., 2020. Evidence that Primary Microrna Bends in the Presence of DGCR8 Seen using Both Saxs and FRET Measurements. Biophysical Journal, 118(3), p.222a.
Type: Poster
Authors: Hasan DeMirci, Bradley B. Tolar, Tzanko Doukov, Aldis Petriceks, Akshaye Pal, Yasuo Yoshikuni, Aharon Gomez, David A. Saez, Esteban Vöhringer-Martinez, Thomas Schwander, Tobias J. Erb, Christopher A. Francis, Soichi Wakatsuki
Citation: DeMirci, H. et al., 2020. Structural adaptation of oxygen tolerance in 4-hydroxybutyrl-CoA dehydratase, a key enzyme of archaeal carbon fixation.
Type: Posted-content
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: José A. Carmona‐Negrón, José M. Liboy‐Lugo, Alberto Santana, Enrique Meléndez
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Timothy R. Stachowski, Mary E. Snell, Edward H. Snell
Citation: Stachowski, T.R., Snell, M.E. & Snell, E.H., 2020. Structural insights into conformational switching in latency-associated peptide between transforming growth factor β-1 bound and unbound states. IUCrJ, 7(2), pp.238-252.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Premila P. Samuel, Mark A. White, William C. Ou, David A. Case, George N. Phillips, John S. Olson
Citation: Samuel, P.P. et al., 2020. The Interplay between Molten Globules and Heme Disassociation Defines Human Hemoglobin Disassembly. Biophysical Journal, 118(6), pp.1381-1400.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Karol Nass, Lars Redecke, M. Perbandt, O. Yefanov, M. Klinge, R. Koopmann, F. Stellato, A. Gabdulkhakov, R. Schönherr, D. Rehders, J. M. Lahey-Rudolph, A. Aquila, A. Barty, S. Basu, R. B. Doak, R. Duden, M. Frank, R. Fromme, S. Kassemeyer, G. Katona, R. Kirian, H. Liu, I. Majoul, J. M. Martin-Garcia, M. Messerschmidt, R. L. Shoeman, U. Weierstall, S. Westenhoff, T. A. White, G. J. Williams, C. H. Yoon, N. Zatsepin, P. Fromme, M. Duszenko, H. N. Chapman, C. Betzel
Citation: Nass, K. et al., 2020. In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors. Nature Communications, 11(1).
Type: Journal-article
Authors: Hongnan Cao, Jonathan D. Walton, Phillip Brumm, George N. Phillips
Citation: Cao, H. et al., 2020. Crystal Structure of α-Xylosidase from Aspergillus niger in Complex with a Hydrolyzed Xyloglucan Product and New Insights in Accurately Predicting Substrate Specificities of GH31 Family Glycosidases. ACS Sustainable Chemistry & Engineering, 8(6), pp.2540-2547.
Type: Journal-article
Authors: Diana C. F. Monteiro, David von Stetten, Claudia Stohrer, Marta Sans, Arwen R. Pearson, Gianluca Santoni, Peter van der Linden, Martin Trebbin
Citation: Monteiro, D.C.F. et al., 2020. 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow. IUCrJ, 7(2), pp.207-219.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Vanja Stojković, Alexander G Myasnikov, Iris D Young, Adam Frost, James S Fraser, Danica Galonić Fujimori
Citation: Stojković, V. et al., 2020. Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit. Nucleic Acids Research.
Type: Journal-article
Authors: Sweta Vangaveti, William A. Cantara, Jessica L. Spears, Hasan DeMirci, Frank V. Murphy, Sri V. Ranganathan, Kathryn L. Sarachan, Paul F. Agris
Citation: Vangaveti, S. et al., 2020. A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine. Journal of Molecular Biology, 432(4), pp.913-929.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Benjamin A. Barad, Lin Liu, Roberto E. Diaz, Ralp Basilio, Steven J. Van Dyken, Richard M. Locksley, James S. Fraser
Citation: Barad, B.A. et al., 2020. Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates. Protein Science.
Type: Journal-article
Authors: Edward H. Snell, Helena Taberman, Charles S. Bury, Mark J. van der Woerd, Elspeth F. Garman
Citation: Snell, E.H. et al., 1999. Structural knowledge or X-ray damage? Dose-dependent case studies on xylose isomerase revealing structural perturbations. Acta Crystallographica Section A Foundations and Advances, 75(a1), pp.a232-a232.
Type: Poster
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Robb Welty, Michael Rau, Suzette Pabit, Mark S. Dunstan, Graeme L. Conn, Lois Pollack, Kathleen B. Hall
Citation: Welty, R. et al., 2019. Ribosomal protein L11 selectively stabilizes a tertiary structure of the GTPase Center rRNA domain. Journal of Molecular Biology.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: E. Sethe Burgie, Jonathan A. Clinger, Mitchell D. Miller, Aaron S. Brewster, Pierre Aller, Agata Butryn, Franklin D. Fuller, Sheraz Gul, Iris D. Young, Cindy C. Pham, In-Sik Kim, Asmit Bhowmick, Lee J. O’Riordan, Kyle D. Sutherlin, Joshua V. Heinemann, Alexander Batyuk, Roberto Alonso-Mori, Mark S. Hunter, Jason E. Koglin, Junko Yano, Vittal K. Yachandra, Nicholas K. Sauter, Aina E. Cohen, Jan Kern, Allen M. Orville, George N. Phillips, Richard D. Vierstra
Citation: Burgie, E.S. et al., 2019. Photoreversible interconversion of a phytochrome photosensory module in the crystalline state. Proceedings of the National Academy of Sciences, 117(1), pp.300-307.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: David C. Wych, James S. Fraser, David L. Mobley, Michael E. Wall
Citation: Wych, D.C. et al., 2019. Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein. Structural Dynamics, 6(6), p.064704.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Kartik Ayyer, Andrew J. Morgan, Andrew Aquila, Hasan DeMirci, Brenda G. Hogue, Richard A. Kirian, P. Lourdu Xavier, Chun Hong Yoon, Henry N. Chapman, Anton Barty
Citation: Ayyer, K. et al., 2019. Low-signal limit of X-ray single particle diffractive imaging. Optics Express, 27(26), p.37816.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Anastasiia Gusach, Aleksandra Luginina, Egor Marin, Rebecca L. Brouillette, Élie Besserer-Offroy, Jean-Michel Longpré, Andrii Ishchenko, Petr Popov, Nilkanth Patel, Taku Fujimoto, Toru Maruyama, Benjamin Stauch, Margarita Ergasheva, Daria Romanovskaia, Anastasiia Stepko, Kirill Kovalev, Mikhail Shevtsov, Valentin Gordeliy, Gye Won Han, Vsevolod Katritch, Valentin Borshchevskiy, Philippe Sarret, Alexey Mishin, Vadim Cherezov
Citation: Gusach, A. et al., 2019. Structural basis of ligand selectivity and disease mutations in cysteinyl leukotriene receptors. Nature Communications, 10(1).
Type: Journal-article
Authors: Alex Plumridge, Kurt Andresen, Lois Pollack
Citation: Plumridge, A., Andresen, K. & Pollack, L., 2019. Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics. Journal of the American Chemical Society.
Type: Journal-article
Authors: Geoffrey W. Grime, Oliver B. Zeldin, Mary E. Snell, Edward D. Lowe, John F. Hunt, Gaetano T. Montelione, Liang Tong, Edward H. Snell, Elspeth F. Garman
Citation: Grime, G.W. et al., 2019. High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application. Journal of the American Chemical Society.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Tobias Claff, Jing Yu, Véronique Blais, Nilkanth Patel, Charlotte Martin, Lijie Wu, Gye Won Han, Brian J. Holleran, Olivier Van der Poorten, Kate L. White, Michael A. Hanson, Philippe Sarret, Louis Gendron, Vadim Cherezov, Vsevolod Katritch, Steven Ballet, Zhi-Jie Liu, Christa E. Müller, Raymond C. Stevens
Citation: Claff, T. et al., 2019. Elucidating the active δ-opioid receptor crystal structure with peptide and small-molecule agonists. Science Advances, 5(11), p.eaax9115.
Type: Journal-article
Authors: Anum A. Glasgow, Yao-Ming Huang, Daniel J. Mandell, Michael Thompson, Ryan Ritterson, Amanda L. Loshbaugh, Jenna Pellegrino, Cody Krivacic, Roland A. Pache, Kyle A. Barlow, Noah Ollikainen, Deborah Jeon, Mark J. S. Kelly, James S. Fraser, Tanja Kortemme
Citation: Glasgow, A.A. et al., 2019. Computational design of a modular protein sense-response system. Science, 366(6468), pp.1024-1028.
Type: Journal-article
Authors: M. L. Shelby, D. Gilbile, T. D. Grant, C. Seuring, B. W. Segelke, W. He, A. C. Evans, T. Pakendorf, P. Fischer, M. S. Hunter, A. Batyuk, M. Barthelmess, A. Meents, M. A. Coleman, T. L. Kuhl, M. Frank
Citation: Shelby, M.L. et al., 2020. A fixed-target platform for serial femtosecond crystallography in a hydrated environment. IUCrJ, 7(1), pp.30-41.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Suraj Pandey, Richard Bean, Tokushi Sato, Ishwor Poudyal, Johan Bielecki, Jorvani Cruz Villarreal, Oleksandr Yefanov, Valerio Mariani, Thomas A. White, Christopher Kupitz, Mark Hunter, Mohamed H. Abdellatif, Saša Bajt, Valerii Bondar, Austin Echelmeier, Diandra Doppler, Moritz Emons, Matthias Frank, Raimund Fromme, Yaroslav Gevorkov, Gabriele Giovanetti, Man Jiang, Daihyun Kim, Yoonhee Kim, Henry Kirkwood, Anna Klimovskaia, Juraj Knoska, Faisal H. M. Koua, Romain Letrun, Stella Lisova, Luis Maia, Victoria Mazalova, Domingo Meza, Thomas Michelat, Abbas Ourmazd, Guido Palmer, Marco Ramilli, Robin Schubert, Peter Schwander, Alessandro Silenzi, Jolanta Sztuk-Dambietz, Alexandra Tolstikova, Henry N. Chapman, Alexandra Ros, Anton Barty, Petra Fromme, Adrian P. Mancuso, Marius Schmidt
Citation: Pandey, S. et al., 2019. Time-resolved serial femtosecond crystallography at the European XFEL. Nature Methods.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Benjamin Stauch, Linda C. Johansson, Vadim Cherezov
Citation: Stauch, B., Johansson, L.C. & Cherezov, V., 2019. Structural Insights into Melatonin Receptors. The FEBS Journal.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Chris Gisriel, Jesse Coe, Romain Letrun, Oleksandr M. Yefanov, Cesar Luna-Chavez, Natasha E. Stander, Stella Lisova, Valerio Mariani, Manuela Kuhn, Steve Aplin, Thomas D. Grant, Katerina Dörner, Tokushi Sato, Austin Echelmeier, Jorvani Cruz Villarreal, Mark S. Hunter, Max O. Wiedorn, Juraj Knoska, Victoria Mazalova, Shatabdi Roy-Chowdhury, Jay-How Yang, Alex Jones, Richard Bean, Johan Bielecki, Yoonhee Kim, Grant Mills, Britta Weinhausen, Jose D. Meza, Nasser Al-Qudami, Saša Bajt, Gerrit Brehm, Sabine Botha, Djelloul Boukhelef, Sandor Brockhauser, Barry D. Bruce, Matthew A. Coleman, Cyril Danilevski, Erin Discianno, Zachary Dobson, Hans Fangohr, Jose M. Martin-Garcia, Yaroslav Gevorkov, Steffen Hauf, Ahmad Hosseinizadeh, Friederike Januschek, Gihan K. Ketawala, Christopher Kupitz, Luis Maia, Maurizio Manetti, Marc Messerschmidt, Thomas Michelat, Jyotirmoy Mondal, Abbas Ourmazd, Gianpietro Previtali, Iosifina Sarrou, Silvan Schön, Peter Schwander, Megan L. Shelby, Alessandro Silenzi, Jolanta Sztuk-Dambietz, Janusz Szuba, Monica Turcato, Thomas A. White, Krzysztof Wrona, Chen Xu, Mohamed H. Abdellatif, James D. Zook, John C. H. Spence, Henry N. Chapman, Anton Barty, Richard A. Kirian, Matthias Frank, Alexandra Ros, Marius Schmidt, Raimund Fromme, Adrian P. Mancuso, Petra Fromme, Nadia A. Zatsepin
Citation: Gisriel, C. et al., 2019. Membrane protein megahertz crystallography at the European XFEL. Nature Communications, 10(1).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Andrii Ishchenko, Benjamin Stauch, Gye Won Han, Alexander Batyuk, Anna Shiriaeva, Chufeng Li, Nadia Zatsepin, Uwe Weierstall, Wei Liu, Eriko Nango, Takanori Nakane, Rie Tanaka, Kensuke Tono, Yasumasa Joti, So Iwata, Isabel Moraes, Cornelius Gati, Vadim Cherezov
Citation: Ishchenko, A. et al., 2019. Toward G protein-coupled receptor structure-based drug design using X-ray lasers. IUCrJ, 6(6), pp.1106-1119.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Yen-Lin Chen, Lois Pollack
Citation: Chen, Y.-L. & Pollack, L., 2019. Salt Dependence of A-Form RNA Duplexes: Structures and Implications. The Journal of Physical Chemistry B.
Type: Journal-article
Authors: Dimitrios Giannakis, Abbas Ourmazd, Joanna Slawinska, Zhizhen Zhao
Citation: Giannakis, D. et al., 2019. Correction to: Spatiotemporal Pattern Extraction by Spectral Analysis of Vector-Valued Observables. Journal of Nonlinear Science.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Aleksandra Luginina, Anastasiia Gusach, Egor Marin, Alexey Mishin, Rebecca Brouillette, Petr Popov, Anna Shiriaeva, Élie Besserer-Offroy, Jean-Michel Longpré, Elizaveta Lyapina, Andrii Ishchenko, Nilkanth Patel, Vitaly Polovinkin, Nadezhda Safronova, Andrey Bogorodskiy, Evelina Edelweiss, Hao Hu, Uwe Weierstall, Wei Liu, Alexander Batyuk, Valentin Gordeliy, Gye Won Han, Philippe Sarret, Vsevolod Katritch, Valentin Borshchevskiy, Vadim Cherezov
Citation: Luginina, A. et al., 2019. Structure-based mechanism of cysteinyl leukotriene receptor inhibition by antiasthmatic drugs. Science Advances, 5(10), p.eaax2518.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Julia K. Rotow, Philippe Gui, Wei Wu, Victoria M. Raymond, Richard B. Lanman, Frederic J. Kaye, Nir Peled, Ferran Fece de la Cruz, Brandon Nadres, Ryan B. Corcoran, Iwei Yeh, Boris C. Bastian, Petr Starostik, Kimberly Newsom, Victor R. Olivas, Alexander M. Wolff, James S. Fraser, Eric A. Collisson, Caroline E. McCoach, D. Ross Camidge, Jose Pacheco, Lyudmila Bazhenova, Tianhong Li, Trever G. Bivona, Collin M. Blakely
Citation: Rotow, J.K. et al., 2019. Co-occurring Alterations in the RAS-MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer. Clinical Cancer Research, 26(2), pp.439-449.
Type: Journal-article
Authors: Michael C. Thompson, Benjamin A. Barad, Alexander M. Wolff, Hyun Sun Cho, Friedrich Schotte, Daniel M. C. Schwarz, Philip Anfinrud, James S. Fraser
Citation: Thompson, M.C. et al., 2019. Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme. Nature Chemistry, 11(11), pp.1058-1066.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Austin Echelmeier, Daihyun Kim, Jorvani Cruz Villarreal, Jesse Coe, Sebastian Quintana, Gerrit Brehm, Ana Egatz-Gomez, Reza Nazari, Raymond G. Sierra, Jason E. Koglin, Alexander Batyuk, Mark S. Hunter, Sébastien Boutet, Nadia Zatsepin, Richard A. Kirian, Thomas D. Grant, Petra Fromme, Alexandra Ros
Citation: Echelmeier, A. et al., 2019. 3D printed droplet generation devices for serial femtosecond crystallography enabled by surface coating. Journal of Applied Crystallography, 52(5), pp.997-1008.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: J. P. J. Chen, K. E. Schmidt, R. A. Kirian, J. J. Donatelli
Citation: Chen, J.P.J. et al., 2019. Reconstruction of Objects from Their Averaged Finite Crystal Diffraction Intensity. 2019 IEEE International Conference on Image Processing (ICIP).
Type: Proceedings-article
Authors: Persis Drell, Dawn A. Bonnell, Jingguang Chen, Sue Clark, Beatriz Roldan Cuenya, Helmut Dosch, Cynthia Friend, Yan Gao, Sharon Hammes-Schiffer, Marc Kastner, Bruce Kay, Stephen R. Leone, Despina Louca, Monica Olvera de la Cruz, Abbas Ourmazd, Philippe Piot, Ian Robertson, Anthony Rollett, Frances Ross, Gary Rubloff, Maria Santore, Esther S. Takeuchi, John Tranquada, Stephen Wasserman
Citation: Drell, P. et al., 2018. A Remarkable Return On Investment In Fundamental Research: 40 Years of Basic Energy Sciences at the Department of Energy.
Type: Report
Authors: Daihyun Kim, Austin Echelmeier, Jorvani Cruz Villarreal, Sahir Gandhi, Sebastian Quintana, Ana Egatz-Gomez, Alexandra Ros
Citation: Kim, D. et al., 2019. Electric Triggering for Enhanced Control of Droplet Generation. Analytical Chemistry, 91(15), pp.9792-9799.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Austin Echelmeier, Mukul Sonker, Alexandra Ros
Citation: Echelmeier, A., Sonker, M. & Ros, A., 2019. Microfluidic sample delivery for serial crystallography using XFELs. Analytical and Bioanalytical Chemistry, 411(25), pp.6535-6547.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Gabriele M. M. Stoffel, David Adrian Saez, Hasan DeMirci, Bastian Vögeli, Yashas Rao, Jan Zarzycki, Yasuo Yoshikuni, Soichi Wakatsuki, Esteban Vöhringer-Martinez, Tobias J. Erb
Citation: Stoffel, G.M.M. et al., 2019. Four amino acids define the CO2binding pocket of enoyl-CoA carboxylases/reductases. Proceedings of the National Academy of Sciences, 116(28), pp.13964-13969.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Helena Taberman, Charles S. Bury, Mark J. van der Woerd, Edward H. Snell, Elspeth F. Garman
Citation: Taberman, H. et al., 2019. Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both. Journal of Synchrotron Radiation, 26(4), pp.931-944.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Gisela Brändén, Greger Hammarin, Rajiv Harimoorthy, Alexander Johansson, David Arnlund, Erik Malmerberg, Anton Barty, Stefan Tångefjord, Peter Berntsen, Daniel P. DePonte, Carolin Seuring, Thomas A. White, Francesco Stellato, Richard Bean, Kenneth R. Beyerlein, Leonard M. G. Chavas, Holger Fleckenstein, Cornelius Gati, Umesh Ghoshdastider, Lars Gumprecht, Dominik Oberthür, David Popp, Marvin Seibert, Thomas Tilp, Marc Messerschmidt, Garth J. Williams, N. Duane Loh, Henry N. Chapman, Peter Zwart, Mengning Liang, Sébastien Boutet, Robert C. Robinson, Richard Neutze
Citation: Brändén, G. et al., 2019. Coherent diffractive imaging of microtubules using an X-ray laser. Nature Communications, 10(1).
Type: Journal-article
Authors: Masoud Mehrjoo, Elke Plönjes, Barbara Keitel, Marion Kuhlmann, Mabel Ruiz-Lopez, Thomas Wodzinski, Klaus Giewekemeyer, Patrik Vagovic, Yoonhee Kim, Mohammadreza Banjafar, Marc Messerschmidt, Tomáš Burian
Citation: Mehrjoo, M. et al., 2019. Spatial characterization of FLASH2 pulses: current status and future plan (Conference Presentation) T. Tschentscher et al., eds. X-Ray Free-Electron Lasers: Advances in Source Development and Instrumentation V.
Type: Proceedings-article
Authors: Dimitrios Giannakis, Abbas Ourmazd, Joanna Slawinska, Zhizhen Zhao
Citation: Giannakis, D. et al., 2019. Spatiotemporal Pattern Extraction by Spectral Analysis of Vector-Valued Observables. Journal of Nonlinear Science.
Type: Journal-article
Authors: J Bayani, C Poncet, CQ Yao, C Crozier, N Anouk, T Piper, C Cunningham, M Sobol, S Aebi, K Benstead, O Bogler, L Dal Lago, J Fraser, FH Hilbers, I Hedenfalk, L Korde, B Linderholm, J Martens, L Middleton, M Murray, C Kelly, C Nilsson, M Nowaczyk, S Peeters, A Peric, P Porter, C Schröder, IT Rubio, KJ Ruddy, C van Asperen, D Van Den Weyngaert, C van Deurzen, E van Leeuwen-Stok, J Vermeij, E Winer, PC Boutros, SH Giordano, F Cardoso, JM Bartlett
Citation: Bayani, J. et al., 2019. Abstract P6-19-01: Evaluation of multiple transcriptomic gene risk signatures in male breast cancer. Poster Session Abstracts.
Type: Proceedings-article
Authors: George D. Calvey, Andrea M. Katz, Lois Pollack
Citation: Calvey, G.D., Katz, A.M. & Pollack, L., 2019. Microfluidic Mixing Injector Holder Enables Routine Structural Enzymology Measurements with Mix-and-Inject Serial Crystallography Using X-ray Free Electron Lasers. Analytical Chemistry.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Benjamin Stauch, Linda C. Johansson, John D. McCorvy, Nilkanth Patel, Gye Won Han, Xi-Ping Huang, Cornelius Gati, Alexander Batyuk, Samuel T. Slocum, Andrii Ishchenko, Wolfgang Brehm, Thomas A. White, Nairie Michaelian, Caleb Madsen, Lan Zhu, Thomas D. Grant, Jessica M. Grandner, Anna Shiriaeva, Reid H. J. Olsen, Alexandra R. Tribo, Saïd Yous, Raymond C. Stevens, Uwe Weierstall, Vsevolod Katritch, Bryan L. Roth, Wei Liu, Vadim Cherezov
Citation: Stauch, B. et al., 2019. Publisher Correction: Structural basis of ligand recognition at the human MT1 melatonin receptor. Nature, 569(7756), pp.E6-E6.
Type: Journal-article
Authors: M. Gertrude Gutierrez, Jacob Deyell, Kate L. White, Lucia C. Dalle Ore, Vadim Cherezov, Raymond C. Stevens, Noah Malmstadt
Citation: Gutierrez, M.G. et al., 2019. The lipid phase preference of the adenosine A2A receptor depends on its ligand binding state. Chemical Communications, 55(40), pp.5724-5727.
Type: Journal-article
Authors: Benjamin Stauch, Linda C. Johansson, John D. McCorvy, Nilkanth Patel, Gye Won Han, Xi-Ping Huang, Cornelius Gati, Alexander Batyuk, Samuel T. Slocum, Andrii Ishchenko, Wolfgang Brehm, Thomas A. White, Nairie Michaelian, Caleb Madsen, Lan Zhu, Thomas D. Grant, Jessica M. Grandner, Anna Shiriaeva, Reid H. J. Olsen, Alexandra R. Tribo, Saïd Yous, Raymond C. Stevens, Uwe Weierstall, Vsevolod Katritch, Bryan L. Roth, Wei Liu, Vadim Cherezov
Citation: Stauch, B. et al., 2019. Structural basis of ligand recognition at the human MT1 melatonin receptor. Nature.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Linda C. Johansson, Benjamin Stauch, John D. McCorvy, Gye Won Han, Nilkanth Patel, Xi-Ping Huang, Alexander Batyuk, Cornelius Gati, Samuel T. Slocum, Chufeng Li, Jessica M. Grandner, Shuming Hao, Reid H. J. Olsen, Alexandra R. Tribo, Sahba Zaare, Lan Zhu, Nadia A. Zatsepin, Uwe Weierstall, Saïd Yous, Raymond C. Stevens, Wei Liu, Bryan L. Roth, Vsevolod Katritch, Vadim Cherezov
Citation: Johansson, L.C. et al., 2019. XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity. Nature.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Adrian P. Mancuso, Andrew Aquila, Lewis Batchelor, Richard J. Bean, Johan Bielecki, Gannon Borchers, Katerina Doerner, Klaus Giewekemeyer, Rita Graceffa, Oliver D. Kelsey, Yoonhee Kim, Henry J. Kirkwood, Alexis Legrand, Romain Letrun, Bradley Manning, Luis Lopez Morillo, Marc Messerschmidt, Grant Mills, Steffen Raabe, Nadja Reimers, Adam Round, Tokushi Sato, Joachim Schulz, Cedric Signe Takem, Marcin Sikorski, Stephan Stern, Prasad Thute, Patrik Vagovič, Britta Weinhausen, Thomas Tschentscher
Citation: Mancuso, A.P. et al., 2019. The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation. Journal of Synchrotron Radiation, 26(3), pp.660-676.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Jose M. Martin-Garcia, Lan Zhu, Derek Mendez, Ming-Yue Lee, Eugene Chun, Chufeng Li, Hao Hu, Ganesh Subramanian, David Kissick, Craig Ogata, Robert Henning, Andrii Ishchenko, Zachary Dobson, Shangji Zhang, Uwe Weierstall, John C. H. Spence, Petra Fromme, Nadia A. Zatsepin, Robert F. Fischetti, Vadim Cherezov, Wei Liu
Citation: Martin-Garcia, J.M. et al., 2019. High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source. IUCrJ, 6(3), pp.412-425.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Halil I Ciftci, Raymond G Sierra, Chun Yoon, Zhen Su, Hiroshi Tateishi, Ryoko Koga, Koiwai Kotaro, Fumiaki Yumoto, Toshiya Senda, Mengling Liang, Soichi Wakatsuki, Masami Otsuka, Mikako Fujita, Hasan DeMirci
Citation: I Ciftci, H. et al., 2019. Serial Femtosecond X-Ray Diffraction of HIV-1 Gag MA-IP6 Microcrystals at Ambient Temperature. International Journal of Molecular Sciences, 20(7), p.1675.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Alexey V. Onufriev, David A. Case
Citation: Onufriev, A.V. & Case, D.A., 2019. Generalized Born Implicit Solvent Models for Biomolecules. Annual Review of Biophysics, 48(1), pp.275-296.
Type: Journal-article
Authors: Katherine A. Niessen, Mengyang Xu, Deepu K. George, Michael C. Chen, Adrian R. Ferré-D’Amaré, Edward H. Snell, Vivian Cody, James Pace, Marius Schmidt, Andrea G. Markelz
Citation: Niessen, K.A. et al., 2019. Protein and RNA dynamical fingerprinting. Nature Communications, 10(1).
Type: Journal-article
Authors: Yingchen Shi, Ke Yin, Xuecheng Tai, Hasan DeMirci, Ahmad Hosseinizadeh, Brenda G. Hogue, Haoyuan Li, Abbas Ourmazd, Peter Schwander, Ivan A. Vartanyants, Chun Hong Yoon, Andrew Aquila, Haiguang Liu
Citation: Shi, Y. et al., 2019. Evaluation of the performance of classification algorithms for XFEL single-particle imaging data.
Type: Component
Authors: Yingchen Shi, Ke Yin, Xuecheng Tai, Hasan DeMirci, Ahmad Hosseinizadeh, Brenda G. Hogue, Haoyuan Li, Abbas Ourmazd, Peter Schwander, Ivan A. Vartanyants, Chun Hong Yoon, Andrew Aquila, Haiguang Liu
Citation: Shi, Y. et al., 2019. Evaluation of the performance of classification algorithms for XFEL single-particle imaging data. IUCrJ, 6(2), pp.331-340.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Yingchen Shi, Ke Yin, Xuecheng Tai, Hasan DeMirci, Ahmad Hosseinizadeh, Brenda G. Hogue, Haoyuan Li, Abbas Ourmazd, Peter Schwander, Ivan A. Vartanyants, Chun Hong Yoon, Andrew Aquila, Haiguang Liu
Citation: Shi, Y. et al., 2019. Evaluation of the performance of classification algorithms for XFEL single-particle imaging data.
Type: Component
Authors: J. P. J. Chen, J. J. Donatelli, K. E. Schmidt, R. A. Kirian
Citation: Chen, J.P.J. et al., 2019. Shape transform phasing of edgy nanocrystals. Acta Crystallographica Section A Foundations and Advances, 75(2), pp.239-259.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Raymond G. Sierra, Alexander Batyuk, Zhibin Sun, Andrew Aquila, Mark S. Hunter, Thomas J. Lane, Mengning Liang, Chun Hong Yoon, Roberto Alonso-Mori, Rebecca Armenta, Jean-Charles Castagna, Michael Hollenbeck, Ted O. Osier, Matt Hayes, Jeff Aldrich, Robin Curtis, Jason E. Koglin, Theodore Rendahl, Evan Rodriguez, Sergio Carbajo, Serge Guillet, Rob Paul, Philip Hart, Kazutaka Nakahara, Gabriella Carini, Hasan DeMirci, E. Han Dao, Brandon M. Hayes, Yashas P. Rao, Matthieu Chollet, Yiping Feng, Franklin D. Fuller, Christopher Kupitz, Takahiro Sato, Matthew H. Seaberg, Sanghoon Song, Tim B. van Driel, Hasan Yavas, Diling Zhu, Aina E. Cohen, Soichi Wakatsuki, Sébastien Boutet
Citation: Sierra, R.G. et al., 2019. The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source. Journal of Synchrotron Radiation, 26(2), pp.346-357.
Type: Journal-article
Authors: Alex Plumridge, Lois Pollack
Citation: Plumridge, A. & Pollack, L., 2019. Following Folding Pathways of Common Riboswitch Motifs with Time-Resolved Single-Molecule FRET. Biophysical Journal, 116(3), p.355a.
Type: Poster
Authors: Suzette A. Pabit, Andrea M. Katz, George D. Calvey, Lois Pollack
Citation: Pabit, S.A. et al., 2019. Time-Resolved Contrast Variation SAXS for Studying RNA-Protein Interactions. Biophysical Journal, 116(3), p.319a-320a.
Type: Poster
Authors: Alex Mauney, Joshua Tokuda, Yujie Chen, Lois Pollack
Citation: Mauney, A. et al., 2019. DNA Sequence and Histone Core Composition Control the Unwrapping of DNA from Nucleosome Core Particles. Biophysical Journal, 116(3), p.214a.
Type: Poster
Authors: Mukul Sonker, Daihyun Kim, Ana Egatz-Gomez, Alexandra Ros
Citation: Sonker, M. et al., 2019. Separation Phenomena in Tailored Micro- and Nanofluidic Environments. Annual Review of Analytical Chemistry, 12(1).
Type: Journal-article
Authors: Medhanjali DasGupta, Dominik Budday, Peter Madzelan, Javier Seravalli, Brandon Hayes, Raymond G. Sierra, Roberto Alonso-Mori, Aaron S. Brewster, Nicholas K. Sauter, Gregory A. Applegate, Virendra Tiwari, David B. Berkowitz, Michael C. Thompson, James S. Fraser, Michael E. Wall, Henry van den Bedem, Mark A. Wilson
Citation: DasGupta, M. et al., 2019. Cysteine modification can gate non-equilibrium conformational dynamics during enzyme catalysis: Supplemental Information.
Type: Posted-content
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Shenshen Hu, Adam R. Offenbacher, Erin M. Thompson, Christine L. Gee, Jarett Wilcoxen, Cody A. M. Carr, Daniil M. Prigozhin, Vanessa Yang, Tom Alber, R. David Britt, James S. Fraser, Judith P. Klinman
Citation: Hu, S. et al., 2019. Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network. Journal of the American Chemical Society, 141(4), pp.1555-1567.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Gennady Ananyev, Shatabdi Roy-Chowdhury, Colin Gates, Petra Fromme, G. Charles Dismukes
Citation: Ananyev, G. et al., 2019. The Catalytic Cycle of Water Oxidation in Crystallized Photosystem II Complexes: Performance and Requirements for Formation of Intermediates. ACS Catalysis, pp.1396-1407.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Shi-chun Du, Lan Zhu, Yu-xing Wang, Jie Liu, Die Zhang, Yu-lu Chen, Qing Peng, Wei Liu, Bin Liu
Citation: Du, S. et al., 2019. SENP1-mediated deSUMOylation of USP28 regulated HIF-1α accumulation and activation during hypoxia response. Cancer Cell International, 19(1).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Richard A. Kirian, Joe P. J. Chen, John C. H. Spence
Citation: Kirian, R.A., Chen, J.P.J. & Spence, J.C.H., 2018. Phasing Serial Crystallography Data. X-ray Free Electron Lasers, pp.235-252.
Type: Book-chapter
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Benjamin Stauch, Linda Johansson, Andrii Ishchenko, Gye Won Han, Alexander Batyuk, Vadim Cherezov
Citation: Stauch, B. et al., 2018. Advances in Structure Determination of G Protein-Coupled Receptors by SFX. X-ray Free Electron Lasers, pp.301-329.
Type: Book-chapter
Authors: Jesse Coe, Alexandra Ros
Citation: Coe, J. & Ros, A., 2018. Small Is Beautiful: Growth and Detection of Nanocrystals. X-ray Free Electron Lasers, pp.59-85.
Type: Book-chapter
Citation: Boutet, S., Fromme, P. & Hunter, M.S. eds., 2018. X-ray Free Electron Lasers.
Type: Book
Authors: Andrew J. Morgan, Kartik Ayyer, Anton Barty, Joe P. J. Chen, Tomas Ekeberg, Dominik Oberthuer, Thomas A. White, Oleksandr Yefanov, Henry N. Chapman
Citation: Morgan, A.J. et al., 2019. Ab initio phasing of the diffraction of crystals with translational disorder. Acta Crystallographica Section A Foundations and Advances, 75(1), pp.25-40.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Scott C. Jensen, Brendan Sullivan, Daniel A. Hartzler, Jose Meza Aguilar, Salah Awel, Saša Bajt, Shibom Basu, Richard Bean, Henry N. Chapman, Chelsie Conrad, Matthias Frank, Raimund Fromme, Jose M. Martin-Garcia, Thomas D. Grant, Michael Heymann, Mark S. Hunter, Gihan Ketawala, Richard A. Kirian, Juraj Knoska, Christopher Kupitz, Xuanxuan Li, Mengning Liang, Stella Lisova, Valerio Mariani, Victoria Mazalova, Marc Messerschmidt, Michael Moran, Garrett Nelson, Dominik Oberthür, Alex Schaffer, Raymond G. Sierra, Natalie Vaughn, Uwe Weierstall, Max O. Wiedorn, P. Lourdu Xavier, Jay-How Yang, Oleksandr Yefanov, Nadia A. Zatsepin, Andrew Aquila, Petra Fromme, Sébastien Boutet, Gerald T. Seidler, Yulia Pushkar
Citation: Jensen, S.C. et al., 2019. X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis. The Journal of Physical Chemistry Letters, pp.441-446.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Tatsuo Oyama, Nicholas G. Hall, Kazuhiro Kobayashi
Citation: Oyama, T., Hall, N.G. & Kobayashi, K., 2018. A generalized parametric divisor method for political apportionment. International Transactions in Operational Research, 28(1), pp.327-355.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Chufeng Li, Xuanxuan Li, Richard Kirian, John C. H. Spence, Haiguang Liu, Nadia A. Zatsepin
Citation: Li, C. et al., 2019. SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data. IUCrJ, 6(1), pp.72-84.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Martin Audet, Kate L. White, Billy Breton, Barbara Zarzycka, Gye Won Han, Yan Lu, Cornelius Gati, Alexander Batyuk, Petr Popov, Jeffrey Velasquez, David Manahan, Hao Hu, Uwe Weierstall, Wei Liu, Wenqing Shui, Vsevolod Katritch, Vadim Cherezov, Michael A. Hanson, Raymond C. Stevens
Citation: Audet, M. et al., 2018. Crystal structure of misoprostol bound to the labor inducer prostaglandin E2 receptor. Nature Chemical Biology, 15(1), pp.11-17.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Daihyun Kim, Mukul Sonker, Alexandra Ros
Citation: Kim, D., Sonker, M. & Ros, A., 2018. Dielectrophoresis: From molecular to micrometer scale analytes. Analytical Chemistry.
Type: Journal-article
Authors: José A. Carmona-Negrón, Alberto Santana, Arnold L. Rheingold, Enrique Meléndez
Citation: Carmona-Negrón, J.A. et al., 2019. Synthesis, structure, docking and cytotoxic studies of ferrocene-hormone conjugates for hormone-dependent breast cancer application. Dalton Transactions.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Yen-Lin Chen, Tongsik Lee, Ron Elber, Lois Pollack
Citation: Chen, Y.-L. et al., 2018. Conformations of an RNA Helix-Junction-Helix Construct revealed by SAXS Refinement of MD Simulations. Biophysical Journal.
Type: Journal-article
Authors: Michael C Thompson, Benjamin A Barad, Alexander M Wolff, Hyun Sun Cho, Friedrich Schotte, Daniel M.C. Schwarz, Philip Anfinrud, James S Fraser
Citation: Thompson, M.C. et al., 2018. Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme:
Type: Posted-content
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Gydo C. P. van Zundert, Brandi M. Hudson, Saulo H. P. de Oliveira, Daniel A. Keedy, Rasmus Fonseca, Amelie Heliou, Pooja Suresh, Kenneth Borrelli, Tyler Day, James S. Fraser, Henry van den Bedem
Citation: Van Zundert, G. et al., 2018. qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps. Journal of Medicinal Chemistry.
Type: Journal-article
Authors: Cecilia M. Casadei, Karol Nass, Anton Barty, Mark S. Hunter, Celestino Padeste, Ching-Ju Tsai, Sébastien Boutet, Marc Messerschmidt, Leonardo Sala, Garth J. Williams, Dmitry Ozerov, Matthew Coleman, Xiao-Dan Li, Matthias Frank, Bill Pedrini
Citation: Casadei, C.M. et al., 2019. Structure-factor amplitude reconstruction from serial femtosecond crystallography of two-dimensional membrane-protein crystals. IUCrJ, 6(1).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Jie Zhu, Cody L. Hoop, David A. Case, Jean Baum
Citation: Zhu, J. et al., 2018. Cryptic binding sites become accessible through surface reconstruction of the type I collagen fibril. Scientific Reports, 8(1).
Type: Journal-article
Authors: Yen-Lin Chen, Julie L. Sutton, Lois Pollack
Citation: Chen, Y.-L., Sutton, J.L. & Pollack, L., 2018. How the Conformations of an Internal Junction Contribute to Fold an RNA Domain. The Journal of Physical Chemistry B.
Type: Journal-article
Authors: Kanupriya Pande, Jeffrey J. Donatelli, Erik Malmerberg, Lutz Foucar, Billy K. Poon, Markus Sutter, Sabine Botha, Shibom Basu, R. Bruce Doak, Katerina Dörner, Sascha W. Epp, Lars Englert, Raimund Fromme, Elisabeth Hartmann, Robert Hartmann, Guenter Hauser, Johan Hattne, Ahmad Hosseinizadeh, Stephan Kassemeyer, Lukas Lomb, Sebastian F. Carron Montero, Andreas Menzel, Daniel Rolles, Artem Rudenko, Marvin M. Seibert, Raymond George Sierra, Peter Schwander, Abbas Ourmazd, Petra Fromme, Nicholas K. Sauter, Michael Bogan, John Bozek, Christoph Bostedt, Ilme Schlichting, Cheryl A. Kerfeld, Petrus H. Zwart
Citation: Pande, K. et al., 2018. Free-electron laser data for multiple-particle fluctuation scattering analysis. Scientific Data, 5, p.180201.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Robb Welty, Suzette A. Pabit, Andrea M. Katz, George D. Calvey, Lois Pollack, Kathleen B. Hall
Citation: Welty, R. et al., 2018. Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure. RNA, 24(12), pp.1828-1838.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Max Rose, Sergey Bobkov, Kartik Ayyer, Ruslan P. Kurta, Dmitry Dzhigaev, Young Yong Kim, Andrew J. Morgan, Chun Hong Yoon, Daniel Westphal, Johan Bielecki, Jonas A. Sellberg, Garth Williams, Filipe R.N.C. Maia, Olexander M. Yefanov, Vyacheslav Ilyin, Adrian P. Mancuso, Henry N. Chapman, Brenda G. Hogue, Andrew Aquila, Anton Barty, Ivan A. Vartanyants
Citation: Rose, M. et al., 2018. Single-particle imaging without symmetry constraints at an X-ray free-electron laser.
Type: Component
Authors: Eaton E. Lattman, Thomas D. Grant, Edward H. Snell
Citation: Lattman, E.E., Grant, T.D. & Snell, E.H., 2018. Biological Small Angle Scattering. Oxford Scholarship Online.
Type: Book
Authors: Eaton E. Lattman, Thomas D. Grant, Edward H. Snell
Citation: Lattman, E.E., Grant, T.D. & Snell, E.H., 2018. Examples of Biological Small Angle Scattering. Oxford Scholarship Online.
Type: Book
Authors: Max Rose, Sergey Bobkov, Kartik Ayyer, Ruslan P. Kurta, Dmitry Dzhigaev, Young Yong Kim, Andrew J. Morgan, Chun Hong Yoon, Daniel Westphal, Johan Bielecki, Jonas A. Sellberg, Garth Williams, Filipe R.N.C. Maia, Olexander M. Yefanov, Vyacheslav Ilyin, Adrian P. Mancuso, Henry N. Chapman, Brenda G. Hogue, Andrew Aquila, Anton Barty, Ivan A. Vartanyants
Citation: Rose, M. et al., 2018. Single-particle imaging without symmetry constraints at an X-ray free-electron laser. IUCrJ, 5(6).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Max F. Hantke, Johan Bielecki, Olena Kulyk, Daniel Westphal, Daniel S. D. Larsson, Martin Svenda, Hemanth K. N. Reddy, Richard A. Kirian, Jakob Andreasson, Janos Hajdu, Filipe R. N. C. Maia
Citation: Hantke, M.F. et al., 2018. Rayleigh-scattering microscopy for tracking and sizing nanoparticles in focused aerosol beams. IUCrJ, 5(6).
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Joanna Slawinska, Abbas Ourmazd, Dimitrios Giannakis
Citation: Slawinska, J., Ourmazd, A. & Giannakis, D., 2018. A New Approach to Signal Processing of Spatiotemporal Data. 2018 IEEE Statistical Signal Processing Workshop (SSP).
Type: Proceedings-article
Authors: Romain D. Arnal, Yun Zhao, Alok K. Mitra, John C. H. Spence, Rick P. Millane
Citation: Arnal, R.D. et al., 2018. The phase problem for two-dimensional crystals. II. Simulations. Acta Crystallographica Section A Foundations and Advances, 74(5), pp.537-544.
Type: Journal-article
Authors: Thibault Annaval, Lu Han, Jeffrey D. Rudolf, Guangbo Xie, Dong Yang, Chin-Yuan Chang, Ming Ma, Ivana Crnovcic, Mitchell D. Miller, Jayashree Soman, Weijun Xu, George N. Phillips, Ben Shen
Citation: Annaval, T. et al., 2018. Biochemical and Structural Characterization of TtnD, a Prenylated FMN-Dependent Decarboxylase from the Tautomycetin Biosynthetic Pathway. ACS Chemical Biology, 13(9), pp.2728-2738.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: Nicole C. Woitowich, Andrei S. Halavaty, Patricia Waltz, Christopher Kupitz, Joseph Valera, Gregory Tracy, Kevin D. Gallagher, Elin Claesson, Takanori Nakane, Suraj Pandey, Garrett Nelson, Rie Tanaka, Eriko Nango, Eiichi Mizohata, Shigeki Owada, Kensure Tono, Yasumasa Joti, Angela C. Nugent, Hardik Patel, Ayesha Mapara, James Hopkins, Phu Duong, Dorina Bizhga, Svetlana E. Kovaleva, Rachael St. Peter, Cynthia N. Hernandez, Wesley B. Ozarowski, Shatabdi Roy-Chowdhuri, Jay-How Yang, Petra Edlund, Heikki Takala, Janne Ihalainen, Jennifer Brayshaw, Tyler Norwood, Ishwor Poudyal, Petra Fromme, John C. H. Spence, Keith Moffat, Sebastian Westenhoff, Marius Schmidt, Emina A. Stojković
Citation: Woitowich, N.C. et al., 2018. Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome. IUCrJ, 5(5), pp.619-634.
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
Authors: E. Han Dao, Frédéric Poitevin, Raymond G. Sierra, Cornelius Gati, Yashas Rao, Halil Ibrahim Ciftci, Fulya Akşit, Alex McGurk, Trevor Obrinski, Paul Mgbam, Brandon Hayes, Casper De Lichtenberg, Fatima Pardo-Avila, Nicholas Corsepius, Lindsey Zhang, Matthew H. Seaberg, Mark S. Hunter, Mengling Liang, Jason E. Koglin, Soichi Wakatsuki, Hasan Demirci
Citation: Dao, E.H. et al., 2018. Structure of the 30S ribosomal decoding complex at ambient temperature. RNA, 24(12), pp.1667-1676.
Type: Journal-article