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  1. 8th BioXFEL International Conference

    09 Dec 2020 | Downloads

  2. How directed evolution reshapes the energy landscape in an enzyme to boost catalysis

    19 Nov 2020 | BioXFEL Publications | Contributor(s): Renee Otten, Ricardo A. P. Pádua, H. Adrian Bunzel, Vy Nguyen, Warintra Pitsawong, MacKenzie Patterson, Shuo Sui, Sarah Perry, Aina E. Cohen, Donald Hilvert, Dorothee Kern

    http://dx.doi.org/10.1126/science.abd3623 The advent of biocatalysts designed computationally and optimized by laboratory evolution provides an opportunity to explore molecular strategies for augmenting catalytic function. Applying a suite of NMR, crystallographic, and stopped-flow techniques to an …

  3. Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source

    19 Nov 2020 | BioXFEL Publications | Contributor(s): 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 Chapman, Alice Contreras, Benedikt J. Daurer, Hasan Demirci, Leonie Flűckiger, Matthias Frank, Janos Hajdu, Max F. Hantke, Brenda Hogue, Ahmad Hosseinizadeh, Mark S. Hunter, H. Olof Jönsson, Richard 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

    http://dx.doi.org/10.1038/s41597-020-00745-2 AbstractSingle Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 …

  4. Molecular-replacement phasing using predicted protein structures from AWSEM-Suite

    26 Oct 2020 | BioXFEL Publications | Contributor(s): Shikai Jin, Mitchell Miller, Mingchen Chen, Nicholas P. Schafer, Xingcheng Lin, Xun Chen, George Phillips, Peter G. Wolynes

    http://dx.doi.org/10.1107/s2052252520013494 The phase problem in X-ray crystallography arises from the fact that only the intensities, and not the phases, of the diffracting electromagnetic waves are measured directly. Molecular replacement can often estimate the relative phases of reflections …

  5. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser

    15 Oct 2020 | BioXFEL Publications | Contributor(s): 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 Kirian, Brenda Hogue, Andrew Aquila, Ivan A. Vartanyants

    http://dx.doi.org/10.1107/s2052252520012798 An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent …

  6. Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase

    15 Oct 2020 | BioXFEL Publications | Contributor(s): 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

    http://dx.doi.org/10.1107/s2052252520012701 Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has …

  7. Crystallization of ApoA1 and ApoE4 Nanolipoprotein Particles and Initial XFEL-Based Structural Studies

    01 Oct 2020 | BioXFEL Publications | Contributor(s): Megan Shelby, Deepshika Gilbile, Thomas D. Grant, William J. Bauer, Brent W. 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 Coleman

    http://dx.doi.org/10.3390/cryst10100886 Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins …

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

    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 …

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

    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 …

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

    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) …

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

    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 …

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

    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 Rafael Maldonado-Hernández and Orestes Quesada and José A. Lasalde-Dominicci

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

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

    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, …

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

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

    http://dx.doi.org/10.1103/physrevlett.125.065502 journal-article 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). Available at: …

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

    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 …

  17. 3D printing of gas-dynamic virtual nozzles and optical characterization of high-speed microjets

    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: …

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

    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 …

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

    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 Thomas, C.S. et al., 2020. Pyridine-2,6-Dithiocarboxylic Acid and Its Metal Complexes: New Inhibitors of New Delhi Metallo …

  20. Carbon nanotube dielectrophoresis: Theory and applications

    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

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

    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 …

  22. Megahertz single-particle imaging at the European XFEL

    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 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Sobolev, E. et al., 2020. Megahertz single-particle imaging at the European XFEL. Communications Physics, 3(1). Available at: http://dx.doi.org/10.1038/s42005-020-0362-y. Egor Sobolev and …

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

    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 …

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

    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 …

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

    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 …

  26. Science in the age of machine learning

    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

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

    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 …

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

    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: …

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

    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: …

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

    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 A Stojković, 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 …

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

    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: …

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

    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: …

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

    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. …

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

    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 Zook, J. et al., 2020. XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia. Structure. Available at: http://dx.doi.org/10.1016/j.str.2020.02.005. James Zook and Mrinal Shekhar …

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

    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: …

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

    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 …

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

    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: …

  38. Serial Crystallography: Preface

    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 …

  39. Reaction Initiation in Enzyme Crystals by Diffusion of Substrate

    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 …

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

    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 …

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

    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 …

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

    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

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

    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. …

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

    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 …

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

    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 …

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

    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. …

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

    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, …

  48. 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

    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 …

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

    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 …

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

    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 …

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

    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 …

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

    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 …

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

    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 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: http://dx.doi.org/10.1016/j.jmb.2019.12.010. Robb Welty and Michael …

  54. 7th Annual BioXFEL International Conference

    23 Dec 2019 | Downloads

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

    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 …

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

    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: …

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

    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 …

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

    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 …

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

    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. …

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

    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 …

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

    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 …

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

    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 …

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

    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 …

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

    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 …

  65. Structural Insights into Melatonin Receptors

    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. …

  66. Membrane protein megahertz crystallography at the European XFEL

    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 …

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

    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. …

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

    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

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

    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: …

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

    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 …

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

    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: …

  72. 3D printed droplet generation devices for serial femtosecond crystallography enabled by surface coating

    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 …

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

    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. …

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

    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 …

  75. Electric Triggering for Enhanced Control of Droplet Generation

    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: …

  76. Microfluidic sample delivery for serial crystallography using XFELs

    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 …

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

    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 …

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

    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 …

  79. 7th Annual BioXFEL International Conference

    23 May 2019 | Downloads

  80. Spatial characterization of FLASH2 pulses: current status and future plan (Conference Presentation)

    14 May 2019 | BioXFEL Publications | Contributor(s): 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

    http://dx.doi.org/10.1117/12.2523254 proceedings-article 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. …

  81. Spatiotemporal Pattern Extraction by Spectral Analysis of Vector-Valued Observables

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

    http://dx.doi.org/10.1007/s00332-019-09548-1 journal-article Giannakis, D. et al., 2019. Spatiotemporal Pattern Extraction by Spectral Analysis of Vector-Valued Observables. Journal of Nonlinear Science. Available at: http://dx.doi.org/10.1007/s00332-019-09548-1. Dimitrios Giannakis and Abbas …

  82. Abstract P6-19-01: Evaluation of multiple transcriptomic gene risk signatures in male breast cancer

    11 May 2019 | BioXFEL Publications | Contributor(s): 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

    http://dx.doi.org/10.1158/1538-7445.sabcs18-p6-19-01 proceedings-article Bayani, J. et al., 2019. Abstract P6-19-01: Evaluation of multiple transcriptomic gene risk signatures in male breast cancer. Poster Session Abstracts. Available at: http://dx.doi.org/10.1158/1538-7445.sabcs18-p6-19-01. J …

  83. Microfluidic Mixing Injector Holder Enables Routine Structural Enzymology Measurements with Mix-and-Inject Serial Crystallography Using X-ray Free Electron Lasers

    07 May 2019 | BioXFEL Publications | Contributor(s): George Douglas Calvey, Andrea Katz, Lois Pollack

    http://dx.doi.org/10.1021/acs.analchem.9b00311 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) 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 …

  84. Publisher Correction: Structural basis of ligand recognition at the human MT1 melatonin receptor

    02 May 2019 | BioXFEL Publications | Contributor(s): Benjamin Stauch, Linda C. Johansson, John D. McCorvy, Nilkanth N Patel, Gye Won Han, Xi-Ping Huang, Cornelius Gati, Alexander Batyuk, Samuel T. Slocum, Andrii Ishchenko, Wolfgang Brehm, Thomas A. White, Nairie Michaelian, Caleb Alexander 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

    http://dx.doi.org/10.1038/s41586-019-1209-0 journal-article Stauch, B. et al., 2019. Publisher Correction: Structural basis of ligand recognition at the human MT1 melatonin receptor. Nature, 569(7756), pp.E6–E6. Available at: http://dx.doi.org/10.1038/s41586-019-1209-0. Benjamin Stauch and …

  85. The lipid phase preference of the adenosine A2A receptor depends on its ligand binding state

    30 Apr 2019 | BioXFEL Publications | Contributor(s): M. Gertrude Gutierrez, Jacob Deyell, Kate L. White, Lucia C. Dalle Ore, Vadim Cherezov, Raymond C. Stevens, Noah Malmstadt

    http://dx.doi.org/10.1039/c8cc10130b As cholesterol fraction increases, ligand-bound receptor occupies more vesicle surface area, demonstrating co-localization with the cholesterol-rich phase. journal-article Gutierrez, M.G. et al., 2019. The lipid phase preference of the adenosine A2A receptor …

  86. Structural basis of ligand recognition at the human MT1 melatonin receptor

    24 Apr 2019 | BioXFEL Publications | Contributor(s): Benjamin Stauch, Linda C. Johansson, John D. McCorvy, Nilkanth N Patel, Gye Won Han, Xi-Ping Huang, Cornelius Gati, Alexander Batyuk, Samuel T. Slocum, Andrii Ishchenko, Wolfgang Brehm, Thomas A. White, Nairie Michaelian, Caleb Alexander 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

    http://dx.doi.org/10.1038/s41586-019-1141-3 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Stauch, B. et al., 2019. Structural basis of ligand recognition at the human MT1 melatonin receptor. Nature. Available at: http://dx.doi.org/10.1038/s41586-019-1141-3. Benjamin Stauch and …

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

    24 Apr 2019 | BioXFEL Publications | Contributor(s): Linda C. Johansson, Benjamin Stauch, John D. McCorvy, Gye Won Han, Nilkanth N 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 Zatsepin, Uwe Weierstall, Saïd Yous, Raymond C. Stevens, Wei Liu, Bryan L. Roth, Vsevolod Katritch, Vadim Cherezov

    http://dx.doi.org/10.1038/s41586-019-1144-0 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Johansson, L.C. et al., 2019. XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity. Nature. Available at: http://dx.doi.org/10.1038/s41586-019-1144-0. …

  88. The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation

    12 Apr 2019 | BioXFEL Publications | Contributor(s): 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

    http://dx.doi.org/10.1107/s1600577519003308 The European X-ray Free-Electron Laser (FEL) became the first operational high-repetition-rate hard X-ray FEL with first lasing in May 2017. Biological structure determination has already benefitted from the unique properties and capabilities of X-ray …

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

    04 Apr 2019 | BioXFEL Publications | Contributor(s): 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 Spence, Petra Fromme, Nadia Zatsepin, Robert F. Fischetti, Vadim Cherezov, Wei Liu

    http://dx.doi.org/10.1107/s205225251900263x Since the first successful serial crystallography (SX) experiment at a synchrotron radiation source, the popularity of this approach has continued to grow showing that third-generation synchrotrons can be viable alternatives to scarce X-ray free-electron …

  90. DENSS: Ab Initio Electron Density Maps from Biological SAXS Data

    20 Mar 2019 | Seminars | Contributor(s): Thomas Grant

    Small angle scattering is an experimental technique used to analyze the molecular structures of a wide variety of biological and non-biological samples in solution. In contrast to X-ray crystallography and cryo-electron microscopy, where 3D electron density maps are calculated, available methods …

  91. Protein and RNA dynamical fingerprinting

    04 Mar 2019 | BioXFEL Publications | Contributor(s): Katherine A. Niessen, Mengyang Xu, Deepu K. George, Michael C. Chen, Adrian R. Ferré-D’Amaré, Edward Snell, Vivian Cody, James Pace, Marius Schmidt, Andrea Markelz

    http://dx.doi.org/10.1038/s41467-019-08926-3 journal-article Niessen, K.A. et al., 2019. Protein and RNA dynamical fingerprinting. Nature Communications, 10(1). Available at: http://dx.doi.org/10.1038/s41467-019-08926-3. Katherine A. Niessen and Mengyang Xu and Deepu K. George and Michael C. …

  92. Evaluation of the performance of classification algorithms for XFEL single-particle imaging data

    01 Mar 2019 | BioXFEL Publications | Contributor(s): Yingchen Shi, Ke Yin, Xuecheng Tai, Hasan Demirci, Ahmad Hosseinizadeh, Brenda Hogue, Haoyuan Li, Abbas Ourmazd, Peter Schwander, Ivan A. Vartanyants, Chun Hong Yoon, Andrew Aquila, Haiguang Liu

    http://dx.doi.org/10.1107/s2052252519001854/cw5020sup1.pdf component Shi, Y. et al., 2019. Evaluation of the performance of classification algorithms for XFEL single-particle imaging data. Available at: http://dx.doi.org/10.1107/s2052252519001854/cw5020sup1.pdf. Yingchen Shi and Ke Yin and …

  93. Evaluation of the performance of classification algorithms for XFEL single-particle imaging data

    01 Mar 2019 | BioXFEL Publications | Contributor(s): Yingchen Shi, Ke Yin, Xuecheng Tai, Hasan Demirci, Ahmad Hosseinizadeh, Brenda Hogue, Haoyuan Li, Abbas Ourmazd, Peter Schwander, Ivan A. Vartanyants, Chun Hong Yoon, Andrew Aquila, Haiguang Liu

    http://dx.doi.org/10.1107/s2052252519001854 Using X-ray free-electron lasers (XFELs), it is possible to determine three-dimensional structures of nanoscale particles using single-particle imaging methods. Classification algorithms are needed to sort out the single-particle diffraction patterns from …

  94. Evaluation of the performance of classification algorithms for XFEL single-particle imaging data

    01 Mar 2019 | BioXFEL Publications | Contributor(s): Yingchen Shi, Ke Yin, Xuecheng Tai, Hasan Demirci, Ahmad Hosseinizadeh, Brenda Hogue, Haoyuan Li, Abbas Ourmazd, Peter Schwander, Ivan A. Vartanyants, Chun Hong Yoon, Andrew Aquila, Haiguang Liu

    http://dx.doi.org/10.1107/s2052252519001854/cw5020sup1.docx component Shi, Y. et al., 2019. Evaluation of the performance of classification algorithms for XFEL single-particle imaging data. Available at: http://dx.doi.org/10.1107/s2052252519001854/cw5020sup1.docx. Yingchen Shi and Ke Yin and …

  95. Shape transform phasing of edgy nanocrystals

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

    http://dx.doi.org/10.1107/s205327331900113x Diffraction patterns from small protein crystals illuminated by highly coherent X-rays often contain measurable interference signals between Bragg peaks. This coherent `shape transform' signal introduces enough additional information to allow the …

  96. Following Folding Pathways of Common Riboswitch Motifs with Time-Resolved Single-Molecule FRET

    15 Feb 2019 | BioXFEL Publications | Contributor(s): Alex Plumridge, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2018.11.1931 poster Plumridge, A. & Pollack, L., 2019. Following Folding Pathways of Common Riboswitch Motifs with Time-Resolved Single-Molecule FRET. Biophysical Journal, 116(3), p.355a. Available at: http://dx.doi.org/10.1016/j.bpj.2018.11.1931. Alex Plumridge …

  97. Time-Resolved Contrast Variation SAXS for Studying RNA-Protein Interactions

    15 Feb 2019 | BioXFEL Publications | Contributor(s): Suzette A. Pabit, Andrea Katz, George Douglas Calvey, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2018.11.1733 poster Pabit, S.A. et al., 2019. Time-Resolved Contrast Variation SAXS for Studying RNA-Protein Interactions. Biophysical Journal, 116(3), p.319a–320a. Available at: http://dx.doi.org/10.1016/j.bpj.2018.11.1733. Suzette A. Pabit and Andrea M. Katz …

  98. DNA Sequence and Histone Core Composition Control the Unwrapping of DNA from Nucleosome Core Particles

    15 Feb 2019 | BioXFEL Publications | Contributor(s): Alex Mauney, Joshua Tokuda, Yujie Chen, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2018.11.1179 poster 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. Available at: http://dx.doi.org/10.1016/j.bpj.2018.11.1179. Alex Mauney and …

  99. Separation Phenomena in Tailored Micro- and Nanofluidic Environments

    30 Jan 2019 | BioXFEL Publications | Contributor(s): Mukul Sonker, Daihyun Kim, Ana Egatz-Gomez, Alexandra Ros

    http://dx.doi.org/10.1146/annurev-anchem-061417-125758 journal-article Sonker, M. et al., 2019. Separation Phenomena in Tailored Micro- and Nanofluidic Environments. Annual Review of Analytical Chemistry, 12(1). Available at: http://dx.doi.org/10.1146/annurev-anchem-061417-125758. Mukul Sonker …

  100. Cysteine modification can gate non-equilibrium conformational dynamics during enzyme catalysis: Supplemental Information

    19 Jan 2019 | BioXFEL Publications | Contributor(s): 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 Thompson, James Fraser, Michael E. Wall, Henry Van Den Bedem, Mark A. Wilson

    http://dx.doi.org/10.1101/524751 Post-translational modification of cysteine residues can regulate protein function and is essential for catalysis by cysteine-dependent enzymes. Covalent modifications neutralize charge on the reactive cysteine thiolate anion and thus alter the active site …