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  1. Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico

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    23 Sep 2020 | BioXFEL Publications | Contributor(s): Aron Broom, Rojo V. Rakotoharisoa, Michael Thompson, Niayesh Zarifi, Erin Nguyen, Nurzhan Mukhametzhanov, Lin Liu, James Fraser, Roberto A. Chica

    http://dx.doi.org/10.1038/s41467-020-18619-x Abstract The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve …

  2. Subthreshold Erosion of an Organic Polymer Induced by Multiple Shots of an X-Ray Free-Electron Laser

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    22 Sep 2020 | BioXFEL Publications | Contributor(s): 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

    http://dx.doi.org/10.1103/physrevapplied.14.034057 journal-article 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). Available at: http://dx.doi.org/10.1103/physrevapplied.14.034057. T. …

  3. Characterizing Enzyme Reactions in Microcrystals for Effective Mix-and-Inject Experiments using X-ray Free-Electron Lasers

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    21 Sep 2020 | BioXFEL Publications | Contributor(s): George Douglas Calvey, Andrea Katz, Kara Zielinski, Boris Dzikovski, Lois Pollack

    http://dx.doi.org/10.1021/acs.analchem.0c02569 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) 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), …

  4. Retrieving functional pathways of biomolecules from single-particle snapshots

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    18 Sep 2020 | BioXFEL Publications | Contributor(s): Ali Dashti, Ghoncheh Mashayekhi, Mrinal Shekhar, Danya Ben Hail, Salah Salah, Peter Schwander, Amedee Des Georges, Abhishek Singharoy, Joachim Frank, Abbas Ourmazd

    http://dx.doi.org/10.1038/s41467-020-18403-x Abstract A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining …

  5. High-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle

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    17 Sep 2020 | BioXFEL Publications | Contributor(s): 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 Stojkovic, Marius Schmidt

    http://dx.doi.org/10.1101/2020.09.16.298463 AbstractPhytochromes are red/far-red light photoreceptors in bacteria to plants, which elicit a variety of important physiological responses. They display a reversible photocycle between the resting (dark) Pr state and the light activated Pfr state, in …

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

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    10 Sep 2020 | BioXFEL Publications | Contributor(s): Austin Echelmeier, Jorvani Cruz Villarreal, Marc Messerschmidt, Daihyun Kim, Jesse David Coe, Darren Gary Thifault, Sabine Botha, Ana Egatz-Gomez, Sahir Ilyas Gandhi, Gerrit Brehm, Chelsie E Conrad, Debra T. Hansen, Caleb Alexander Madsen, Saša Bajt, J. Domingo Meza-Aguilar, Dominik Oberthür, Max Oliver 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 Spence, Henry Chapman, Nadia Zatsepin, Petra Fromme, Richard Kirian, Alexandra Ros

    http://dx.doi.org/10.1038/s41467-020-18156-7 Abstract Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal …

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

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    10 Sep 2020 | BioXFEL Publications | Contributor(s): 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 Kaushylal 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

    http://dx.doi.org/10.1101/2020.09.09.287987 AbstractThe COVID19 pandemic has resulted in 25+ million reported infections and nearly 850.000 deaths. Research to identify effective therapies for COVID19 includes: i) designing a vaccine as future protection; ii) structure-based drug design; and iii) …

  8. Exploring Serum Transferrin Regulation of Nonferric Metal Therapeutic Function and Toxicity

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    30 Aug 2020 | BioXFEL Publications | Contributor(s): 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 Rodriguez, 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 Tinoco

    http://dx.doi.org/10.3390/inorganics8090048 Serum transferrin (sTf) plays a pivotal role in regulating iron biodistribution and homeostasis within the body. The molecular details of sTf Fe(III) binding blood transport, and cellular delivery through transferrin receptor-mediated endocytosis are …

  9. The crystal structure ofAbsH3: A putative flavin adenine dinucleotide‐dependent reductase in the abyssomicin biosynthesis pathway

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    27 Aug 2020 | BioXFEL Publications | Contributor(s): Jonathan Clinger, Xiachang Wang, Wenlong Cai, Yanyan Zhu, Mitchell Miller, Chang‐Guo Zhan, Steven G. Van Lanen, Jon S. Thorson, George Phillips

    http://dx.doi.org/10.1002/prot.25994 journal-article 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. Available …

  10. Biophysical characterization dataset of native nicotinic acetylcholine receptor in lipid-like detergent complexes

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    26 Aug 2020 | BioXFEL Publications | Contributor(s): Rafael Maldonado-Hernandez, Orestes Quesada, José A. Lasalde-Dominicci

    http://dx.doi.org/10.1016/j.dib.2020.106230 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Maldonado-Hernández, R., Quesada, O. & Lasalde-Dominicci, J.A., 2020. Biophysical characterization dataset of native nicotinic acetylcholine receptor in lipid-like detergent complexes. Data …

  11. Covalent Capture of Collagen Triple Helices Using Lysine–Aspartate and Lysine–Glutamate Pairs

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    21 Aug 2020 | BioXFEL Publications | Contributor(s): Sarah A. H. Hulgan, Abhishek A. Jalan, I-Che Li, Douglas R. Walker, Mitchell Miller, Abigael Kosgei, Weijun Xu, George Phillips, Jeffrey D. Hartgerink

    http://dx.doi.org/10.1021/acs.biomac.0c00878 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) 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. Available at: …

  12. Need for Speed: Examining Protein Behavior during CryoEM Grid Preparation at Different Timescales

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    18 Aug 2020 | BioXFEL Publications | Contributor(s): David P. Klebl, Molly S.C. Gravett, Dimitrios Kontziampasis, David J. Wright, Robin S. Bon, Diana Monteiro, Martin Trebbin, Frank Sobott, Howard D. White, Michele C. Darrow, Rebecca F. Thompson, Stephen P. Muench

    http://dx.doi.org/10.1016/j.str.2020.07.018 journal-article 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. Available at: http://dx.doi.org/10.1016/j.str.2020.07.018. David P. Klebl …

  13. Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering

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    11 Aug 2020 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Lois Pollack

    http://dx.doi.org/10.1107/s2052252520008830 Macromolecular structures can be determined from solution X-ray scattering. Small-angle X-ray scattering (SAXS) provides global structural information on length scales of 10s to 100s of Ångstroms, and many algorithms are available to convert SAXS data …

  14. Microfluidic polyimide gas dynamic virtual nozzles for serial crystallography

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    07 Aug 2020 | BioXFEL Publications | Contributor(s): Mohammad Vakili, Ramakrishna Vasireddi, Paul V. Gwozdz, Diana Monteiro, Michael Heymann, Robert H. Blick, Martin Trebbin

    http://dx.doi.org/10.1063/5.0012806 journal-article Vakili, M. et al., 2020. Microfluidic polyimide gas dynamic virtual nozzles for serial crystallography. Review of Scientific Instruments, 91(8), p.085108. Available at: http://dx.doi.org/10.1063/5.0012806. Mohammad Vakili and Ramakrishna …

  15. Construction of gateway-compatible baculovirus expression vectors for high-throughput protein expression and in vivo microcrystal screening

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    07 Aug 2020 | BioXFEL Publications | Contributor(s): Yanyang Tang, Justin Saul, Nirupa Nagaratnam, Jose M. Martin-Garcia, Petra Fromme, Ji Qiu, Joshua LaBaer

    http://dx.doi.org/10.1038/s41598-020-70163-2 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Tang, Y. et al., 2020. Construction of gateway-compatible baculovirus expression vectors for high-throughput protein expression and in vivo microcrystal screening. Scientific Reports, …

  16. Inversion of Many-Beam Bragg Intensities for Phasing by Iterated Projections: Removal of Multiple Scattering Artifacts from Diffraction Data

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    06 Aug 2020 | BioXFEL Publications | Contributor(s): Jeffrey J. Donatelli, John Spence

    http://dx.doi.org/10.1103/physrevlett.125.065502 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) 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. …

  17. Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED

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    30 Jul 2020 | BioXFEL Publications | Contributor(s): Lan Zhu, Guanhong Bu, Liang Jing, Dan Shi, Ming-Yue Lee, Tamir Gonen, Wei Liu, Brent L. Nannenga

    http://dx.doi.org/10.1016/j.str.2020.07.006 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Zhu, L. et al., 2020. Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED. Structure, 28(10), pp.1149–1159.e4. Available at: …

  18. From Static Structures to Continuous Conformational Changes on the Energy Landscapes

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    30 Jul 2020 | BioXFEL Publications | Contributor(s): Ghoncheh Mashayekhi, Ali Dashti, Peter Schwander, Abbas Ourmazd

    http://dx.doi.org/10.1017/s1431927620018723 journal-article Mashayekhi, G. et al., 2020. From Static Structures to Continuous Conformational Changes on the Energy Landscapes. Microscopy and Microanalysis, 26(S2), pp.1614–1615. Available at: http://dx.doi.org/10.1017/s1431927620018723. Ghoncheh …

  19. Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers

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    22 Jul 2020 | BioXFEL Publications | Contributor(s): Suraj Pandey, Ishwor Poudyal, Tek Narsingh Malla

    http://dx.doi.org/10.3390/cryst10070628 With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating the structure of transient states along the reaction coordinate. X-ray free electron lasers (XFELs) have enabled TRX …

  20. Ptychographic X-ray speckle tracking with multi-layer Laue lens systems

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    08 Jul 2020 | BioXFEL Publications | Contributor(s): 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 Chapman, Saša Bajt

    http://dx.doi.org/10.1107/s1600576720006925 The ever-increasing brightness of synchrotron radiation sources demands improved X-ray optics to utilize their capability for imaging and probing biological cells, nano-devices and functional matter on the nanometre scale with chemical sensitivity. Hard …

  21. Advances in methods for atomic resolution macromolecular structure determination

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    02 Jul 2020 | BioXFEL Publications | Contributor(s): Michael Thompson, Todd O. Yeates, Jose A. Rodriguez

    http://dx.doi.org/10.12688/f1000research.25097.1 Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. …

  22. 3D printing of gas-dynamic virtual nozzles and optical characterization of high-speed microjets

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    26 Jun 2020 | BioXFEL Publications | Contributor(s): Reza Nazari, Sahba Zaare, Roberto C. Alvarez, Konstantinos Karpos, Trent Engelman, Caleb Alexander Madsen, Garrett Charles Nelson, John Spence, Uwe Weierstall, Ronald J. Adrian, Richard Kirian

    http://dx.doi.org/10.1364/oe.390131 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) 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. Available at: …

  23. Diffusion in multilayers, studied by quantitative chemical mapping at the atomic level

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    18 Jun 2020 | BioXFEL Publications | Contributor(s): Y. Kim, A. Ourmazd

    http://dx.doi.org/10.1017/s0424820100174904 Using chemical lattice imaging in combination with vector pattern recognition, we study diffusion and interdiffusion at single interfaces in mulilayered semiconductors quantitatively with atomic plane resolution. 20 periods of 50Å C-doped GaAs/50Å …

  24. Pyridine-2,6-Dithiocarboxylic Acid and Its Metal Complexes: New Inhibitors of New Delhi Metallo β-Lactamase-1

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    02 Jun 2020 | BioXFEL Publications | Contributor(s): Chris S. Thomas, Doug R. Braun, Jose Luis Olmos, Scott R. Rajski, George Phillips, David Andes, Tim S. Bugni

    http://dx.doi.org/10.3390/md18060295 Keywords: NDM-1 inhibitors; marine-derived Streptomyces sp.; carbapenem-resistant Enterobacteriaceae; metal chelators journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Thomas, C.S. et al., 2020. Pyridine-2,6-Dithiocarboxylic Acid and Its Metal …

  25. Carbon nanotube dielectrophoresis: Theory and applications

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    31 May 2020 | BioXFEL Publications | Contributor(s): Mohammad Towshif Rabbani, Mukul Sonker, Alexandra Ros

    http://dx.doi.org/10.1002/elps.202000049 journal-article Rabbani, M.T., Sonker, M. & Ros, A., 2020. Carbon nanotube dielectrophoresis: Theory and applications. ELECTROPHORESIS. Available at: http://dx.doi.org/10.1002/elps.202000049. Mohammad Towshif Rabbani and Mukul Sonker and Alexandra Ros

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

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    29 May 2020 | BioXFEL Publications | Contributor(s): Nirupa Nagaratnam, Yanyang Tang, Sabine Botha, Justin Saul, Chufeng Li, Hao Hu, Sahba Zaare, Mark S. Hunter, David Lowry, Uwe Weierstall, Nadia Zatsepin, John Spence, Ji Qiu, Joshua LaBaer, Petra Fromme, Jose M. Martin-Garcia

    http://dx.doi.org/10.1107/s2053230x20006172 μNS is a 70 kDa major nonstructural protein of avian reoviruses, which cause significant economic losses in the poultry industry. They replicate inside viral factories in host cells, and the μNS protein has been suggested to be the minimal viral …

  27. Megahertz single-particle imaging at the European XFEL

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    29 May 2020 | BioXFEL Publications | Contributor(s): 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 Chapman, Grzegorz Chojnowski, Benedikt J. Daurer, Katerina Dörner, Tomas Ekeberg, Leonie Flückiger, Oxana Galzitskaya, Luca Gelisio, Steffen Hauf, Brenda Hogue, Daniel A. Horke, Ahmad Hosseinizadeh, Vyacheslav Ilyin, Chulho Jung, Chan Kim, Yoonhee Kim, Richard 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 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

    http://dx.doi.org/10.1038/s42005-020-0362-y AbstractThe emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL is …

  28. Targeted DNA sequencing analysis to reveal genetic diversity and androgen-receptor alteration in advanced EGFR mutant lung adenocarcinoma.

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    25 May 2020 | BioXFEL Publications | Contributor(s): Wei Wu, Ross A. Okimoto, Collin Michael Blakely, James Fraser, Trever G. Bivona

    http://dx.doi.org/10.1200/jco.2020.38.15_suppl.9526 9526 Background: Lung cancer remains the leading cause of death from cancer around the world. Several oncogenic drivers have been identified from large cancer genome projects focused mainly on profiling early-stage lung cancers. Targeted …

  29. First Experiments in Structural Biology at the European X-ray Free-Electron Laser

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    25 May 2020 | BioXFEL Publications | Contributor(s): Grant Mills, Richard Bean, Adrian P. Mancuso

    http://dx.doi.org/10.3390/app10103642 Ultrabright pulses produced in X-ray free-electron lasers (XFELs) offer new possibilities for industry and research, particularly for biochemistry and pharmaceuticals. The unprecedented brilliance of these next-generation sources enables structure determination …

  30. Length-Selective Dielectrophoretic Manipulation of Single-Walled Carbon Nanotubes

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    25 May 2020 | BioXFEL Publications | Contributor(s): Mohammad T. Rabbani, Christoph F. Schmidt, Alexandra Ros

    http://dx.doi.org/10.1021/acs.analchem.0c00794 journal-article Rabbani, M.T., Schmidt, C.F. & Ros, A., 2020. Length-Selective Dielectrophoretic Manipulation of Single-Walled Carbon Nanotubes. Analytical Chemistry. Available at: http://dx.doi.org/10.1021/acs.analchem.0c00794. Mohammad T. Rabbani …

  31. Science in the age of machine learning

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    21 May 2020 | BioXFEL Publications | Contributor(s): Abbas Ourmazd

    http://dx.doi.org/10.1038/s42254-020-0191-7 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Ourmazd, A., 2020. Science in the age of machine learning. Nature Reviews Physics. Available at: http://dx.doi.org/10.1038/s42254-020-0191-7. Abbas Ourmazd

  32. Prochlorococcus phage ferredoxin: Structural characterization and electron transfer to cyanobacterial sulfite reductases

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    20 May 2020 | BioXFEL Publications | Contributor(s): Ian J. Campbell, Jose Luis Olmos, Weijun Xu, Dimithree Kahanda, Joshua T. Atkinson, Othneil Noble Sparks, Mitchell Miller, George Phillips, George N. Bennett, Jonathan J. Silberg

    http://dx.doi.org/10.1074/jbc.ra120.013501 Marine cyanobacteria are infected by phages whose genomes encode ferredoxin (Fd) electron carriers. These Fds are thought to redirect the energy harvested from light to phage-encoded oxidoreductases that enhance viral fitness, but it is  unclear how the …

  33. Femtosecond timing synchronization at megahertz repetition rates for an x-ray free-electron laser

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    18 May 2020 | BioXFEL Publications | Contributor(s): 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 Chapman, Adrian P. Mancuso

    http://dx.doi.org/10.1364/optica.396728 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Sato, T. et al., 2020. Femtosecond timing synchronization at megahertz repetition rates for an x-ray free-electron laser. Optica, 7(6), p.716. Available at: …

  34. Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser Pulses

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    04 May 2020 | BioXFEL Publications | Contributor(s): Richard Kirian, Henry Chapman

    http://dx.doi.org/10.1007/978-3-030-23201-6_27 book-chapter 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. Available at: …

  35. An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020)

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    01 May 2020 | BioXFEL Publications | Contributor(s): LaRinda A. Holland, Emily A. Kaelin, Rabia Maqsood, Bereket Estifanos, Lily I. Wu, Arvind Varsani, Rolf U. Halden, Brenda Hogue, Matthew Scotch, Efrem S. Lim

    http://dx.doi.org/10.1128/jvi.00711-20 journal-article 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). Available at: …

  36. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

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    30 Apr 2020 | BioXFEL Publications | Contributor(s): 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 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 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

    http://dx.doi.org/10.1038/s41586-020-2286-9 journal-article Gordon, D.E. et al., 2020. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature, 583(7816), pp.459–468. Available at: http://dx.doi.org/10.1038/s41586-020-2286-9. David E. Gordon and Gwendolyn M. Jang and …

  37. An 81 base-pair deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)

    0.0 out of 5 stars 

    22 Apr 2020 | BioXFEL Publications | Contributor(s): LaRinda A. Holland, Emily A. Kaelin, Rabia Maqsood, Bereket Estifanos, Lily I. Wu, Arvind Varsani, Rolf U. Halden, Brenda Hogue, Matthew Scotch, Efrem S. Lim

    http://dx.doi.org/10.1101/2020.04.17.20069641 On January 26 2020, the first Coronavirus Disease 2019 (COVID-19) case was reported in Arizona of an individual with travel history (3rd case in the US) (1). Here, we report on early SARS-CoV-2 sentinel surveillance in Tempe, Arizona (USA). Genomic …

  38. Dynamics of rare gas solids irradiated by electron beams

    0.0 out of 5 stars 

    10 Apr 2020 | BioXFEL Publications | Contributor(s): J. Candanedo, C. Caleman, N. Tîmneanu, O. Beckstein, J. C. H. Spence

    http://dx.doi.org/10.1063/1.5134801 journal-article Candanedo, J. et al., 2020. Dynamics of rare gas solids irradiated by electron beams. The Journal of Chemical Physics, 152(14), p.144303. Available at: http://dx.doi.org/10.1063/1.5134801. J. Candanedo and C. Caleman and N. Tîmneanu and O. …

  39. The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

    0.0 out of 5 stars 

    30 Mar 2020 | BioXFEL Publications | Contributor(s): 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 William Bosman, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, So Iwata, Shigeki Owada, Keith Moffat, Gerrit Groenhof, Emina Stojkovic, Janne A Ihalainen, Marius Schmidt, Sebastian Westenhoff

    http://dx.doi.org/10.7554/elife.53514 Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial …

  40. Sample deposition onto cryo-EM grids: from sprays to jets and back

    0.0 out of 5 stars 

    25 Mar 2020 | BioXFEL Publications | Contributor(s): David P. Klebl, Diana Monteiro, Dimitrios Kontziampasis, Florian Kopf, Frank Sobott, Howard D. White, Martin Trebbin, Stephen P. Muench

    http://dx.doi.org/10.1107/s2059798320002958 Despite the great strides made in the field of single-particle cryogenic electron microscopy (cryo-EM) in microscope design, direct electron detectors and new processing suites, the area of sample preparation is still far from ideal. Traditionally, sample …

  41. Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding

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    24 Mar 2020 | BioXFEL Publications | Contributor(s): Suvrajit Maji, Hstau Liao, Ali Dashti, Ghoncheh Mashayekhi, Abbas Ourmazd, Joachim Frank

    http://dx.doi.org/10.1021/acs.jcim.9b01115 journal-article 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. Available at: …

  42. Using Machine Learning to Achieve Accurate Estimates of Fetal Gestational Age and Personalized Predictions of Fetal Growth

    0.0 out of 5 stars 

    24 Mar 2020 | BioXFEL Publications | Contributor(s): 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 And Newborn Gro Group

    http://dx.doi.org/10.2139/ssrn.3471997 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) 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. Available at: …

  43. Single-particle imaging by x-ray free-electron lasers—How many snapshots are needed?

    0.0 out of 5 stars 

    20 Mar 2020 | BioXFEL Publications | Contributor(s): I. Poudyal, M. Schmidt, P. Schwander

    http://dx.doi.org/10.1063/1.5144516 journal-article 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. Available at: http://dx.doi.org/10.1063/1.5144516. I. Poudyal and M. …

  44. XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia

    0.0 out of 5 stars 

    09 Mar 2020 | BioXFEL Publications | Contributor(s): James D Zook, Mrinal Shekhar, Debra Hansen, Chelsie E 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 David Coe, Mark S. Hunter, Meng Liang, Uwe Weierstall, Garret Nelson, Daniel James, Benjamin Stauch, Felicia Craciunescu, Darren Gary Thifault, Wei Liu, Vadim Cherezov, Abhishek Singharoy, Petra Fromme

    http://dx.doi.org/10.1016/j.str.2020.02.005 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Zook, J. et al., 2020. XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia. Structure. Available at: …

  45. Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility

    0.0 out of 5 stars 

    07 Mar 2020 | BioXFEL Publications | Contributor(s): Darya Marchany-Rivera, Clyde A. Smith, Josiris D. Rodriguez-Perez, Juan J Lopez-Garriga

    http://dx.doi.org/10.1016/j.jinorgbio.2020.111055 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Marchany-Rivera, D. et al., 2020. Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility. Journal of Inorganic Biochemistry, 207, p.111055. Available at: …

  46. Structure-based discovery of potent and selective melatonin receptor agonists

    0.0 out of 5 stars 

    02 Mar 2020 | BioXFEL Publications | Contributor(s): Nilkanth N Patel, Xi Ping Huang, Jessica M Grandner, Linda C Johansson, Benjamin Stauch, John D McCorvy, Yongfeng Liu, Bryan Roth, Vsevolod Katritch

    http://dx.doi.org/10.7554/elife.53779 Melatonin receptors MT1 and MT2 are involved in synchronizing circadian rhythms and are important targets for treating sleep and mood disorders, type-2 diabetes and cancer. Here, we performed large scale structure-based virtual screening for new ligand …

  47. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

    0.0 out of 5 stars 

    25 Feb 2020 | BioXFEL Publications | Contributor(s): Alexander M. Wolff, Iris Diane 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 Lazarou, Takashi Nomura, Shigeki Owada, Avi J. Samelson, Tomoyuki Tanaka, Rie Tanaka, Erin M. Thompson, Henry Van Den Bedem, Rahel Woldeyes, Fumiaki Yumoto, Wei Zhao, Kensuke Tono, Sebastien Boutet, So Iwata, Tamir Gonen, Nicholas K. Sauter, James Fraser, Michael Thompson

    http://dx.doi.org/10.1107/s205225252000072x Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods …

  48. Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes

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    24 Feb 2020 | BioXFEL Publications | Contributor(s): Tyler D. Huber, Jonathan Clinger, Yang Liu, Weijun Xu, Mitchell Miller, George Phillips, Jon S. Thorson

    http://dx.doi.org/10.1021/acschembio.9b00943 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) 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. Available at: …

  49. Serial Crystallography: Preface

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    24 Feb 2020 | BioXFEL Publications | Contributor(s): John Spence

    http://dx.doi.org/10.3390/cryst10020135 The history of serial crystallography (SC) has its origins in the earliest attempts to merge data from several crystals. This preface provides an overview of some recent work, with a survey of the rapid advances made over the past decade in both sample …

  50. Reaction Initiation in Enzyme Crystals by Diffusion of Substrate

    0.0 out of 5 stars 

    14 Feb 2020 | BioXFEL Publications | Contributor(s): Marius Schmidt

    http://dx.doi.org/10.3390/cryst10020116 Ever since the first structure of an enzyme, lysozyme, was solved, scientists have been eager to explore how these molecules perform their catalytic function. There has been an overwhelmingly large body of publications that report the X-ray structures of …

  51. Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

    0.0 out of 5 stars 

    10 Feb 2020 | BioXFEL Publications | Contributor(s): 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

    http://dx.doi.org/10.1038/s41586-020-2027-0 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Stein, R.M. et al., 2020. Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. Nature. Available at: http://dx.doi.org/10.1038/s41586-020-2027-0. Reed M. Stein and …

  52. Prochlorococcusphage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases

    0.0 out of 5 stars 

    08 Feb 2020 | BioXFEL Publications | Contributor(s): Ian J. Campbell, Jose L. Olmos, Weijun Xu, Dimithree Kahanda, Joshua T. Atkinson, Othneil N. Sparks, Mitchell Miller, George Phillips, George N. Bennett, Jonathan J. Silberg

    http://dx.doi.org/10.1101/2020.02.07.937771 AbstractMarine cyanobacteria are infected by phage whose genomes encode ferredoxin (Fd) electron carriers. While these Fds are thought to redirect the energy harvested from light to phage-encoded oxidoreductases that enhance viral fitness, it is not clear …

  53. Convolutional Neural Networks Bridge Molecular Models and Solution X-ray Scattering Experiments

    0.0 out of 5 stars 

    07 Feb 2020 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2019.11.1706 poster Chen, Y.-L. & Pollack, L., 2020. Convolutional Neural Networks Bridge Molecular Models and Solution X-ray Scattering Experiments. Biophysical Journal, 118(3), p.301a. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.1706. Yen-Lin Chen and …

  54. Rhodopsin's Ultra-Fast Activation Dynamics in Bilayer and Micelle Environments

    0.0 out of 5 stars 

    07 Feb 2020 | BioXFEL Publications | Contributor(s): 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 Kirian, Michael F. Brown, Alan Grossfield

    http://dx.doi.org/10.1016/j.bpj.2019.11.669 journal-article Salas-Estrada, L.A. et al., 2020. Rhodopsin’s Ultra-Fast Activation Dynamics in Bilayer and Micelle Environments. Biophysical Journal, 118(3), p.92a. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.669. Leslie A. Salas-Estrada …

  55. Discovering Design Principles to Re-Engineer Functional RNA Elements

    0.0 out of 5 stars 

    07 Feb 2020 | BioXFEL Publications | Contributor(s): Alex Plumridge, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2019.11.556 poster Plumridge, A. & Pollack, L., 2020. Discovering Design Principles to Re-Engineer Functional RNA Elements. Biophysical Journal, 118(3), p.70a. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.556. Alex Plumridge and Lois Pollack

  56. Probing Mg2+-Mediated RNA-RNA Interactions in the Presence of Metabolites

    0.0 out of 5 stars 

    07 Feb 2020 | BioXFEL Publications | Contributor(s): Derrick R. Lin, Suzette A. Pabit, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2019.11.551 poster 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. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.551. Derrick R. Lin and Suzette A. …

  57. Quantitative Analysis of Salt-Induced RNA Duplex Variations by Wide-Angle X-ray Scattering (WAXS)

    0.0 out of 5 stars 

    07 Feb 2020 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2019.11.548 poster 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. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.548. Yen-Lin Chen and …

  58. DNA Sequence and Histone Core Composition Determine the Unwrapping Pathways in Nucleosomes

    0.0 out of 5 stars 

    07 Feb 2020 | BioXFEL Publications | Contributor(s): Alex Mauney, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2019.11.2706 poster Mauney, A. & Pollack, L., 2020. DNA Sequence and Histone Core Composition Determine the Unwrapping Pathways in Nucleosomes. Biophysical Journal, 118(3), p.489a. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.2706. Alex Mauney and Lois …

  59. Membrane Protein Dynamics Revealed by X-Ray Scattering with a Femtosecond Free-Electron Laser

    0.0 out of 5 stars 

    07 Feb 2020 | BioXFEL Publications | Contributor(s): 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 Kirian, Michael F. Brown

    http://dx.doi.org/10.1016/j.bpj.2019.11.2097 journal-article 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. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.2097. Thomas D. Grant …

  60. Viral RNA Folding Studied through Contrast Variation Small Angle- X Ray Scattering

    0.0 out of 5 stars 

    07 Feb 2020 | BioXFEL Publications | Contributor(s): Josue San Emeterio, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2019.11.1319 journal-article Emeterio, J. S., & Pollack, L. (2020). Viral RNA Folding Studied through Contrast Variation Small Angle- X Ray Scattering. Biophysical Journal, 118(3), 222a. https://doi.org/10.1016/j.bpj.2019.11.1319 Josue San Emeterio and Lois Pollack

  61. Evidence that Primary Microrna Bends in the Presence of DGCR8 Seen using Both Saxs and FRET Measurements

    0.0 out of 5 stars 

    07 Feb 2020 | BioXFEL Publications | Contributor(s): Suzette A. Pabit, Yen-Lin Chen, Grace A. Usher, Erik C. Cook, Lois Pollack, Scott A. Showalter

    http://dx.doi.org/10.1016/j.bpj.2019.11.1318 poster 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. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.1318. Suzette A. …

  62. Structural adaptation of oxygen tolerance in 4-hydroxybutyrl-CoA dehydratase, a key enzyme of archaeal carbon fixation

    0.0 out of 5 stars 

    07 Feb 2020 | BioXFEL Publications | Contributor(s): 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

    http://dx.doi.org/10.1101/2020.02.05.935528 AbstractAutotrophic microorganisms that convert inorganic carbon into organic matter were key players in the evolution of life on Earth. As the early atmosphere became oxygenated, microorganisms needed to develop mechanisms for oxygen protection, …

  63. Synthesis and structural studies of 16‐ferrocenemethyl‐estra‐1,3,5(10)‐triene‐3,17β‐diol and its interaction with human serum albumin by fluorescence spectroscopy and in silico docking approaches

    0.0 out of 5 stars 

    06 Feb 2020 | BioXFEL Publications | Contributor(s): José A. Carmona‐Negrón, José M. Liboy‐Lugo, Alberto Santana, Enrique Meléndez

    http://dx.doi.org/10.1002/aoc.5483 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Carmona‐Negrón, J.A. et al., 2020. Synthesis and structural studies of 16‐ferrocenemethyl‐estra‐1,3,5(10)‐triene‐3,17β‐diol and its interaction with human serum albumin by …

  64. Structural insights into conformational switching in latency-associated peptide between transforming growth factor β-1 bound and unbound states

    0.0 out of 5 stars 

    05 Feb 2020 | BioXFEL Publications | Contributor(s): Timothy R. Stachowski, Mary E. Snell, Edward Snell

    http://dx.doi.org/10.1107/s205225251901707x Transforming growth factor β-1 (TGFβ-1) is a secreted signalling protein that directs many cellular processes and is an attractive target for the treatment of several diseases. The primary endogenous activity regulatory mechanism for TGFβ-1 is …

  65. The Interplay between Molten Globules and Heme Disassociation Defines Human Hemoglobin Disassembly

    0.0 out of 5 stars 

    04 Feb 2020 | BioXFEL Publications | Contributor(s): Premila P. Samuel, Mark A. White, William C. Ou, David Case, George Phillips, John S. Olson

    http://dx.doi.org/10.1016/j.bpj.2020.01.031 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) 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. Available at: …

  66. In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors

    0.0 out of 5 stars 

    30 Jan 2020 | BioXFEL Publications | Contributor(s): 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

    http://dx.doi.org/10.1038/s41467-020-14484-w journal-article Nass, K. et al., 2020. In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors. Nature Communications, 11(1). Available at: http://dx.doi.org/10.1038/s41467-020-14484-w. Karol …

  67. 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

    0.0 out of 5 stars 

    23 Jan 2020 | BioXFEL Publications | Contributor(s): Hongnan Cao, Jonathan D. Walton, Phillip Brumm, George Phillips

    http://dx.doi.org/10.1021/acssuschemeng.9b07073 journal-article 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 …

  68. 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow

    0.0 out of 5 stars 

    16 Jan 2020 | BioXFEL Publications | Contributor(s): Diana Monteiro, David Von Stetten, Claudia Stohrer, Marta Sans, Arwen R. Pearson, Gianluca Santoni, Peter Van Der Linden, Martin Trebbin

    http://dx.doi.org/10.1107/s2052252519016865 Serial crystallography has enabled the study of complex biological questions through the determination of biomolecular structures at room temperature using low X-ray doses. Furthermore, it has enabled the study of protein dynamics by the capture of …

  69. Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit

    0.0 out of 5 stars 

    14 Jan 2020 | BioXFEL Publications | Contributor(s): Vanja Stojković, Alexander G Myasnikov, Iris Diane Young, Adam Frost, James Fraser, Danica Galonić Fujimori

    http://dx.doi.org/10.1093/nar/gkaa037 Abstract Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA …

  70. A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine

    0.0 out of 5 stars 

    13 Jan 2020 | BioXFEL Publications | Contributor(s): Sweta Vangaveti, William A. Cantara, Jessica L. Spears, Hasan Demirci, Frank V. Murphy, Sri V. Ranganathan, Kathryn L. Sarachan, Paul F. Agris

    http://dx.doi.org/10.1016/j.jmb.2019.12.016 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) 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), …

  71. Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates

    0.0 out of 5 stars 

    12 Jan 2020 | BioXFEL Publications | Contributor(s): Benjamin A. Barad, Lin Liu, Roberto E. Diaz, Ralp Basilio, Steven J. Van Dyken, Richard M. Locksley, James Fraser

    http://dx.doi.org/10.1002/pro.3822 journal-article Barad, B.A. et al., 2020. Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates. Protein Science. Available at: http://dx.doi.org/10.1002/pro.3822. Benjamin A. Barad and Lin Liu and Roberto E. Diaz …

  72. Structural knowledge or X-ray damage? Dose-dependent case studies on xylose isomerase revealing structural perturbations

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    03 Jan 2020 | BioXFEL Publications | Contributor(s): Edward Snell, Helena Taberman, Charles S. Bury, Mark J. Van Der Woerd, Elspeth F. Garman

    http://dx.doi.org/10.1107/s010876731909771x poster NSF-STC Biology with X-ray Lasers (NSF-1231306) 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 …

  73. Ribosomal protein L11 selectively stabilizes a tertiary structure of the GTPase Center rRNA domain

    0.0 out of 5 stars 

    23 Dec 2019 | BioXFEL Publications | Contributor(s): Robb Welty, Michael Rau, Suzette Pabit, Mark S. Dunstan, Graeme L. Conn, Lois Pollack, Kathleen B. Hall

    http://dx.doi.org/10.1016/j.jmb.2019.12.010 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Welty, R. et al., 2019. Ribosomal protein L11 selectively stabilizes a tertiary structure of the GTPase Center rRNA domain. Journal of Molecular Biology. Available at: …

  74. 7th Annual BioXFEL International Conference

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    23 Dec 2019 | Downloads

    …

  75. Photoreversible interconversion of a phytochrome photosensory module in the crystalline state

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    18 Dec 2019 | BioXFEL Publications | Contributor(s): E. Sethe Burgie, Jonathan Clinger, Mitchell Miller, Aaron S. Brewster, Pierre Aller, Agata Butryn, Franklin D. Fuller, Sheraz Gul, Iris Diane 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 Phillips, Richard D. Vierstra

    http://dx.doi.org/10.1073/pnas.1912041116 A major barrier to defining the structural intermediates that arise during the reversible photointerconversion of phytochromes between their biologically inactive and active states has been the lack of crystals that faithfully undergo this transition within …

  76. Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

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    18 Dec 2019 | BioXFEL Publications | Contributor(s): David C. Wych, James Fraser, David L. Mobley, Michael E. Wall

    http://dx.doi.org/10.1063/1.5132692 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) 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. Available at: …

  77. Low-signal limit of X-ray single particle diffractive imaging

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    12 Dec 2019 | BioXFEL Publications | Contributor(s): Kartik Ayyer, Andrew J. Morgan, Andrew Aquila, Hasan Demirci, Brenda Hogue, Richard Kirian, P. Lourdu Xavier, Chun Hong Yoon, Henry Chapman, Anton Barty

    http://dx.doi.org/10.1364/oe.27.037816 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Ayyer, K. et al., 2019. Low-signal limit of X-ray single particle diffractive imaging. Optics Express, 27(26), p.37816. Available at: http://dx.doi.org/10.1364/oe.27.037816. Kartik Ayyer and …

  78. Structural basis of ligand selectivity and disease mutations in cysteinyl leukotriene receptors

    0.0 out of 5 stars 

    06 Dec 2019 | BioXFEL Publications | Contributor(s): Anastasiia Gusach, Aleksandra Luginina, Egor Marin, Rebecca L. Brouillette, Élie Besserer-Offroy, Jean-Michel Longpré, Andrii Ishchenko, Petr Popov, Nilkanth N 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

    http://dx.doi.org/10.1038/s41467-019-13348-2 journal-article Gusach, A. et al., 2019. Structural basis of ligand selectivity and disease mutations in cysteinyl leukotriene receptors. Nature Communications, 10(1). Available at: http://dx.doi.org/10.1038/s41467-019-13348-2. Anastasiia Gusach and …

  79. Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics

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    05 Dec 2019 | BioXFEL Publications | Contributor(s): Alex Plumridge, Kurt Andresen, Lois Pollack

    http://dx.doi.org/10.1021/jacs.9b04461 journal-article Plumridge, A., Andresen, K. & Pollack, L., 2019. Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics. Journal of the American Chemical Society. Available at: http://dx.doi.org/10.1021/jacs.9b04461. …

  80. High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application

    0.0 out of 5 stars 

    03 Dec 2019 | BioXFEL Publications | Contributor(s): Geoffrey W. Grime, Oliver B. Zeldin, Mary E. Snell, Edward D. Lowe, John F. Hunt, Gaetano T. Montelione, Liang Tong, Edward Snell, Elspeth F. Garman

    http://dx.doi.org/10.1021/jacs.9b09186 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) 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 …

  81. Elucidating the active δ-opioid receptor crystal structure with peptide and small-molecule agonists

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    27 Nov 2019 | BioXFEL Publications | Contributor(s): Tobias Claff, Jing Yu, Véronique Blais, Nilkanth N 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

    http://dx.doi.org/10.1126/sciadv.aax9115 Selective activation of the δ-opioid receptor (DOP) has great potential for the treatment of chronic pain, benefitting from ancillary anxiolytic and antidepressant-like effects. Moreover, DOP agonists show reduced adverse effects as compared to μ-opioid …

  82. Computational design of a modular protein sense-response system

    0.0 out of 5 stars 

    25 Nov 2019 | BioXFEL Publications | Contributor(s): 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 Fraser, Tanja Kortemme

    http://dx.doi.org/10.1126/science.aax8780 Sensing and responding to signals is a fundamental ability of living systems, but despite substantial progress in the computational design of new protein structures, there is no general approach for engineering arbitrary new protein sensors. Here, we …

  83. A fixed-target platform for serial femtosecond crystallography in a hydrated environment

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    21 Nov 2019 | BioXFEL Publications | Contributor(s): 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

    http://dx.doi.org/10.1107/s2052252519014003 For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while …

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

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    18 Nov 2019 | BioXFEL Publications | Contributor(s): Suraj Pandey, Richard Bean, Tokushi Sato, Ishwor Poudyal, Johan Bielecki, Jorvani Cruz Villarreal, Oleksandr Yefanov, Valerio Mariani, Thomas A. White, Christopher Kupitz, Mark S. 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 Hammad Mekky 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 Chapman, Alexandra Ros, Anton Barty, Petra Fromme, Adrian P. Mancuso, Marius Schmidt

    http://dx.doi.org/10.1038/s41592-019-0628-z journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Pandey, S. et al., 2019. Time-resolved serial femtosecond crystallography at the European XFEL. Nature Methods. Available at: http://dx.doi.org/10.1038/s41592-019-0628-z. Suraj Pandey and …

  85. Structural Insights into Melatonin Receptors

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    06 Nov 2019 | BioXFEL Publications | Contributor(s): Benjamin Stauch, Linda C. Johansson, Vadim Cherezov

    http://dx.doi.org/10.1111/febs.15128 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Stauch, B., Johansson, L.C. & Cherezov, V., 2019. Structural Insights into Melatonin Receptors. The FEBS Journal. Available at: http://dx.doi.org/10.1111/febs.15128. Benjamin Stauch and Linda C. …

  86. Membrane protein megahertz crystallography at the European XFEL

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    04 Nov 2019 | BioXFEL Publications | Contributor(s): Chris Gisriel, Jesse David Coe, Romain Letrun, Oleksandr M. Yefanov, Cesar Luna-Chavez, Natasha 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 Oliver 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 Coleman, Cyril Danilevski, Erin Discianno, Zachary Dobson, Hans Fangohr, Jose M. Martin-Garcia, Yaroslav Gevorkov, Steffen Hauf, Ahmad Hosseinizadeh, Friederike Januschek, Gihan Kaushylal Ketawala, Christopher Kupitz, Luis Maia, Maurizio Manetti, Marc Messerschmidt, Thomas Michelat, Jyotirmoy Mondal, Abbas Ourmazd, Gianpietro Previtali, Iosifina Sarrou, Silvan Schön, Peter Schwander, Megan Shelby, Alessandro Silenzi, Jolanta Sztuk-Dambietz, Janusz Szuba, Monica Turcato, Thomas A. White, Krzysztof Wrona, Chen Xu, Mohamed H. Abdellatif, James D Zook, John Spence, Henry Chapman, Anton Barty, Richard Kirian, Matthias Frank, Alexandra Ros, Marius Schmidt, Raimund Fromme, Adrian P. Mancuso, Petra Fromme, Nadia Zatsepin

    http://dx.doi.org/10.1038/s41467-019-12955-3 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Gisriel, C. et al., 2019. Membrane protein megahertz crystallography at the European XFEL. Nature Communications, 10(1). Available at: http://dx.doi.org/10.1038/s41467-019-12955-3. Chris …

  87. Toward G protein-coupled receptor structure-based drug design using X-ray lasers

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    24 Oct 2019 | BioXFEL Publications | Contributor(s): 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

    http://dx.doi.org/10.1107/s2052252519013137 Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. …

  88. Salt Dependence of A-Form RNA Duplexes: Structures and Implications

    0.0 out of 5 stars 

    23 Oct 2019 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Lois Pollack

    http://dx.doi.org/10.1021/acs.jpcb.9b07502 journal-article Chen, Y.-L. & Pollack, L., 2019. Salt Dependence of A-Form RNA Duplexes: Structures and Implications. The Journal of Physical Chemistry B. Available at: http://dx.doi.org/10.1021/acs.jpcb.9b07502. Yen-Lin Chen and Lois Pollack

  89. Correction to: Spatiotemporal Pattern Extraction by Spectral Analysis of Vector-Valued Observables

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    23 Oct 2019 | BioXFEL Publications | Contributor(s): Dimitrios Giannakis, Abbas Ourmazd, Joanna Slawinska, Zhizhen Zhao

    http://dx.doi.org/10.1007/s00332-019-09586-9 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Giannakis, D. et al., 2019. Correction to: Spatiotemporal Pattern Extraction by Spectral Analysis of Vector-Valued Observables. Journal of Nonlinear Science. Available at: …

  90. Structure-based mechanism of cysteinyl leukotriene receptor inhibition by antiasthmatic drugs

    0.0 out of 5 stars 

    09 Oct 2019 | BioXFEL Publications | Contributor(s): 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 N 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

    http://dx.doi.org/10.1126/sciadv.aax2518 The G protein–coupled cysteinyl leukotriene receptor CysLT1R mediates inflammatory processes and plays a major role in numerous disorders, including asthma, allergic rhinitis, cardiovascular disease, and cancer. Selective CysLT1R antagonists are widely …

  91. Co-occurring Alterations in the RAS–MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer

    0.0 out of 5 stars 

    23 Sep 2019 | BioXFEL Publications | Contributor(s): 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 Fraser, Eric A. Collisson, Caroline E. McCoach, D. Ross Camidge, Jose Pacheco, Lyudmila Bazhenova, Tianhong Li, Trever G. Bivona, Collin M. Blakely

    http://dx.doi.org/10.1158/1078-0432.ccr-19-1667 Abstract Purpose: Although patients with advanced-stage non–small cell lung cancers (NSCLC) harboring MET exon 14 skipping mutations (METex14) often benefit from MET tyrosine kinase inhibitor (TKI) …

  92. Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme

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    16 Sep 2019 | BioXFEL Publications | Contributor(s): Michael Thompson, Benjamin A. Barad, Alexander M. Wolff, Hyun Sun Cho, Friedrich Schotte, Daniel M. C. Schwarz, Philip Anfinrud, James Fraser

    http://dx.doi.org/10.1038/s41557-019-0329-3 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) 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. Available at: …

  93. 3D printed droplet generation devices for serial femtosecond crystallography enabled by surface coating

    0.0 out of 5 stars 

    29 Aug 2019 | BioXFEL Publications | Contributor(s): Austin Echelmeier, Daihyun Kim, Jorvani Cruz Villarreal, Jesse David Coe, Sebastian E Quintana, Gerrit Brehm, Ana Egatz-Gomez, Reza Nazari, Raymond G. Sierra, Jason E. Koglin, Alexander Batyuk, Mark S. Hunter, Sébastien Boutet, Nadia Zatsepin, Richard Kirian, Thomas D. Grant, Petra Fromme, Alexandra Ros

    http://dx.doi.org/10.1107/s1600576719010343 The role of surface wetting properties and their impact on the performance of 3D printed microfluidic droplet generation devices for serial femtosecond crystallography (SFX) are reported. SFX is a novel crystallography method enabling structure …

  94. Reconstruction of Objects from Their Averaged Finite Crystal Diffraction Intensity

    0.0 out of 5 stars 

    26 Aug 2019 | BioXFEL Publications | Contributor(s): J. P. J. Chen, K. E. Schmidt, R. A. Kirian, J. J. Donatelli

    http://dx.doi.org/10.1109/icip.2019.8804468 proceedings-article 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). Available at: http://dx.doi.org/10.1109/icip.2019.8804468. …

  95. A Remarkable Return On Investment In Fundamental Research: 40 Years of Basic Energy Sciences at the Department of Energy

    0.0 out of 5 stars 

    02 Aug 2019 | BioXFEL Publications | Contributor(s): 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

    http://dx.doi.org/10.2172/1545686 report Drell, P. et al., 2018. A Remarkable Return On Investment In Fundamental Research: 40 Years of Basic Energy Sciences at the Department of Energy. Available at: http://dx.doi.org/10.2172/1545686. Persis Drell and Dawn A. Bonnell and Jingguang Chen and Sue …

  96. Electric Triggering for Enhanced Control of Droplet Generation

    0.0 out of 5 stars 

    01 Jul 2019 | BioXFEL Publications | Contributor(s): Daihyun Kim, Austin Echelmeier, Jorvani Cruz Villarreal, Sahir Ilyas Gandhi, Sebastian E Quintana, Ana Egatz-Gomez, Alexandra Ros

    http://dx.doi.org/10.1021/acs.analchem.9b01449 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Kim, D. et al., 2019. Electric Triggering for Enhanced Control of Droplet Generation. Analytical Chemistry, 91(15), pp.9792–9799. Available at: …

  97. Microfluidic sample delivery for serial crystallography using XFELs

    0.0 out of 5 stars 

    27 Jun 2019 | BioXFEL Publications | Contributor(s): Austin Echelmeier, Mukul Sonker, Alexandra Ros

    http://dx.doi.org/10.1007/s00216-019-01977-x journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Echelmeier, A., Sonker, M. & Ros, A., 2019. Microfluidic sample delivery for serial crystallography using XFELs. Analytical and Bioanalytical Chemistry, 411(25), pp.6535–6547. Available …

  98. Four amino acids define the CO2binding pocket of enoyl-CoA carboxylases/reductases

    0.0 out of 5 stars 

    26 Jun 2019 | BioXFEL Publications | Contributor(s): 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

    http://dx.doi.org/10.1073/pnas.1901471116 Carboxylases are biocatalysts that capture and convert carbon dioxide (CO2) under mild conditions and atmospheric concentrations at a scale of more than 400 Gt annually. However, how these enzymes bind and control the gaseous CO2molecule during catalysis is …

  99. Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both

    0.0 out of 5 stars 

    24 Jun 2019 | BioXFEL Publications | Contributor(s): Helena Taberman, Charles S. Bury, Mark J. Van Der Woerd, Edward Snell, Elspeth F. Garman

    http://dx.doi.org/10.1107/s1600577519005599 Xylose isomerase (XI) is an industrially important metalloprotein studied for decades. Its reaction mechanism has been postulated to involve movement of the catalytic metal cofactor to several different conformations. Here, a dose-dependent approach was …

  100. Coherent diffractive imaging of microtubules using an X-ray laser

    0.0 out of 5 stars 

    13 Jun 2019 | BioXFEL Publications | Contributor(s): 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 Chapman, Peter Zwart, Mengning Liang, Sébastien Boutet, Robert C. Robinson, Richard Neutze

    http://dx.doi.org/10.1038/s41467-019-10448-x journal-article Brändén, G. et al., 2019. Coherent diffractive imaging of microtubules using an X-ray laser. Nature Communications, 10(1). Available at: http://dx.doi.org/10.1038/s41467-019-10448-x. Gisela Brändén and Greger Hammarin and Rajiv …