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  1. Comprehensive characterization of gas dynamic virtual nozzles for x-ray free-electron laser experiments

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    26 Nov 2024 | BioXFEL Publications | Contributor(s): Konstantinos Karpos, Sahba Zaare, Dimitra Manatou, Roberto C. Alvarez, Vivek Krishnan, Clint Ottmar, Jodi Gilletti, Aian Pableo, Diandra Doppler, Adil Ansari, Reza Nazari, Alexandra Ros, Richard Kirian

    https://doi.org/10.1063/4.0000262 We introduce a hardware–software system for rapidly characterizing liquid microjets for x-ray diffraction experiments. An open-source python-based software package allows for programmatic and automated data collection and analysis. We show how jet speed, length, …

  2. Comprehensive Research on Past and Future Therapeutic Strategies Devoted to Treatment of Amyotrophic Lateral Sclerosis

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    22 Feb 2022 | BioXFEL Publications | Contributor(s): Belgin Sever, Halilibrahim Ciftci, Hasan Demirci, Hilal Sever, Firdevs Ocak, Burak Yulug, Hiroshi Tateishi, Takahisa Tateishi, Masami Otsuka, Mikako Fujita, Ayşe Nazlı Başak

    http://dx.doi.org/10.3390/ijms23052400 Amyotrophic lateral sclerosis (ALS) is a rapidly debilitating fatal neurodegenerative disorder, causing muscle atrophy and weakness, which leads to paralysis and eventual death. ALS has a multifaceted nature affected by many pathological mechanisms, including …

  3. Computational crystallization

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    11 Jan 2016 | BioXFEL Publications | Contributor(s): Irem Altan, Patrick Charbonneau, Edward Snell

    http://dx.doi.org/10.1016/j.abb.2016.01.004 Irem Altan and Patrick Charbonneau and Edward H. Snell Altan, I., Charbonneau, P. & Snell, E.H., 2016. Computational crystallization. Archives of Biochemistry and Biophysics. Available at: http://dx.doi.org/10.1016/j.abb.2016.01.004. journal-article

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

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    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 …

  5. Computational design of thermostabilizing point mutations for G protein-coupled receptors

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    21 Jun 2018 | BioXFEL Publications | Contributor(s): Petr Popov, Yao Peng, Ling Shen, Raymond C Stevens, Vadim Cherezov, Zhi-Jie Liu, Vsevolod Katritch

    http://dx.doi.org/10.7554/elife.34729 Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational approach to …

  6. Computing a Bayesian multi-state model of a protein structure from an X-ray diffraction pattern

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    08 Feb 2024 | BioXFEL Publications | Contributor(s): Matthew P. Hancock, James Fraser, Andrej Sali

    http://dx.doi.org/10.1016/j.bpj.2023.11.1276 journal-article Hancock, M. P., Fraser, J. S., & Sali, A. (2024). Computing a Bayesian multi-state model of a protein structure from an X-ray diffraction pattern. Biophysical Journal, 123(3), 200a–201a. https://doi.org/10.1016/j.bpj.2023.11.1276 …

  7. Concentration of Sindbis virus with optimized gradient insulator-based dielectrophoresis

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    08 Feb 2016 | BioXFEL Publications | Contributor(s): Jie Ding, Robert M Lawrence, Paul V. Jones, Brenda Hogue, Mark A. Hayes

    http://dx.doi.org/10.1039/c5an02430g Jie Ding and Robert M. Lawrence and Paul V. Jones and Brenda G. Hogue and Mark A. Hayes Ding, J. et al., 2016. Concentration of Sindbis virus with optimized gradient insulator-based dielectrophoresis. Analyst. Available at: http://dx.doi.org/10.1039/c5an02430g. …

  8. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II

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    30 Nov 2015 | BioXFEL Publications | Contributor(s): Raymond G Sierra, Cornelius Gati, Hartawan Laksmono, E Han Dao, Sheraz Gul, Franklin Fuller, Jan Kern, Ruchira Chatterjee, Mohamed Ibrahim, Aaron S Brewster, Iris Diane Young, Tara Michels-Clark, Andrew Aquila, Mengning Liang, Mark S. Hunter, Jason E Koglin, Sébastien Boutet, Elia A Junco, Brandon Hayes, Michael J Bogan, Christina Y Hampton, Elisabetta V Puglisi, Nicholas K Sauter, Claudiu A Stan, Athina Zouni, Junko Yano, Vittal K Yachandra, S Michael Soltis, Joseph D Puglisi, Hasan Demirci

    http://dx.doi.org/10.1038/nmeth.3667 Raymond G Sierra and Cornelius Gati and Hartawan Laksmono and E Han Dao and Sheraz Gul and Franklin Fuller and Jan Kern and Ruchira Chatterjee and Mohamed Ibrahim and Aaron S Brewster and Iris D Young and Tara Michels-Clark and Andrew Aquila and Mengning Liang …

  9. Confirmation of TTC8 as a disease gene for nonsyndromic autosomal recessive retinitis pigmentosa (RP51)

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    21 Jul 2015 | BioXFEL Publications | Contributor(s): S. Goyal, M. Jäger, P.N. Robinson, V. Vanita

    http://dx.doi.org/10.1111/cge.12644 S. Goyal and M. Jäger and P.N. Robinson and V. Vanita Goyal, S. et al., 2015. Confirmation of TTC8 as a disease gene for nonsyndromic autosomal recessive retinitis pigmentosa (RP51) . Clinical Genetics, 89(4), pp.454–460. Available at: …

  10. Conformational dynamics of adenylate kinase in crystals

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    21 Feb 2024 | BioXFEL Publications | Contributor(s): Junhyung Kim, Sojin Moon, Tod D. Romo, Yifei Yang, Euiyoung Bae, George Phillips

    http://dx.doi.org/10.1063/4.0000205 Adenylate kinase is a ubiquitous enzyme in living systems and undergoes dramatic conformational changes during its catalytic cycle. For these reasons, it is widely studied by genetic, biochemical, and biophysical methods, both experimental and theoretical. We …

  11. Conformational landscape of a virus by single-particle X-ray scattering

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    14 Aug 2017 | BioXFEL Publications | Contributor(s): Ahmad Hosseinizadeh, Ghoncheh Mashayekhi, Jeremy Copperman, Peter Schwander, Ali Dashti, Reyhaneh Sepehr, Russell Fung, Marius Schmidt, Chun Hong Yoon, Brenda Hogue, Garth J Williams, Andrew Aquila, Abbas Ourmazd

    http://dx.doi.org/10.1038/nmeth.4395 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Hosseinizadeh, A. et al., 2017. Conformational landscape of a virus by single-particle X-ray scattering. Nature Methods. Available at: http://dx.doi.org/10.1038/nmeth.4395. Ahmad Hosseinizadeh and …

  12. Conformational variation of proteins at room temperature is not dominated by radiation damage

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    21 Dec 2016 | BioXFEL Publications | Contributor(s): Silvia Russi, Ana González, Lillian R. Kenner, Daniel A. Keedy, James Fraser, Henry Van Den Bedem

    Protein crystallography data collection at synchrotrons is routinely carried out at cryogenic temperatures to mitigate radiation damage. Although damage still takes place at 100 K and below, the immobilization of free radicals increases the lifetime of the crystals by approximately 100-fold. …

  13. Conformations of an RNA Helix-Junction-Helix Construct revealed by SAXS Refinement of MD Simulations

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    22 Nov 2018 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Tongsik Lee, Ron Elber, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2018.11.020 journal-article Chen, Y.-L. et al., 2018. Conformations of an RNA Helix-Junction-Helix Construct revealed by SAXS Refinement of MD Simulations. Biophysical Journal. Available at: http://dx.doi.org/10.1016/j.bpj.2018.11.020. Yen-Lin Chen and Tongsik Lee …

  14. Conformations of macromolecules and their complexes from heterogeneous datasets

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    09 Jun 2014 | BioXFEL Publications | Contributor(s): P. Schwander, R. Fung, A. Ourmazd

    http://dx.doi.org/10.1098/rstb.2013.0567 P. Schwander and R. Fung and A. Ourmazd Schwander, P., Fung, R. & Ourmazd, A., 2014. Conformations of macromolecules and their complexes from heterogeneous datasets. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), …

  15. Connecting glutamine synthetase biophysics to the cellular environment

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    11 Feb 2022 | BioXFEL Publications | Contributor(s): Eric R. Greene, Erin Thompson, D. John Lee, Angelika Arada, Daphne Chen, James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.11.1035 journal-article Greene, E. R., Thompson, E., Lee, D. J., Arada, A., Chen, D., & Fraser, J. (2022). Connecting glutamine synthetase biophysics to the cellular environment. Biophysical Journal, 121(3), 348a. https://doi.org/10.1016/j.bpj.2021.11.1035 …

  16. 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, …

  17. Continuous Changes in Structure Mapped by Manifold Embedding of Single-Particle Data in Cryo-EM

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    14 Feb 2016 | BioXFEL Publications | Contributor(s): Joachim Frank, Abbas Ourmazd

    http://dx.doi.org/10.1016/j.ymeth.2016.02.007 Joachim Frank and Abbas Ourmazd Frank, J. & Ourmazd, A., 2016. Continuous Changes in Structure Mapped by Manifold Embedding of Single-Particle Data in Cryo-EM. Methods. Available at: http://dx.doi.org/10.1016/j.ymeth.2016.02.007. NSF-STC Biology with …

  18. Continuous diffraction of molecules and disordered molecular crystals

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    07 Jul 2017 | BioXFEL Publications | Contributor(s): Henry Chapman, Oleksandr M. Yefanov, Kartik Ayyer, Thomas A. White, Anton Barty, Andrew Morgan, Valerio Mariani, Dominik Oberthuer, Kanupriya Pande

    http://dx.doi.org/10.1107/s160057671700749x The intensities of far-field diffraction patterns of orientationally aligned molecules obey Wilson statistics, whether those molecules are in isolation (giving rise to a continuous diffraction pattern) or arranged in a crystal (giving rise to Bragg …

  19. Continuous organelle separation in an insulator‐based dielectrophoretic device

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    29 Dec 2021 | BioXFEL Publications | Contributor(s): Ricardo Ortiz, Domin Koh, Dai Hyun Kim, Mohammad Towshif Rabbani, Cesar Anguaya Velasquez, Mukul Sonker, Edgar A. Arriaga, Alexandra Ros

    http://dx.doi.org/10.1002/elps.202100326 journal-article Ortiz, R., Koh, D., Kim, D. H., Rabbani, M. T., Anguaya Velasquez, C., Sonker, M., Arriaga, E. A., & Ros, A. (2022). Continuous organelle separation in an insulator‐based dielectrophoretic device. ELECTROPHORESIS, 43(12), 1283–1296. …

  20. Continuous Separation of DNA Molecules by Size Using Insulator-Based Dielectrophoresis

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    12 Dec 2016 | BioXFEL Publications | Contributor(s): Paul V. Jones, Gabriel L. Salmon, Alexandra Ros

    journal-article http://dx.doi.org/10.1021/acs.analchem.6b03369 Jones, P.V., Salmon, G.L. & Ros, A., 2017. Continuous Separation of DNA Molecules by Size Using Insulator-Based Dielectrophoresis. Analytical Chemistry, 89(3), pp.1531–1539. Available at: …

  21. Contrast variation SAXS: Sample preparation protocols, experimental procedures, and data analysis

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    22 Sep 2022 | BioXFEL Publications | Contributor(s): Josue San Emeterio, Suzette A. Pabit, Lois Pollack

    http://dx.doi.org/10.1016/bs.mie.2022.08.007 book-chapter San Emeterio, J., Pabit, S. A., & Pollack, L. (2022). Contrast variation SAXS: Sample preparation protocols, experimental procedures, and data analysis. Methods in Enzymology, 41–83. https://doi.org/10.1016/bs.mie.2022.08.007 Josue San …

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

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    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 …

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

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    20 Jan 2022 | BioXFEL Publications | Contributor(s): Esra Ayan, Busra Yuksel, Ebru Destan, Fatma Betul Ertem, Gunseli Yildirim, Meryem Eren, 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, Alexander Batyuk, Valerio Mariani, Zhen Su, Frederic Poitevin, Chun Hong Yoon, Christopher Kupitz, Aina Cohen, Tzanko Doukov, Raymond G. Sierra, Çağdaş Dağ, Hasan Demirci

    http://dx.doi.org/10.1038/s42003-021-02903-7 AbstractMultimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile …

  24. Coordinating the impact of structural genomics on the human α-helical transmembrane proteome

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    05 Feb 2013 | BioXFEL Publications | Contributor(s): Ursula Pieper, Avner Schlessinger, Edda Kloppmann, Geoffrey A Chang, James J Chou, Mark E Dumont, Brian G Fox, Petra Fromme, Wayne A Hendrickson, Michael G Malkowski, Douglas C Rees, David L Stokes, Michael H B Stowell, Michael C Wiener, Burkhard Rost, Robert Stroud, Raymond C Stevens, Andrej Sali

    journal-article http://dx.doi.org/10.1038/nsmb.2508 Pieper, U. et al., 2013. Coordinating the impact of structural genomics on the human α-helical transmembrane proteome. Nature Structural & Molecular Biology, 20(2), pp.135–138. Available at: http://dx.doi.org/10.1038/nsmb.2508. Ursula Pieper …

  25. Copper Based Antibacterial Compounds: Potential Targeting Pathways and Current Drug Design Trends.

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    28 Apr 2023 | BioXFEL Publications | Contributor(s): Aixa M. Orta-Rivera, Yazmary Meléndez-Contés, Nataniel Rivera-Berríos, Adriana M. Gómez-Cardona, Andrés Ramos-Rodríguez, Claudia Cruz-Santiago, Christian González-Dumeng, Janangelis López, Jansteven Escribano, Jared J. Rivera-Otero, Josean Díaz-Rivera, Sebastián C. Díaz-Vélez, Zulemaría Feliciano-Delgado, Arthur Tinoco

    http://dx.doi.org/10.20944/preprints202304.1124.v1 Classical antibacterial drugs were designed to target specific bacterial properties distinct from host human cells to maximize potency and selectivity. These designs were quite effective as they could be easily derivatized to bear next generation …

  26. Coronavirus envelope (E) protein remains at the site of assembly

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    26 Feb 2015 | BioXFEL Publications | Contributor(s): Pavithra Venkatagopalan, Sasha M. Daskalova, Lisa A. Lopez, Kelly A. Dolezal, Brenda Hogue

    journal-article http://dx.doi.org/10.1016/j.virol.2015.02.005 Venkatagopalan, P. et al., 2015. Coronavirus envelope (E) protein remains at the site of assembly. Virology, 478, pp.75–85. Available at: http://dx.doi.org/10.1016/j.virol.2015.02.005. Pavithra Venkatagopalan and Sasha M. Daskalova …

  27. Coronavirus M Protein Trafficking in Epithelial Cells Utilizes a Myosin Vb Splice Variant and Rab10

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    10 Jan 2024 | BioXFEL Publications | Contributor(s): Lynne A. Lapierre, Joseph T. Roland, Elizabeth H. Manning, Catherine Caldwell, Honor L. Glenn, Pierre-Olivier Vidalain, Frederic Tangy, Brenda Hogue, C. A. M. De Haan, James R. Goldenring

    http://dx.doi.org/10.3390/cells13020126 The membrane (M) glycoprotein of coronaviruses (CoVs) serves as the nidus for virion assembly. Using a yeast two-hybrid screen, we identified the interaction of the cytosolic tail of Murine Hepatitis Virus (MHV-CoV) M protein with Myosin Vb (MYO5B), …

  28. 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: …

  29. Correlated motions in enzymes

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    03 May 2022 | BioXFEL Publications | Contributor(s): Nozomi Ando, Steve P. Meisburger, David Case

    http://dx.doi.org/10.1096/fasebj.2022.36.s1.0i154 Correlated motions in proteins arising from the collective movements of residues have long been proposed to be fundamentally important to key properties of proteins, from catalysis and allostery to evolvability. Recent breakthroughs in structural …

  30. Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

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    12 Oct 2017 | BioXFEL Publications | Contributor(s): Ruslan P. Kurta, Jeffrey J. Donatelli, Chun Hong Yoon, Peter Berntsen, Johan Bielecki, Benedikt J. Daurer, Hasan Demirci, Petra Fromme, Max Felix Hantke, Filipe R. N. C. Maia, Anna Munke, Carl Nettelblad, Kanupriya Pande, Hemanth K. N. Reddy, Jonas A. Sellberg, Raymond G. Sierra, Martin Svenda, Gijs Van Der Schot, Ivan A. Vartanyants, Garth J. Williams, P. Lourdu Xavier, Andrew Aquila, Peter H. Zwart, Adrian P. Mancuso

    http://dx.doi.org/10.1103/physrevlett.119.158102 journal-article Kurta, R.P. et al., 2017. Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses. Physical Review Letters, 119(15). Available at: http://dx.doi.org/10.1103/physrevlett.119.158102. Ruslan P. …

  31. Corrigendum: Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

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    30 Jun 2015 | BioXFEL Publications | Contributor(s): Johan Hattne, Nathaniel Echols, Rosalie Tran, Jan Kern, Richard J Gildea, Aaron S Brewster, Roberto Alonso-Mori, Carina Glöckner, Julia Hellmich, Hartawan Laksmono, Raymond G Sierra, Benedikt Lassalle-Kaiser, Alyssa Lampe, Guangye Han, Sheraz Gul, Dörte DiFiore, Despina Milathianaki, Alan R Fry, Alan Miahnahri, William E White, Donald W Schafer, M Marvin Seibert, Jason E Koglin, Dimosthenis Sokaras, Tsu-Chien Weng, Jonas Sellberg, Matthew J Latimer, Pieter Glatzel, Petrus H Zwart, Ralf W Grosse-Kunstleve, Michael J Bogan, Marc Messerschmidt, Garth J Williams, Sébastien Boutet, Johannes Messinger, Athina Zouni, Junko Yano, Uwe Bergmann, Vittal K Yachandra, Paul D Adams, Nicholas K Sauter

    http://dx.doi.org/10.1038/nmeth0715-692d Johan Hattne and Nathaniel Echols and Rosalie Tran and Jan Kern and Richard J Gildea and Aaron S Brewster and Roberto Alonso-Mori and Carina Glöckner and Julia Hellmich and Hartawan Laksmono and Raymond G Sierra and Benedikt Lassalle-Kaiser and Alyssa Lampe …

  32. Corrigendum: Diffraction data of core-shell nanoparticles from an X-ray free electron laser

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    24 Oct 2017 | BioXFEL Publications | Contributor(s): Xuanxuan Li, Chun-Ya Chiu, Hsiang-Ju Wang, Stephan Kassemeyer, Sabine Botha, Robert L Shoeman, Robert M Lawrence, Christopher Kupitz, Richard Kirian, Daniel James, Dingjie Wang, Garrett Charles Nelson, Marc Messerschmidt, Sébastien Boutet, Garth J Williams, Elisabeth Hartmann, Aliakbar Jafarpour, Lutz M Foucar, Anton Barty, Henry Chapman, Mengning Liang, Andreas Menzel, Fenglin Wang, Shibom Basu, Raimund Fromme, R.Bruce Doak, Petra Fromme, Uwe Weierstall, Michael H Huang, John Spence, Ilme Schlichting, Brenda Hogue, Haiguang Liu

    http://dx.doi.org/10.1038/sdata.2017.154 journal-article Li, X. et al., 2017. Corrigendum: Diffraction data of core-shell nanoparticles from an X-ray free electron laser. Scientific Data, 4, p.170154. Available at: http://dx.doi.org/10.1038/sdata.2017.154. Xuanxuan Li and Chun-Ya Chiu and …

  33. Corrigendum: Double-flow focused liquid injector for efficient serial femtosecond crystallography

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    21 Jun 2017 | BioXFEL Publications | Contributor(s): Dominik Oberthuer, Juraj Knoška, Max Oliver Wiedorn, Kenneth R. Beyerlein, David Bushnell, Elena G. Kovaleva, Michael Heymann, Lars Gumprecht, Richard Kirian, Anton Barty, Valerio Mariani, Aleksandra Tolstikova, Luigi Adriano, Salah Awel, Miriam Barthelmess, Katerina Dörner, P. Lourdu Xavier, Oleksandr Yefanov, Daniel R. James, Garrett Charles Nelson, Dingjie Wang, George Douglas Calvey, Yujie Chen, Andrea Schmidt, Michael Szczepek, Stefan Frielingsdorf, Oliver Lenz, Edward Snell, Philip J. Robinson, Božidar Šarler, Grega Belšak, Marjan Maček, Fabian Wilde, Andrew Aquila, Sébastien Boutet, Mengning Liang, Mark S. Hunter, Patrick Scheerer, John D. Lipscomb, Uwe Weierstall, Roger Kornberg, John Spence, Lois Pollack, Henry Chapman, Saša Bajt

    http://dx.doi.org/10.1038/srep46846 journal-article Oberthuer, D. et al., 2017. Corrigendum: Double-flow focused liquid injector for efficient serial femtosecond crystallography. Scientific Reports, 7, p.46846. Available at: http://dx.doi.org/10.1038/srep46846. Dominik Oberthuer and Juraj …

  34. 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: …

  35. Covariance mapping of two-photon double core hole states in C2H2and C2H6produced by an x-ray free electron laser

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    02 Jul 2015 | BioXFEL Publications | Contributor(s): M Mucke, V Zhaunerchyk, L J Frasinski, R J Squibb, M Siano, J H D Eland, P Linusson, P Salén, P V D Meulen, R D Thomas, M Larsson, L Foucar, J Ullrich, K Motomura, S Mondal, K Ueda, T Osipov, L Fang, B F Murphy, N Berrah, C Bostedt, J D Bozek, S Schorb, M Messerschmidt, J M Glownia, J P Cryan, R N Coffee, O Takahashi, S Wada, M N Piancastelli, R Richter, K C Prince, R Feifel

    http://dx.doi.org/10.1088/1367-2630/17/7/073002 M Mucke and V Zhaunerchyk and L J Frasinski and R J Squibb and M Siano and J H D Eland and P Linusson and P Salén and P v d Meulen and R D Thomas and M Larsson and L Foucar and J Ullrich and K Motomura and S Mondal and K Ueda and T Osipov and L Fang …

  36. Critical assessment of the emission spectra of various photosystem II core complexes

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    03 Apr 2015 | BioXFEL Publications | Contributor(s): Jinhai Chen, Adam Kell, Khem Acharya, Christopher Kupitz, Petra Fromme, Ryszard Jankowiak

    http://dx.doi.org/10.1007/s11120-015-0128-7 Jinhai Chen and Adam Kell and Khem Acharya and Christopher Kupitz and Petra Fromme and Ryszard Jankowiak Chen, J. et al., 2015. Critical assessment of the emission spectra of various photosystem II core complexes. Photosynthesis Research, 124(3), …

  37. Critical Role of Water Molecules in Proton Translocation by the Membrane-Bound Transhydrogenase

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    22 Jun 2017 | BioXFEL Publications | Contributor(s): Pius S. Padayatti, Josephine H. Leung, Paween Mahinthichaichan, Emad Tajkhorshid, Andrii Ishchenko, Vadim Cherezov, S. Michael Soltis, J. Baz Jackson, C. David Stout, Robert B. Gennis, Qinghai Zhang

    http://dx.doi.org/10.1016/j.str.2017.05.022 journal-article Padayatti, P.S. et al., 2017. Critical Role of Water Molecules in Proton Translocation by the Membrane-Bound Transhydrogenase. Structure, 25(7), pp.1111–1119.e3. Available at: http://dx.doi.org/10.1016/j.str.2017.05.022. Pius S. …

  38. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

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    04 Feb 2021 | BioXFEL Publications | Contributor(s): Catherine L. Lawson, Andriy Kryshtafovych, Paul D. Adams, Pavel V. Afonine, Matthew L. Baker, Benjamin A. Barad, Paul Bond, Tom Burnley, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kevin Cowtan, Ken A. Dill, Frank DiMaio, Daniel P. Farrell, James Fraser, Mark A. Herzik, Soon Wen Hoh, Jie Hou, Li-Wei Hung, Maxim Igaev, Agnel P. Joseph, Daisuke Kihara, Dilip Kumar, Sumit Mittal, Bohdan Monastyrskyy, Mateusz Olek, Colin M. Palmer, Ardan Patwardhan, Alberto Perez, Jonas Pfab, Grigore D. Pintilie, Jane S. Richardson, Peter B. Rosenthal, Daipayan Sarkar, Luisa U. Schäfer, Michael F. Schmid, Gunnar F. Schröder, Mrinal Shekhar, Dong Si, Abishek Singharoy, Genki Terashi, Thomas C. Terwilliger, Andrea Vaiana, Liguo Wang, Zhe Wang, Stephanie A. Wankowicz, Christopher J. Williams, Martyn Winn, Tianqi Wu, Xiaodi Yu, Kaiming Zhang, Helen M. Berman, Wah Chiu

    http://dx.doi.org/10.1038/s41592-020-01051-w AbstractThis paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate …

  39. CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

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    22 Sep 2021 | BioXFEL Publications | Contributor(s): Mrinal Shekhar, Genki Terashi, Chitrak Gupta, Daipayan Sarkar, Gaspard Debussche, Nicholas J. Sisco, Jonathan Nguyen, Arup Mondal, John Vant, Petra Fromme, Wade D. Van Horn, Emad Tajkhorshid, Daisuke Kihara, Ken Dill, Alberto Perez, Abhishek Singharoy

    http://dx.doi.org/10.1016/j.matt.2021.09.004 journal-article Shekhar, M., Terashi, G., Gupta, C., Sarkar, D., Debussche, G., Sisco, N. J., Nguyen, J., Mondal, A., Vant, J., Fromme, P., Van Horn, W. D., Tajkhorshid, E., Kihara, D., Dill, K., Perez, A., & Singharoy, A. (2021). CryoFold: Determining …

  40. Cryptic binding sites become accessible through surface reconstruction of the type I collagen fibril

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    05 Nov 2018 | BioXFEL Publications | Contributor(s): Jie Zhu, Cody L. Hoop, David Case, Jean Baum

    http://dx.doi.org/10.1038/s41598-018-34616-z journal-article Zhu, J. et al., 2018. Cryptic binding sites become accessible through surface reconstruction of the type I collagen fibril. Scientific Reports, 8(1). Available at: http://dx.doi.org/10.1038/s41598-018-34616-z. Jie Zhu and Cody L. Hoop …

  41. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites

    0.0 out of 5 stars 

    05 Feb 2016 | BioXFEL Publications | Contributor(s): Peter Cimermancic, Patrick Weinkam, T. Justin Rettenmaier, Leon Bichmann, Daniel A. Keedy, Rahel Woldeyes, Dina Schneidman-Duhovny, Omar N. Demerdash, Julie C. Mitchell, James A. Wells, James Fraser, Andrej Sali

    http://dx.doi.org/10.1016/j.jmb.2016.01.029 Peter Cimermancic and Patrick Weinkam and T. Justin Rettenmaier and Leon Bichmann and Daniel A. Keedy and Rahel A. Woldeyes and Dina Schneidman-Duhovny and Omar N. Demerdash and Julie C. Mitchell and James A. Wells and James S. Fraser and Andrej Sali …

  42. Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR

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    29 May 2014 | BioXFEL Publications | Contributor(s): Daniel A. Keedy, Henry Van den Bedem, David A. Sivak, Gregory A. Petsko, Dagmar Ringe, Mark A. Wilson, James S. Fraser

    http://dx.doi.org/10.1016/j.str.2014.04.016 Daniel A. Keedy and Henry van den Bedem and David A. Sivak and Gregory A. Petsko and Dagmar Ringe and Mark A. Wilson and James S. Fraser Keedy, D.A. et al., 2014. Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis …

  43. Crystal Structure of 4-Hydroxybutyryl-CoA Synthetase (ADP-forming): A Key Enzyme in the Thaumarchaeal Hydroxypropionate/Hydroxybutyrate cycle

    0.0 out of 5 stars 

    31 Jul 2023 | BioXFEL Publications | Contributor(s): Hasan Demirci, J Johnson, Bradley Tolar, Bilge Tosun, Yasuo Yoshikuni, Christopher Francis, Soichi Wakatsuki

    http://dx.doi.org/10.21203/rs.3.rs-3173078/v1 Abstract The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway. The Nitrosopumilus maritimus 4-hydroxybutyryl-CoA …

  44. Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand

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    17 May 2017 | BioXFEL Publications | Contributor(s): Xianjun Zhang, Fei Zhao, Yiran Wu, Jun Yang, Gye Won Han, Suwen Zhao, Andrii Ishchenko, Lintao Ye, Xi Lin, Kang Ding, Venkatasubramanian Dharmarajan, Patrick R. Griffin, Cornelius Gati, Garrett Charles Nelson, Mark S. Hunter, Michael A. Hanson, Vadim Cherezov, Raymond C. Stevens, Wenfu Tan, Houchao Tao, Fei Xu

    http://dx.doi.org/10.1038/ncomms15383 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Zhang, X. et al., 2017. Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand. Nature Communications, 8, p.15383. Available at: …

  45. Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature

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    11 Jul 2017 | BioXFEL Publications | Contributor(s): Izumi Ishigami, Nadia Zatsepin, Masahide Hikita, Chelsie E Conrad, Garrett Charles Nelson, Jesse David Coe, Shibom Basu, Thomas D. Grant, Matthew H. Seaberg, Raymond G. Sierra, Mark S. Hunter, Petra Fromme, Raimund Fromme, Syun-Ru Yeh, Denis L. Rousseau

    http://dx.doi.org/10.1073/pnas.1705628114 Cytochromecoxidase (CcO), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton …

  46. Crystal Structure of Human Protein N-Terminal Glutamine Amidohydrolase, an Initial Component of the N-End Rule Pathway

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    30 Oct 2014 | BioXFEL Publications | Contributor(s): Mi Seul Park, Eduard Bitto, Kyung Rok Kim, Craig A. Bingman, Mitchell Miller, Hyun-Jung Kim, Byung Woo Han, George Phillips

    http://dx.doi.org/10.1371/journal.pone.0111142 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Park, M.S. et al., 2014. Crystal Structure of Human Protein N-Terminal Glutamine Amidohydrolase, an Initial Component of the N-End Rule Pathway T. J. Boggon, ed. PLoS ONE, 9(10), …

  47. Crystal structure of misoprostol bound to the labor inducer prostaglandin E2 receptor

    0.0 out of 5 stars 

    29 Nov 2018 | BioXFEL Publications | Contributor(s): Martin Audet, Kate L. White, Billy Breton, Barbara Zarzycka, Gye Won Han, Yan Lu, Cornelius Gati, Alexander Batyuk, Petr Popov, Jeffrey Velasquez, David Manahan, Hao Hu, Uwe Weierstall, Wei Liu, Wenqing Shui, Vsevolod Katritch, Vadim Cherezov, Michael A. Hanson, Raymond C. Stevens

    http://dx.doi.org/10.1038/s41589-018-0160-y journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Audet, M. et al., 2018. Crystal structure of misoprostol bound to the labor inducer prostaglandin E2 receptor. Nature Chemical Biology, 15(1), pp.11–17. Available at: …

  48. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

    0.0 out of 5 stars 

    22 Jul 2015 | BioXFEL Publications | Contributor(s): Yanyong Kang, X. Edward Zhou, Xiang Gao, Yuanzheng He, Wei Liu, Andrii Ishchenko, Anton Barty, Thomas A. White, Oleksandr Yefanov, Gye Won Han, Qingping Xu, Parker W. De Waal, Jiyuan Ke, M. H. Eileen Tan, Chenghai Zhang, Arne Moeller, Graham M. West, Bruce D. Pascal, Ned Van Eps, Lydia N. Caro, Sergey A. Vishnivetskiy, Regina J. Lee, Kelly M. Suino-Powell, Xin Gu, Kuntal Pal, Jinming Ma, Xiaoyong Zhi, Sébastien Boutet, Garth J. Williams, Marc Messerschmidt, Cornelius Gati, Nadia Zatsepin, Dingjie Wang, Daniel James, Shibom Basu, Shatabdi Roy-Chowdhury, Chelsie E Conrad, Jesse David Coe, Haiguang Liu, Stella Lisova, Christopher Kupitz, Ingo Grotjohann, Raimund Fromme, Yi Jiang, Minjia Tan, Huaiyu Yang, Jun Li, Meitian Wang, Zhong Zheng, Dianfan Li, Nicole Howe, Yingming Zhao, Jörg Standfuss, Kay Diederichs, Yuhui Dong, Clinton S. Potter, Bridget Carragher, Martin Caffrey, Hualiang Jiang, Henry Chapman, John Spence, Petra Fromme, Uwe Weierstall, Oliver P. Ernst, Vsevolod Katritch, Vsevolod V. Gurevich, Patrick R. Griffin, Wayne L. Hubbell, Raymond C. Stevens, Vadim Cherezov, Karsten Melcher, H. Eric Xu

    http://dx.doi.org/10.1038/nature14656 Yanyong Kang and X. Edward Zhou and Xiang Gao and Yuanzheng He and Wei Liu and Andrii Ishchenko and Anton Barty and Thomas A. White and Oleksandr Yefanov and Gye Won Han and Qingping Xu and Parker W. de Waal and Jiyuan Ke and M. H. Eileen Tan and Chenghai Zhang …

  49. Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027

    0.0 out of 5 stars 

    13 Jul 2016 | BioXFEL Publications | Contributor(s): Tingting Huang, Chin-Yuan Chang, Jeremy R Lohman, Jeffrey D Rudolf, Youngchang Kim, Changsoo Chang, Dong Yang, Ming Ma, Xiaohui Yan, Ivana Crnovcic, Lance Bigelow, Shonda Clancy, Craig A Bingman, Ragothaman M Yennamalli, Gyorgy Babnigg, Andrzej Joachimiak, George Phillips, Ben Shen

    http://dx.doi.org/10.1038/ja.2016.88 Tingting Huang and Chin-Yuan Chang and Jeremy R Lohman and Jeffrey D Rudolf and Youngchang Kim and Changsoo Chang and Dong Yang and Ming Ma and Xiaohui Yan and Ivana Crnovcic and Lance Bigelow and Shonda Clancy and Craig A Bingman and Ragothaman M Yennamalli and …

  50. Crystal structure of SsfS6, the putativeC-glycosyltransferase involved in SF2575 biosynthesis

    0.0 out of 5 stars 

    23 Mar 2013 | BioXFEL Publications | Contributor(s): Fengbin Wang, Maoquan Zhou, Shanteri Singh, Ragothaman M. Yennamalli, Craig A. Bingman, Jon S. Thorson, George Phillips

    http://dx.doi.org/10.1002/prot.24289 journal-article Wang, F. et al., 2013. Crystal structure of SsfS6, the putativeC-glycosyltransferase involved in SF2575 biosynthesis. Proteins: Structure, Function, and Bioinformatics, 81(7), pp.1277–1282. Available at: http://dx.doi.org/10.1002/prot.24289. …

  51. Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus

    0.0 out of 5 stars 

    21 Oct 2024 | BioXFEL Publications | Contributor(s): Jerome Johnson, Bradley B. Tolar, Bilge Tosun, Yasuo Yoshikuni, Christopher A. Francis, Soichi Wakatsuki, Hasan Demirci

    https://doi.org/10.1038/s42003-024-06432-x AbstractThe 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway. The Nitrosopumilus maritimus 4-hydroxybutyryl-CoA synthetase …

  52. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine

    0.0 out of 5 stars 

    23 Jan 2015 | BioXFEL Publications | Contributor(s): L. Qin, I. Kufareva, L. G. Holden, C. Wang, Y. Zheng, C. Zhao, G. Fenalti, H. Wu, G. W. Han, V. Cherezov, R. Abagyan, R. C. Stevens, T. M. Handel

    http://dx.doi.org/10.1126/science.1261064 L. Qin and I. Kufareva and L. G. Holden and C. Wang and Y. Zheng and C. Zhao and G. Fenalti and H. Wu and G. W. Han and V. Cherezov and R. Abagyan and R. C. Stevens and T. M. Handel Qin, L. et al., 2015. Crystal structure of the chemokine receptor CXCR4 in …

  53. Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from arabidopsis thaliana in complex with AMP

    0.0 out of 5 stars 

    28 Apr 2015 | BioXFEL Publications | Contributor(s): Do Jin Kim, Eduard Bitto, Craig A. Bingman, Hyun-Jung Kim, Byung Woo Han, George Phillips

    http://dx.doi.org/10.1002/prot.24821 Do Jin Kim and Eduard Bitto and Craig A. Bingman and Hyun-Jung Kim and Byung Woo Han and George N. Phillips Kim, D.J. et al., 2015. Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from arabidopsis thaliana in …

  54. Crystal structure of the protein fromArabidopsis thalianagene At5g06450, a putative DnaQ-like exonuclease domain-containing protein with homohexameric assembly

    0.0 out of 5 stars 

    24 Apr 2013 | BioXFEL Publications | Contributor(s): David W. Smith, Mi Ra Han, Joon Sung Park, Kyung Rok Kim, Taeho Yeom, Ji Yeon Lee, Do Jin Kim, Craig A. Bingman, Hyun-Jung Kim, Kyubong Jo, Byung Woo Han, George Phillips

    http://dx.doi.org/10.1002/prot.24315 journal-article Smith, D.W. et al., 2013. Crystal structure of the protein fromArabidopsis thalianagene At5g06450, a putative DnaQ-like exonuclease domain-containing protein with homohexameric assembly. Proteins: Structure, Function, and Bioinformatics, 81(9), …

  55. Crystal Structure of the Zorbamycin-Binding Protein ZbmA, the Primary Self-Resistance Element in Streptomyces flavoviridis ATCC21892

    0.0 out of 5 stars 

    29 Oct 2015 | BioXFEL Publications | Contributor(s): Jeffrey D. Rudolf, Lance Bigelow, Changsoo Chang, Marianne E. Cuff, Jeremy R. Lohman, Chin-Yuan Chang, Ming Ma, Dong Yang, Shonda Clancy, Gyorgy Babnigg, Andrzej Joachimiak, George Phillips, Ben Shen

    http://dx.doi.org/10.1021/acs.biochem.5b01008 Jeffrey D. Rudolf and Lance Bigelow and Changsoo Chang and Marianne E. Cuff and Jeremy R. Lohman and Chin-Yuan Chang and Ming Ma and Dong Yang and Shonda Clancy and Gyorgy Babnigg and Andrzej Joachimiak and George N. Phillips and Ben Shen Rudolf, J.D. …

  56. 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 …

  57. Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 inStreptomyces globisporus

    0.0 out of 5 stars 

    25 Aug 2016 | BioXFEL Publications | Contributor(s): Chin-Yuan Chang, Jeremy R. Lohman, Hongnan Cao, Kemin Tan, Jeffrey D. Rudolf, Ming Ma, Weijun Xu, Craig A. Bingman, Ragothaman M. Yennamalli, Lance Bigelow, Gyorgy Babnigg, Xiaohui Yan, Andrzej Joachimiak, George Phillips, Ben Shen

    http://dx.doi.org/10.1021/acs.biochem.6b00713 Chin-Yuan Chang and Jeremy R. Lohman and Hongnan Cao and Kemin Tan and Jeffrey D. Rudolf and Ming Ma and Weijun Xu and Craig A. Bingman and Ragothaman M. Yennamalli and Lance Bigelow and Gyorgy Babnigg and Xiaohui Yan and Andrzej Joachimiak and George …

  58. Crystallization of a self-assembled three-dimensional DNA nanostructure

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    30 Jan 2013 | BioXFEL Publications | Contributor(s): Kimberly N. Rendek, Raimund Fromme, Ingo Grotjohann, Petra Fromme

    journal-article http://dx.doi.org/10.1107/s1744309112052128 Rendek, K.N. et al., 2013. Crystallization of a self-assembled three-dimensional DNA nanostructure. Acta Crystallographica Section F Structural Biology and Crystallization Communications, 69(2), pp.141–146. Available at: …

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

    0.0 out of 5 stars 

    01 Oct 2020 | BioXFEL Publications | Contributor(s): Megan Shelby, Deepshika Gilbile, Thomas Grant, William Bauer, Brent W. Segelke, Wei He, Angela Evans, Natalia Crespo, Pontus Fischer, Tim Pakendorf, Vincent Hennicke, Mark S. Hunter, Alex Batyuk, Miriam Barthelmess, Alke Meents, Tonya 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 …

  60. Crystallization of Membrane Proteins: An Overview

    0.0 out of 5 stars 

    01 Jun 2017 | BioXFEL Publications | Contributor(s): Andrii Ishchenko, Enrique E. Abola, Vadim Cherezov

    http://dx.doi.org/10.1007/978-1-4939-7000-1_5 book-chapter Ishchenko, A., Abola, E.E. & Cherezov, V., 2017. Crystallization of Membrane Proteins: An Overview. Protein Crystallography, pp.117–141. Available at: http://dx.doi.org/10.1007/978-1-4939-7000-1_5. Andrii Ishchenko and Enrique E. Abola …

  61. Crystallization of Photosystem II for Time-Resolved Structural Studies Using an X-ray Free Electron Laser

    0.0 out of 5 stars 

    18 Apr 2015 | BioXFEL Publications | Contributor(s): Jesse David Coe, Christopher Kupitz, Shibom Basu, Chelsie E Conrad, Shatabdi Roy-Chowdhury, Raimund Fromme, Petra Fromme

    http://dx.doi.org/10.1016/bs.mie.2015.01.011 Jesse Coe and Christopher Kupitz and Shibom Basu and Chelsie E. Conrad and Shatabdi Roy-Chowdhury and Raimund Fromme and Petra Fromme Coe, J. et al., 2015. Crystallization of Photosystem II for Time-Resolved Structural Studies Using an X-ray Free …

  62. Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel

    0.0 out of 5 stars 

    05 Nov 2013 | BioXFEL Publications | Contributor(s): Bahige G. Abdallah, Christopher Kupitz, Petra Fromme, Alexandra Ros

    http://dx.doi.org/10.1021/nn402515q Bahige G. Abdallah and Christopher Kupitz and Petra Fromme and Alexandra Ros Abdallah, B.G. et al., 2013. Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel. ACS Nano, 7(12), pp.10534–10543. Available at: …

  63. Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel

    0.0 out of 5 stars 

    09 Oct 2015 | Teaching Materials

    Traditional macroscale protein crystallization is accomplished nontrivially by exploring a range of protein concentrations and buffers in solution until a suitable combination is attained. This methodology is time-consuming and resource-intensive, hindering protein structure determination. Even …

  64. Crystallization screening: the influence of history on current practice

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    26 Jun 2014 | BioXFEL Publications | Contributor(s): Joseph Luft, Janet Newman, Edward Snell

    While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed. …

  65. Crystallographic data processing for free-electron laser sources

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    14 Jun 2013 | BioXFEL Publications | Contributor(s): Thomas A. White, Anton Barty, Francesco Stellato, James Holton, Richard Kirian, Nadia Zatsepin, Henry Chapman

    A processing pipeline for diffraction data acquired using the `serial crystallography' methodology with a free-electron laser source is described with reference to the crystallographic analysis suiteCrystFELand the pre-processing programCheetah. A detailed analysis of the nature and impact of …

  66. Crystallographic Methods - Crystallographic Symmetry - Part I

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    20 Oct 2014 | Teaching Materials | Contributor(s): Edward Snell

    Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

  67. Crystallographic Methods - Crystallographic Symmetry - Part II

    0.0 out of 5 stars 

    20 Oct 2014 | Teaching Materials

    Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

  68. Crystallographic Methods - Crystallographic Symmetry - Part III

    0.0 out of 5 stars 

    22 Oct 2014 | Teaching Materials | Contributor(s): Edward Snell

    Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

  69. Crystallographic Methods - Geometrical Crystallography - Part I

    0.0 out of 5 stars 

    19 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing Geometrical crystallography     Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation and the Ewald construction; Reciprocal space and the reciprocal lattice Rupp, ch. 5

  70. Crystallographic Methods - Geometrical Crystallography - Part II

    0.0 out of 5 stars 

    04 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing Geometrical crystallography     Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation and the Ewald construction; Reciprocal space and the reciprocal lattice Rupp, ch. 5

  71. Crystallographic Methods - Introduction and Overview

    0.0 out of 5 stars 

    25 Aug 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing Introduction     Protein structural elements: 1° aa sequence,  2° α-helix, β strand, β sheet, loop, 3° domain fold,  4° domain assembly; Overview of biomacromolecular crystallography

  72. Crystallographic Methods - X-ray Diffraction Physics - Part I

    0.0 out of 5 stars 

    08 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  73. Crystallographic Methods - X-ray Diffraction Physics - Part II

    0.0 out of 5 stars 

    11 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  74. Crystallographic Methods - X-ray Diffraction Physics - Part III

    0.0 out of 5 stars 

    15 Sep 2014 | Teaching Materials

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  75. Crystallographic Methods - X-ray Diffraction Physics - Part IV

    0.0 out of 5 stars 

    18 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  76. Crystallographic Methods - X-ray Diffraction Physics - Part IX

    0.0 out of 5 stars 

    03 Oct 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  77. Crystallographic Methods - X-ray Diffraction Physics - Part V

    0.0 out of 5 stars 

    22 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  78. Crystallographic Methods - X-ray Diffraction Physics - Part VI

    0.0 out of 5 stars 

    25 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  79. Crystallographic Methods - X-ray Diffraction Physics - Part VII

    0.0 out of 5 stars 

    28 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  80. Crystallographic Methods - X-ray Diffraction Physics - Part VIII

    0.0 out of 5 stars 

    01 Oct 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  81. Crystallographic Methods of Structural Biology

    0.0 out of 5 stars 

    18 Sep 2016 | Courses | Contributor(s): Robert H Blessing, Edward Snell

    The goal of the course is that students acquire sufficient knowledge and understanding of the basic principles of biomolecular crystal structure analysis that they will be able to comfortably, and with interest and insight, read and comprehend the articles in Volume F of the International Tables …

  82. Crystallography with an XFEL

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    21 Jul 2015 | Seminars | Contributor(s): Marc Messerschmidt

    Dr. Marc Messerschmidt discusses the design and operation of the X-ray free electron laser at the LCLS. Be sure to grab the attached MP3 audio file to follow along. Topics discussed include: - XFEL fundamentals - LCLS machine capabilities and energy spectrum - Beamlines and instrumentation for …

  83. Crystallography: Sources of inspiration

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    28 Jan 2014 | BioXFEL Publications | Contributor(s): Sean McSweeney, Petra Fromme

    http://dx.doi.org/10.1038/505620a Sean McSweeney and Petra Fromme McSweeney, S. & Fromme, P., 2014. Crystallography: Sources of inspiration. Nature, 505(7485), pp.620–621. Available at: http://dx.doi.org/10.1038/505620a. journal-article

  84. CrystFEL Tutorial

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    03 Sep 2014 | Teaching Materials

    Tom White (CFEL)

  85. Curiosity: a tool for exploring density features in crystallographic and cryoEM maps

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    11 Feb 2022 | BioXFEL Publications | Contributor(s): Iris Diane Young, James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.11.2781 journal-article Young, I. D., & Fraser, J. S. (2022). Curiosity: a tool for exploring density features in crystallographic and cryoEM maps. Biophysical Journal, 121(3), 528a. https://doi.org/10.1016/j.bpj.2021.11.2781 Iris D. Young and James S. Fraser

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

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    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 …

  87. Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization

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    30 Jan 2017 | BioXFEL Publications | Contributor(s): Madison B. Adolph, Anjuman Ara, Yuqing Feng, Cristina J. Wittkopp, Michael Emerman, James Fraser, Linda Chelico

    journal-article http://dx.doi.org/10.1093/nar/gkx066 Adolph, M.B. et al., 2017. Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization. Nucleic Acids Research, 45(6), pp.3378–3394. Available at: http://dx.doi.org/10.1093/nar/gkx066. …

  88. Damage threshold of amorphous carbon mirror for 177eV FEL radiation

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    10 Nov 2010 | BioXFEL Publications | Contributor(s): Sh. Dastjani Farahani, Jaromir Chalupsky, T. Burian, Henry Chapman, A.J. Gleeson, V. Hajkoya, L. Juha, M. Jurek, Dorota Klinger, Harald Sinn, R. Sobierajski, M. Störmer, K. Tiedtke, S. Toleikis, Thomas Tschentscher, H. Wabnitz, Jerome Gaudin

    http://dx.doi.org/10.1016/j.nima.2010.10.133 journal-article Dastjani Farahani, S. et al., 2011. Damage threshold of amorphous carbon mirror for 177eV FEL radiation. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, …

  89. Dan Salah Tawfik (1955‐2021)—A giant of protein evolution

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    28 May 2021 | BioXFEL Publications | Contributor(s): Mikael H Elias, James Fraser, Shina Caroline Lynn Kamerlin, Wayne M Patrick, Colin J Jackson

    http://dx.doi.org/10.15252/embr.202153256 journal-article Elias, M.H. et al., 2021. Dan Salah Tawfik (1955‐2021)—A giant of protein evolution. EMBO reports. Available at: http://dx.doi.org/10.15252/embr.202153256. Mikael H Elias and James S Fraser and Shina Caroline Lynn Kamerlin and Wayne M …

  90. Data Analysis and Sample Delivery

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    29 Aug 2014 | Teaching Materials

    John Spence (ASU/LBNL) How XFEL MX differs from MX and why we do it.

  91. Data Analysis Scripts

    5.0 out of 5 stars 

    21 Jul 2015 | Downloads

    A repository of useful scripts for the analysis of XFEL data. 

  92. Data assimilation in operator algebras

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    17 Feb 2023 | BioXFEL Publications | Contributor(s): David Freeman, Dimitrios Giannakis, Brian Mintz, Abbas Ourmazd, Joanna Slawinska

    http://dx.doi.org/10.1073/pnas.2211115120 We develop an algebraic framework for sequential data assimilation of partially observed dynamical systems. In this framework, Bayesian data assimilation is embedded in a nonabelian operator algebra, which provides a representation of observables by …

  93. Data publication with the structural biology data grid supports live analysis

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    07 Mar 2016 | BioXFEL Publications | Contributor(s): Peter A. Meyer, Stephanie Socias, Jason Key, Elizabeth Ransey, Emily C. Tjon, Alejandro Buschiazzo, Ming Lei, Chris Botka, James Withrow, David Neau, Kanagalaghatta Rajashankar, Karen S. Anderson, Richard H. Baxter, Stephen C. Blacklow, Titus J. Boggon, Alexandre M. J. J. Bonvin, Dominika Borek, Tom J. Brett, Amedeo Caflisch, Chung-I Chang, Walter J. Chazin, Kevin D. Corbett, Michael S. Cosgrove, Sean Crosson, Sirano Dhe-Paganon, Enrico Di Cera, Catherine L. Drennan, Michael J. Eck, Brandt F. Eichman, Qing R. Fan, Adrian R. Ferré-D'Amaré, J. Christopher Fromme, K. Christopher Garcia, Rachelle Gaudet, Peng Gong, Stephen C. Harrison, Ekaterina E. Heldwein, Zongchao Jia, Robert J. Keenan, Andrew C. Kruse, Marc Kvansakul, Jason S. McLellan, Yorgo Modis, Yunsun Nam, Zbyszek Otwinowski, Emil F. Pai, Pedro José Barbosa Pereira, Carlo Petosa, C. S. Raman, Tom A. Rapoport, Antonina Roll-Mecak, Michael K. Rosen, Gabby Rudenko, Joseph Schlessinger, Thomas U. Schwartz, Yousif Shamoo, Holger Sondermann, Yizhi J. Tao, Niraj H. Tolia, Oleg V. Tsodikov, Kenneth D. Westover, Hao Wu, Ian Foster, James Fraser, Filipe R. N C. Maia, Tamir Gonen, Tom Kirchhausen, Kay Diederichs, Mercè Crosas, Piotr Sliz

    journal-article http://dx.doi.org/10.1038/ncomms10882 Meyer, P.A. et al., 2016. Data publication with the structural biology data grid supports live analysis. Nature Communications, 7, p.10882. Available at: http://dx.doi.org/10.1038/ncomms10882. Peter A. Meyer and Stephanie Socias and Jason Key …

  94. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure

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    27 Sep 2016 | BioXFEL Publications | Contributor(s): Jacques-Philippe Colletier, Michael R. Sawaya, Mari Gingery, Jose A. Rodriguez, Duilio Cascio, Aaron S. Brewster, Tara Michels-Clark, Robert H. Hice, Nicolas Coquelle, Sébastien Boutet, Garth J. Williams, Marc Messerschmidt, Daniel P. DePonte, Raymond G. Sierra, Hartawan Laksmono, Jason E. Koglin, Mark S. Hunter, Hyun-Woo Park, Monarin Uervirojnangkoorn, Dennis K. Bideshi, Axel T. Brunger, Brian A. Federici, Nicholas K. Sauter, David S. Eisenberg

    http://dx.doi.org/10.1038/nature19825 Jacques-Philippe Colletier and Michael R. Sawaya and Mari Gingery and Jose A. Rodriguez and Duilio Cascio and Aaron S. Brewster and Tara Michels-Clark and Robert H. Hice and Nicolas Coquelle and Sébastien Boutet and Garth J. Williams and Marc Messerschmidt and …

  95. De novo protein crystal structure determination from X-ray free-electron laser data

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    22 Nov 2013 | BioXFEL Publications | Contributor(s): Thomas R. M. Barends, Lutz Foucar, Sabine Botha, R. Bruce Doak, Robert L. Shoeman, Karol Nass, Jason E. Koglin, Garth J. Williams, Sébastien Boutet, Marc Messerschmidt, Ilme Schlichting

    http://dx.doi.org/10.1038/nature12773 journal-article Barends, T.R.M. et al., 2013. De novo protein crystal structure determination from X-ray free-electron laser data. Nature, 505(7482), pp.244–247. Available at: http://dx.doi.org/10.1038/nature12773. Thomas R. M. Barends and Lutz Foucar and …

  96. De novo protein structure determination by heavy-atom soaking in lipidic cubic phase and SIRAS phasing using serial synchrotron crystallography

    0.0 out of 5 stars 

    08 Aug 2018 | BioXFEL Publications | Contributor(s): S. Botha, D. Baitan, K. E. J. Jungnickel, D. Oberthür, C. Schmidt, S. Stern, M. O. Wiedorn, M. Perbandt, H. N. Chapman, C. Betzel

    http://dx.doi.org/10.1107/s2052252518009223 During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application …

  97. Decoding hidden structural information in solution wide-angle X-ray scattering (WAXS): from ensemble modeling to machine learning

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    21 Oct 2021 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Lois Pollack

    http://dx.doi.org/10.1107/s0108767321098731 journal-article Chen, Y.-L., & Pollack, L. (2021). Decoding hidden structural information in solution wide-angle X-ray scattering (WAXS): from ensemble modeling to machine learning. Acta Crystallographica Section A Foundations and Advances, 77(a1), …

  98. Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases

    0.0 out of 5 stars 

    01 Mar 2024 | BioXFEL Publications | Contributor(s): Edwin G. Peña-Martínez, Jose Arcadio Rodriguez-Martinez

    http://dx.doi.org/10.31083/j.fbs1601004 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Peña-Martínez, E. G., & Rodríguez-Martínez, J. A. (2024). Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases. Frontiers in …

  99. Deconvoluting receptor trafficking, regulation, and function using massively parallel assays

    0.0 out of 5 stars 

    11 Feb 2022 | BioXFEL Publications | Contributor(s): David Nedrud, Yungui He, Daniel Schmidt, James Fraser, Willow Coyote-Maestas

    http://dx.doi.org/10.1016/j.bpj.2021.11.2700 journal-article Nedrud, D., He, Y., Schmidt, D., Fraser, J., & Coyote-Maestas, W. (2022). Deconvoluting receptor trafficking, regulation, and function using massively parallel assays. Biophysical Journal, 121(3), 2a. …

  100. Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment

    0.0 out of 5 stars 

    09 Jun 2014 | BioXFEL Publications | Contributor(s): K. Pande, P. Schwander, M. Schmidt, D. K. Saldin

    http://dx.doi.org/10.1098/rstb.2013.0332 K. Pande and P. Schwander and M. Schmidt and D. K. Saldin Pande, K. et al., 2014. Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment. Philosophical Transactions of the Royal Society B: …