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Deterministic Ratchet for Sub-micrometer (Bio)particle Separation

06 Mar 2018 | BioXFEL Publications | Contributor(s): Daihyun Kim, Jinghui Luo, Edgar A. Arriaga, Alexandra Ros

http://dx.doi.org/10.1021/acs.analchem.7b03774 journal-article Kim, D. et al., 2018. Deterministic Ratchet for Sub-micrometer (Bio)particle Separation. Analytical Chemistry. Available at: http://dx.doi.org/10.1021/acs.analchem.7b03774. Daihyun Kim and Jinghui Luo and Edgar A. Arriaga and …

Development of a ceramic injection molding process for liquid jet nozzles to be applied for X-ray free-electron lasers

24 Jul 2017 | BioXFEL Publications | Contributor(s): Volker Piotter, Alexander Klein, Klaus Plewa, Kenneth R. Beyerlein, Henry Chapman, Saša Bajt

http://dx.doi.org/10.1007/s00542-017-3493-7 journal-article Piotter, V. et al., 2017. Development of a ceramic injection molding process for liquid jet nozzles to be applied for X-ray free-electron lasers. Microsystem Technologies. Available at: http://dx.doi.org/10.1007/s00542-017-3493-7. …

Development of a photophoretic optical guide for femtosecond x-ray diffractive imaging of aerosolized nanoparticles (Conference Presentation)

10 Nov 2016 | BioXFEL Publications | Contributor(s): Richard Kirian, Salah Awel, Max Oliver Wiedorn, Daniel Horke, Nils Roth, Niko O. Eckerskorn, Jochen Küpper, Henry Chapman, Andrei V. Rode

http://dx.doi.org/10.1117/12.2239171 Richard A. Kirian and Salah Awel and Max Wiedorn and Daniel Horke and Nils Roth and Niko O. Eckerskorn and Jochen Küpper and Henry N. Chapman and Andrei V. Rode Kirian, R.A. et al., 2016. Development of a photophoretic optical guide for femtosecond x-ray …

Development of coherent scattering and diffractive imaging and the COSMIC facility at the Advanced Light Source

22 Mar 2013 | BioXFEL Publications | Contributor(s): D Shapiro, S Roy, R Celestre, W Chao, D Doering, M Howells, S Kevan, D Kilcoyne, J Kirz, S Marchesini, K A Seu, A Schirotzek, J Spence, T Tyliszczak, T Warwick, D Voronov, H A Padmore

http://dx.doi.org/10.1088/1742-6596/425/19/192011 journal-article Shapiro, D. et al., 2013. Development of coherent scattering and diffractive imaging and the COSMIC facility at the Advanced Light Source. Journal of Physics: Conference Series, 425(19), p.192011. Available at: …

Developments Towards Imaging Nanoscale Biology with XFELs: Some Recent Examples and a Glance to the Future

10 Aug 2018 | BioXFEL Publications | Contributor(s): Adrian P. Mancuso, Andrew Aquila, Richard Bean, Johan Bielecki, Carsten Fortmann-Grote, Klaus Giewekemeyer, Yoonhee Kim, Ruslan Kurta, Romain Letrun, Masoud Mehrjoo, Marc Messerschmidt, Grant Mills, Adam Round, Tokushi Sato, Joachim Schulz, Marcin Sikorski, Stephan Stern, Patrik Vagovic, Thomas Tschentscher

http://dx.doi.org/10.1017/s143192761801276x journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Mancuso, A.P. et al., 2018. Developments Towards Imaging Nanoscale Biology with XFELs: Some Recent Examples and a Glance to the Future. Microscopy and Microanalysis, 24(S2), pp.76–77. …

Dielectrophoresis of lambda-DNA using 3D carbon electrodes

24 Jan 2013 | BioXFEL Publications | Contributor(s): Rodrigo Martinez-Duarte, Fernanda Camacho-Alanis, Philippe Renaud, Alexandra Ros

http://dx.doi.org/10.1002/elps.201200447 journal-article Martinez-Duarte, R. et al., 2013. Dielectrophoresis of lambda-DNA using 3D carbon electrodes. ELECTROPHORESIS, 34(7), pp.1113–1122. Available at: http://dx.doi.org/10.1002/elps.201200447. Rodrigo Martinez-Duarte and Fernanda …

Dielectrophoresis: From molecular to micrometer scale analytes

27 Nov 2018 | BioXFEL Publications | Contributor(s): Daihyun Kim, Mukul Sonker, Alexandra Ros

http://dx.doi.org/10.1021/acs.analchem.8b05454 journal-article Kim, D., Sonker, M. & Ros, A., 2018. Dielectrophoresis: From molecular to micrometer scale analytes. Analytical Chemistry. Available at: http://dx.doi.org/10.1021/acs.analchem.8b05454. Daihyun Kim and Mukul Sonker and Alexandra Ros

Dielectrophoretic Sorting of Membrane Protein Nanocrystals

04 Sep 2013 | BioXFEL Publications | Contributor(s): Bahige G. Abdallah, Tzu-Chiao Chao, Christopher Kupitz, Petra Fromme, Alexandra Ros

http://dx.doi.org/10.1021/nn403760q Bahige G. Abdallah and Tzu-Chiao Chao and Christopher Kupitz and Petra Fromme and Alexandra Ros Abdallah, B.G. et al., 2013. Dielectrophoretic Sorting of Membrane Protein Nanocrystals. ACS Nano, 7(10), pp.9129–9137. Available at: …

Difference structures from time-resolved small-angle and wide-angle x-ray scattering

17 May 2018 | BioXFEL Publications | Contributor(s): Prakash Nepal, D. K. Saldin

http://dx.doi.org/10.1103/physrevb.97.195426 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Nepal, P. & Saldin, D.K., 2018. Difference structures from time-resolved small-angle and wide-angle x-ray scattering. Physical Review B, 97(19). Available at: …

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 …

Diffraction before destruction

09 Jun 2014 | BioXFEL Publications | Contributor(s): H. N. Chapman, C. Caleman, N. Timneanu

http://dx.doi.org/10.1098/rstb.2013.0313 H. N. Chapman and C. Caleman and N. Timneanu Chapman, H.N., Caleman, C. & Timneanu, N., 2014. Diffraction before destruction. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), pp.20130313–20130313. Available at: …

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 …

Diffraction data of core-shell nanoparticles from an X-ray free electron laser

11 Apr 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.2017.48 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Li, X. et al., 2017. Diffraction data of core-shell nanoparticles from an X-ray free electron laser. Scientific Data, 4, p.170048. Available at: http://dx.doi.org/10.1038/sdata.2017.48. …

Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins

18 Apr 2015 | BioXFEL Publications | Contributor(s): Michael E. Wall, Thomas C. Terwilliger, James Fraser, Paul D. Adams, Nicholas K. Sauter, Andrew VanBenschoten

http://dx.doi.org/10.1016/j.bpj.2013.11.2171 journal-article Wall, M.E. et al., 2014. Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins. Biophysical Journal, 106(2), p.384a. Available at: http://dx.doi.org/10.1016/j.bpj.2013.11.2171. Michael E. Wall and Thomas C. Terwilliger …

Diffuse X-Ray Scattering to Model Protein Motions

04 Feb 2014 | BioXFEL Publications | Contributor(s): Michael E. Wall, Paul D. Adams, James S. Fraser, Nicholas K. Sauter

http://dx.doi.org/10.1016/j.str.2014.01.002 journal-article Wall, M.E. et al., 2014. Diffuse X-Ray Scattering to Model Protein Motions. Structure, 22(2), pp.182–184. Available at: http://dx.doi.org/10.1016/j.str.2014.01.002. Michael E. Wall and Paul D. Adams and James S. Fraser and …

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 …

DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

24 Feb 2023 | BioXFEL Publications | Contributor(s): Christian B. Macdonald, David Nedrud, Patrick Rockefeller Grimes, Donovan Trinidad, James Fraser, Willow Coyote-Maestas

http://dx.doi.org/10.1186/s13059-023-02880-6 AbstractInsertions and deletions (indels) enable evolution and cause disease. Due to technical challenges, indels are left out of most mutational scans, limiting our understanding of them in disease, biology, and evolution. We develop a low cost and bias …

Direct Observation of the Mechanism of Antibiotic Resistance by Mix-and-Inject at the European XFEL

26 Nov 2020 | BioXFEL Publications | Contributor(s): Suraj Pandey, George Douglas Calvey, Andrea Katz, Tek Narsingh Malla, Faisal Hammad Mekky Koua, Jose M. Martin-Garcia, Ishwor Poudyal, Jay-How Yang, Mohammad Vakili, Oleksandr Yefanov, Kara Zielinski, Saša Bajt, Salah Awel, Katerina Dörner, Matthias Frank, Luca Gelisio, Rebecca Jeanne Jernigan, Henry Kirkwood, Marco Kloos, Jayanath Koliyadu, Valerio Mariani, Mitchell Miller, Grant Mills, Garrett Charles Nelson, Jose L. Olmos, Alireza Sadri, Tokushi Sato, Alexandra Tolstikova, Weijun Xu, Abbas Ourmazd, John Spence, Peter Schwander, Anton Barty, Henry Chapman, Petra Fromme, Adrian P. Mancuso, George Phillips, Richard Bean, Lois Pollack, Marius Schmidt

http://dx.doi.org/10.1101/2020.11.24.396689 AbstractIn this study, we follow the diffusion and buildup of occupancy of the substrate ceftriaxone in M. tuberculosis β-lactamase BlaC microcrystals by structural analysis of the enzyme substrate complex at single millisecond time resolution. We also …

Direct phasing in femtosecond nanocrystallography. I. Diffraction characteristics

15 Jan 2014 | BioXFEL Publications | Contributor(s): Joe Chen, John Spence, Rick P. Millane

X-ray free-electron lasers solve a number of difficulties in protein crystallography by providing intense but ultra-short pulses of X-rays, allowing collection of useful diffraction data from nanocrystals. Whereas the diffraction from large crystals corresponds only to samples of the Fourier …

Direct phasing in femtosecond nanocrystallography. II. Phase retrieval

15 Jan 2014 | BioXFEL Publications | Contributor(s): Joe Chen, John Spence, Rick P. Millane

X-ray free-electron laser diffraction patterns from protein nanocrystals provide information on the diffracted amplitudes between the Bragg reflections, offering the possibility of direct phase retrieval without the use of ancillary experimental diffraction data [Spenceet al.(2011).Opt. Express,19, …

Direct Phasing of Finite Crystals Illuminated with a Free-Electron Laser

12 Feb 2015 | BioXFEL Publications | Contributor(s): Richard Kirian, Richard J. Bean, Kenneth R. Beyerlein, Miriam Barthelmess, Chun Hong Yoon, Fenglin Wang, Flavio Capotondi, Emanuele Pedersoli, Anton Barty, Henry Chapman

http://dx.doi.org/10.1103/physrevx.5.011015 Richard A. Kirian and Richard J. Bean and Kenneth R. Beyerlein and Miriam Barthelmess and Chun Hong Yoon and Fenglin Wang and Flavio Capotondi and Emanuele Pedersoli and Anton Barty and Henry N. Chapman Kirian, R.A. et al., 2015. Direct Phasing of …

Direct Structural and Chemical Characterization of the Photolytic Intermediates of Methylcobalamin Using Time-Resolved X-ray Absorption Spectroscopy

06 Mar 2018 | BioXFEL Publications | Contributor(s): GANESH SUBRAMANIAN, Xiaoyi Zhang, Gerdenis Kodis, Qingyu Kong, Cunming Liu, Andrew Chizmeshya, Uwe Weierstall, John Spence

http://dx.doi.org/10.1021/acs.jpclett.8b00083 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Subramanian, G. et al., 2018. Direct Structural and Chemical Characterization of the Photolytic Intermediates of Methylcobalamin Using Time-Resolved X-ray Absorption Spectroscopy. The …

Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

11 Jan 2022 | BioXFEL Publications | Contributor(s): Kaitlyn Tsai, Vanja Stojković, Lianet Noda-Garcia, Iris Diane Young, Alexander G Myasnikov, Jordan Kleinman, Ali Palla, Stephen N Floor, Adam Frost, James Fraser, Dan S Tawfik, Danica Galonić Fujimori

http://dx.doi.org/10.7554/elife.70017 Alteration of antibiotic binding sites through modification of ribosomal RNA (rRNA) is a common form of resistance to ribosome-targeting antibiotics. The rRNA-modifying enzyme Cfr methylates an adenosine nucleotide within the peptidyl transferase center, …

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

Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine

25 Sep 2014 | BioXFEL Publications | Contributor(s): Brianna B. Williams, Andrew H. Van Benschoten, Peter Cimermancic, Mohamed S. Donia, Michael Zimmermann, Mao Taketani, Atsushi Ishihara, Purna C. Kashyap, James S. Fraser, Michael A. Fischbach

http://dx.doi.org/10.1016/j.chom.2014.09.001 journal-article Williams, B.B. et al., 2014. Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine. Cell Host & Microbe, 16(4), pp.495–503. Available at: …

Discovery and Clinical Proof-of-Concept of RLY-2608, a First-in-Class Mutant-Selective Allosteric PI3Kα Inhibitor That Decouples Antitumor Activity from Hyperinsulinemia

02 Nov 2023 | BioXFEL Publications | Contributor(s): Andreas Varkaris, Ermira Pazolli, Hakan Gunaydin, Qi Wang, Levi Pierce, Alessandro A. Boezio, Artemisa Bulku, Lucian DiPietro, Cary Fridrich, Adam Frost, Fabrizio Giordanetto, Erika P. Hamilton, Katherine Harris, Michael Holliday, Tamieka L. Hunter, Amanda Iskandar, Yongli Ji, Alexandre Larivée, Jonathan R. LaRochelle, André Lescarbeau, Fabien Llambi, Brenda Lormil, Mary M. Mader, Brenton G. Mar, Iain Martin, Thomas H. McLean, Klaus Michelsen, Yakov Pechersky, Erika Puente-Poushnejad, Kevin Raynor, Dipali Rogala, Ramin Samadani, Alison M. Schram, Kelley Shortsleeves, Sweta Swaminathan, Shahein Tajmir, Gege Tan, Yong Tang, Roberto Valverde, Bryan Wehrenberg, Jeremy Wilbur, Bret R. Williams, Hongtao Zeng, Hanmo Zhang, W. Patrick Walters, Beni B. Wolf, David E. Shaw, Donald A. Bergstrom, James Watters, James Fraser, Pascal D. Fortin, D. Randal Kipp

http://dx.doi.org/10.1158/2159-8290.cd-23-0944 Abstract PIK3CA (PI3Kα) is a lipid kinase commonly mutated in cancer, including ∼40% of hormone receptor–positive breast cancer. The most frequently observed mutants occur in the kinase and …

Discovery of allosteric binding sites by crystallographic fragment screening

07 Nov 2020 | BioXFEL Publications | Contributor(s): Tobias Krojer, James Fraser, Frank Von Delft

http://dx.doi.org/10.1016/j.sbi.2020.08.004 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Krojer, T., Fraser, J.S. & von Delft, F., 2020. Discovery of allosteric binding sites by crystallographic fragment screening. Current Opinion in Structural Biology, 65, pp.209–216. …

Dismantling antibiotic resistance one variant at a time: in vitro and computational analysis of VatD

11 Feb 2022 | BioXFEL Publications | Contributor(s): Alexis M. Kelley, Christian B. Macdonald, James Fraser

http://dx.doi.org/10.1016/j.bpj.2021.11.2487 journal-article Kelley, A. M., Macdonald, C. B., & Fraser, J. (2022). Dismantling antibiotic resistance one variant at a time: in vitro and computational analysis of VatD. Biophysical Journal, 121(3), 48a. https://doi.org/10.1016/j.bpj.2021.11.2487 …

Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure

25 Sep 2018 | BioXFEL Publications | Contributor(s): Robb Welty, Suzette A. Pabit, Andrea Katz, George Douglas Calvey, Lois Pollack, Kathleen B. Hall

http://dx.doi.org/10.1261/rna.068361.118 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Welty, R. et al., 2018. Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure. RNA, 24(12), pp.1828–1838. Available at: …

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 …

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 …

Dose efficient Compton X-ray microscopy

10 Apr 2018 | BioXFEL Publications | Contributor(s): P. Villanueva-Perez, S. Bajt, H. N. Chapman

http://dx.doi.org/10.1364/optica.5.000450 journal-article Villanueva-Perez, P., Bajt, S. & Chapman, H.N., 2018. Dose efficient Compton X-ray microscopy. Optica, 5(4), p.450. Available at: http://dx.doi.org/10.1364/optica.5.000450. P. Villanueva-Perez and S. Bajt and H. N. Chapman

Double-flow focused liquid injector for efficient serial femtosecond crystallography

16 Mar 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/srep44628 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Oberthuer, D. et al., 2017. Double-flow focused liquid injector for efficient serial femtosecond crystallography. Scientific Reports, 7, p.44628. Available at: http://dx.doi.org/10.1038/srep44628. …

Double-focusing mixing jet for XFEL study of chemical kinetics

06 Oct 2014 | BioXFEL Publications | Contributor(s): Dingjie Wang, Uwe Weierstall, Lois Pollack, John Spence

Several liquid sample injection methods have been developed to satisfy the requirements for serial femtosecond X-ray nanocrystallography, which enables radiation-damage-free determination of molecular structure at room temperature. Time-resolved nanocrystallography would combine structure analysis …

Double-focusing mixing jet for XFEL study of chemical kinetics

13 Oct 2015 | Teaching Materials

Several liquid sample injection methods have been developed to satisfy the requirements for serial femtosecond X-ray nanocrystallography, which enables radiation-damage-free determination of molecular structure at room temperature. Time-resolved nanocrystallography would combine structure analysis …

Draft Genome Sequence of the Filamentous Cyanobacterium Leptolyngbya sp. Strain Heron Island J, Exhibiting Chromatic Acclimation

07 Feb 2014 | BioXFEL Publications | Contributor(s): R. Paul, R. E. Jinkerson, K. Buss, J. Steel, R. Mohr, W. R. Hess, M. Chen, P. Fromme

journal-article http://dx.doi.org/10.1128/genomea.01166-13 Paul, R. et al., 2014. Draft Genome Sequence of the Filamentous Cyanobacterium Leptolyngbya sp. Strain Heron Island J, Exhibiting Chromatic Acclimation. Genome Announcements, 2(1), pp.e01166–13–e01166–13. Available at: …

Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers

02 Mar 2017 | BioXFEL Publications | Contributor(s): Franklin D Fuller, Sheraz Gul, Ruchira Chatterjee, E Sethe Burgie, Iris Diane Young, Hugo Lebrette, Vivek Srinivas, Aaron S Brewster, Tara Michels-Clark, Jonathan Clinger, Babak Andi, Mohamed Ibrahim, Ernest Pastor, Casper De Lichtenberg, Rana Hussein, Christopher J Pollock, Miao Zhang, Claudiu A Stan, Thomas Kroll, Thomas Fransson, Clemens Weninger, Markus Kubin, Pierre Aller, Louise Lassalle, Philipp Bräuer, Mitchell Miller, Muhamed Amin, Sergey Koroidov, Christian G Roessler, Marc Allaire, Raymond G Sierra, Peter T Docker, James M Glownia, Silke Nelson, Jason E Koglin, Diling Zhu, Matthieu Chollet, Sanghoon Song, Henrik Lemke, Mengning Liang, Dimosthenis Sokaras, Roberto Alonso-Mori, Athina Zouni, Johannes Messinger, Uwe Bergmann, Amie K Boal, J Martin Bollinger, Carsten Krebs, Martin Högbom, George Phillips, Richard D Vierstra, Nicholas K Sauter, Allen M Orville, Jan Kern, Vittal K Yachandra, Junko Yano

journal-article http://dx.doi.org/10.1038/nmeth.4195 NSF-STC Biology with X-ray Lasers (NSF-1231306) Fuller, F.D. et al., 2017. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nature Methods, 14(4), pp.443–449. Available at: …

Dynamics from noisy data with extreme timing uncertainty

26 Apr 2016 | BioXFEL Publications | Contributor(s): R. Fung, A. Ourmazd, A. M. Hanna, O. Vendrell, S. Ramakrishna, T. Seideman, R. Santra

http://dx.doi.org/10.1038/nature17627 R. Fung and A. Ourmazd and A. M. Hanna and O. Vendrell and S. Ramakrishna and T. Seideman and R. Santra and A. Ourmazd Fung, R. et al., 2016. Dynamics from noisy data with extreme timing uncertainty. Nature, 532(7600), pp.471–475. Available at: …

Dynamics of rare gas solids irradiated by electron beams

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

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

Dynamics retrieval from stochastically weighted incomplete data by low-pass spectral analysis

16 Aug 2022 | BioXFEL Publications | Contributor(s): Cecilia M. Casadei, Ahmad Hosseinizadeh, Gebhard F.X. Schertler, Abbas Ourmazd, Robin Santra

http://dx.doi.org/10.1063/4.0000156 Time-resolved serial femtosecond crystallography (TR-SFX) provides access to protein dynamics on sub-picosecond timescales, and with atomic resolution. Due to the nature of the experiment, these datasets are often highly incomplete and the measured diffracted …

E pluribus unum, no more: from one crystal, many conformations

09 Aug 2014 | BioXFEL Publications | Contributor(s): Rahel Woldeyes, David A Sivak, James Fraser

http://dx.doi.org/10.1016/j.sbi.2014.07.005 Rahel A Woldeyes and David A Sivak and James S Fraser Woldeyes, R.A., Sivak, D.A. & Fraser, J.S., 2014. E pluribus unum, no more: from one crystal, many conformations. Current Opinion in Structural Biology, 28, pp.56–62. Available at: …

Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser

22 Mar 2021 | BioXFEL Publications | Contributor(s): Ji-Hye Yun, Xuanxuan Li, Jianing Yue, Jae-Hyun Park, Zeyu Jin, Chufeng Li, Hao Hu, Yingchen Shi, Suraj Pandey, Sergio Carbajo, Sébastien Boutet, Mark S. Hunter, Mengning Liang, Raymond G. Sierra, Thomas J. Lane, Liang Zhou, Uwe Weierstall, Nadia Zatsepin, Mio Ohki, Jeremy R. H. Tame, Sam-Yong Park, John Spence, Wenkai Zhang, Marius Schmidt, Weontae Lee, Haiguang Liu

http://dx.doi.org/10.1073/pnas.2020486118 Chloride ion–pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl− into cells. How the ClR initiates the transport is elusive. Here, we show the dynamics of ion transport observed with time-resolved serial …

Editorial overview: Biophysical and molecular biological methods

28 Nov 2016 | BioXFEL Publications | Contributor(s): Petra Fromme, Andrej Sali

http://dx.doi.org/10.1016/j.sbi.2016.11.015 journal-article Fromme, P. & Sali, A., 2016. Editorial overview: Biophysical and molecular biological methods. Current Opinion in Structural Biology, 40, pp.ix–xi. Available at: http://dx.doi.org/10.1016/j.sbi.2016.11.015. Petra Fromme and Andrej Sali

Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases

13 Jun 2014 | BioXFEL Publications | Contributor(s): Sojin Moon, Ryan M. Bannen, Thomas J. Rutkoski, George Phillips, Euiyoung Bae

http://dx.doi.org/10.1002/prot.24627 journal-article Moon, S. et al., 2014. Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases. Proteins: Structure, Function, and Bioinformatics, 82(10), …

Effectiveness of different types of Masks in Aerosol Dispersion in SARS–CoV-2 Infection

17 Jun 2021 | BioXFEL Publications | Contributor(s): Gokhan Tanisali, Ahmet Sozak, Abdul Samet Bulut, Tolga Ziya Sander, Ozlem Dogan, Çağdaş Dağ, Mehmet Gönen, Fusun Can, Hasan Demirci, Onder Ergonul

http://dx.doi.org/10.1016/j.ijid.2021.06.029 journal-article Tanisali, G. et al., 2021. Effectiveness of different types of Masks in Aerosol Dispersion in SARS–CoV-2 Infection. International Journal of Infectious Diseases. Available at: http://dx.doi.org/10.1016/j.ijid.2021.06.029. Gokhan …

Effects of self-seeding and crystal post-selection on the quality of Monte Carlo-integrated SFX data

21 Apr 2015 | BioXFEL Publications | Contributor(s): Thomas Barends, Thomas A. White, Anton Barty, Lutz Foucar, Marc Messerschmidt, Roberto Alonso-Mori, Sabine Botha, Henry Chapman, R. Bruce Doak, Lorenzo Galli, Cornelius Gati, Matthias Gutmann, Jason Koglin, Anders Markvardsen, Karol Nass, Dominik Oberthur, Robert L. Shoeman, Ilme Schlichting, Sébastien Boutet

Serial femtosecond crystallography (SFX) is an emerging method for data collection at free-electron lasers (FELs) in which single diffraction snapshots are taken from a large number of crystals. The partial intensities collected in this way are then combined in a scheme called Monte Carlo …

Efficient Computation of k-Nearest Neighbour Graphs for Large High-Dimensional Data Sets on GPU Clusters

23 Sep 2013 | BioXFEL Publications | Contributor(s): Ali Dashti, Ivan Komarov, Roshan M. D’Souza

http://dx.doi.org/10.1371/journal.pone.0074113 journal-article Dashti, A., Komarov, I. & D’Souza, R.M., 2013. Efficient Computation of k-Nearest Neighbour Graphs for Large High-Dimensional Data Sets on GPU Clusters A. Gursoy, ed. PLoS ONE, 8(9), p.e74113. Available at: …

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: …

Electrically stimulated droplet injector for reduced sample consumption in serial crystallography

29 Sep 2022 | BioXFEL Publications | Contributor(s): Mukul Sonker, Diandra Doppler, Ana Egatz-Gomez, Sahba Zaare, Mohammad T. Rabbani, Abhik Manna, Jorvani Cruz Villarreal, Garrett Charles Nelson, Gihan Kaushylal Ketawala, Konstantinos Karpos, Roberto C. Alvarez, Reza Nazari, Darren Gary Thifault, Rebecca Jeanne Jernigan, Dominik Oberthür, Huijong Han, Raymond Sierra, Mark S. Hunter, Alexander Batyuk, Christopher Kupitz, Robert E. Sublett, Frederic Poitevin, Stella Lisova, Valerio Mariani, Alexandra Tolstikova, Sebastien Boutet, Marc Messerschmidt, J. Domingo Meza-Aguilar, Raimund Fromme, Jose M. Martin-Garcia, Sabine Botha, Petra Fromme, Thomas D. Grant, Richard Kirian, Alexandra Ros

http://dx.doi.org/10.1016/j.bpr.2022.100081 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Sonker, M., Doppler, D., Egatz-Gomez, A., Zaare, S., Rabbani, M. T., Manna, A., Cruz Villarreal, J., Nelson, G., Ketawala, G. K., Karpos, K., Alvarez, R. C., Nazari, R., Thifault, D., …

Electron Crystallography, Charge-Density Mapping and Nanodiffraction

24 Aug 2016 | BioXFEL Publications | Contributor(s): John Spence

book-chapter http://dx.doi.org/10.1007/978-3-319-26651-0_5 Spence, J., 2016. Electron Crystallography, Charge-Density Mapping and Nanodiffraction. Transmission Electron Microscopy, pp.145–166. Available at: http://dx.doi.org/10.1007/978-3-319-26651-0_5. John Spence

Electron microscopy of gold nanoparticles at atomic resolution

21 Aug 2014 | BioXFEL Publications | Contributor(s): M. Azubel, J. Koivisto, S. Malola, D. Bushnell, G. L. Hura, A. L. Koh, H. Tsunoyama, T. Tsukuda, M. Pettersson, H. Hakkinen, R. D. Kornberg

http://dx.doi.org/10.1126/science.1251959 journal-article Azubel, M. et al., 2014. Electron microscopy of gold nanoparticles at atomic resolution. Science, 345(6199), pp.909–912. Available at: http://dx.doi.org/10.1126/science.1251959. M. Azubel and J. Koivisto and S. Malola and D. Bushnell …

Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse

29 Apr 2015 | BioXFEL Publications | Contributor(s): L. Galli, S.-K. Son, M. Klinge, S. Bajt, A. Barty, R. Bean, C. Betzel, K. R. Beyerlein, C. Caleman, R. B. Doak, M. Duszenko, H. Fleckenstein, C. Gati, B. Hunt, R. A. Kirian, M. Liang, M. H. Nanao, K. Nass, D. Oberthür, L. Redecke, R. Shoeman, F. Stellato, C. H. Yoon, T. A. White, O. Yefanov, J. Spence, H. N. Chapman

http://dx.doi.org/10.1063/1.4919398 L. Galli and S.-K. Son and M. Klinge and S. Bajt and A. Barty and R. Bean and C. Betzel and K. R. Beyerlein and C. Caleman and R. B. Doak and M. Duszenko and H. Fleckenstein and C. Gati and B. Hunt and R. A. Kirian and M. Liang and M. H. Nanao and K. Nass and D. …

Electrophysiology of Viral Envelope Protein Ion Channels in Lipid Membranes Across Apertures in Polystyrene and Silicon

27 Jan 2010 | BioXFEL Publications | Contributor(s): Nipun Chaplot, Latrice Faulkner, Sasha Daskalova, Brenda Hogue, Michael Goryll

http://dx.doi.org/10.1016/j.bpj.2009.12.300 journal-article Chaplot, N. et al., 2010. Electrophysiology of Viral Envelope Protein Ion Channels in Lipid Membranes Across Apertures in Polystyrene and Silicon. Biophysical Journal, 98(3), p.52a. Available at: …

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 …

Elucidating the Role of Microprocessor Protein DGCR8 in Bending RNA Structures

13 Nov 2020 | BioXFEL Publications | Contributor(s): Suzette A. Pabit, Yen-Lin Chen, Emery T. Usher, Erik C. Cook, Lois Pollack, Scott A. Showalter

http://dx.doi.org/10.1016/j.bpj.2020.10.038 journal-article Pabit, S.A. et al., 2020. Elucidating the Role of Microprocessor Protein DGCR8 in Bending RNA Structures. Biophysical Journal, 119(12), pp.2524–2536. Available at: http://dx.doi.org/10.1016/j.bpj.2020.10.038. Suzette A. Pabit and …

Embedding classical dynamics in a quantum computer

03 May 2022 | BioXFEL Publications | Contributor(s): Dimitrios Giannakis, Abbas Ourmazd, Philipp Pfeffer, Jörg Schumacher, Joanna Slawinska

http://dx.doi.org/10.1103/physreva.105.052404 journal-article Giannakis, D., Ourmazd, A., Pfeffer, P., Schumacher, J., & Slawinska, J. (2022). Embedding classical dynamics in a quantum computer. Physical Review A, 105(5). https://doi.org/10.1103/physreva.105.052404 Dimitrios Giannakis and Abbas …

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

17 Aug 2015 | BioXFEL Publications | Contributor(s): Benjamin A Barad, Nathaniel Echols, Ray Yu-Ruei Wang, Yifan Cheng, Frank DiMaio, Paul D Adams, James Fraser

http://dx.doi.org/10.1038/nmeth.3541 Benjamin A Barad and Nathaniel Echols and Ray Yu-Ruei Wang and Yifan Cheng and Frank DiMaio and Paul D Adams and James S Fraser Barad, B.A. et al., 2015. EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy. Nat Meth, 12(10), …

Enabling membrane protein structure and dynamics with X-ray free electron lasers

11 Jun 2014 | BioXFEL Publications | Contributor(s): Geoffrey K Feld, Matthias Frank

http://dx.doi.org/10.1016/j.sbi.2014.05.002 journal-article Feld, G.K. & Frank, M., 2014. Enabling membrane protein structure and dynamics with X-ray free electron lasers. Current Opinion in Structural Biology, 27, pp.69–78. Available at: http://dx.doi.org/10.1016/j.sbi.2014.05.002. Geoffrey K …

Endosomal GPCR signaling turned off by negative feedback actions of PKA and v-ATPase

27 Jul 2014 | BioXFEL Publications | Contributor(s): Alexandre Gidon, Mohammad M Al-Bataineh, Frederic G Jean-Alphonse, Hilary P Stevenson, Tomoyuki Watanabe, Claire Louet, Ashok Khatri, Guillermo Calero, Núria M Pastor-Soler, Thomas J Gardella, Jean-Pierre Vilardaga

http://dx.doi.org/10.1038/nchembio.1589 journal-article Gidon, A. et al., 2014. Endosomal GPCR signaling turned off by negative feedback actions of PKA and v-ATPase. Nature Chemical Biology, 10(9), pp.707–709. Available at: http://dx.doi.org/10.1038/nchembio.1589. Alexandre Gidon and Mohammad …

Energy landscape of the SARS-CoV-2 reveals extensive conformational heterogeneity

08 Mar 2022 | BioXFEL Publications | Contributor(s): Ghoncheh Mashayekhi, John Vant, Abhigna Polavarapu, Abbas Ourmazd, Abhishek Singharoy

http://dx.doi.org/10.1016/j.crstbi.2022.02.001 journal-article Mashayekhi, G., Vant, J., Polavarapu, A., Ourmazd, A., & Singharoy, A. (2022). Energy landscape of the SARS-CoV-2 reveals extensive conformational heterogeneity. Current Research in Structural Biology, 4, 68–77. …

Energy Landscapes

07 Oct 2015 | Teaching Materials | Contributor(s): Ali Dashti

Energy landscapes and continuous conformational mapping of molecular machines.

Energy landscapes from cryo-EM snapshots: a benchmarking study

25 Jan 2023 | BioXFEL Publications | Contributor(s): Raison Dsouza, Ghoncheh Mashayekhi, Roshanak Etemadpour, Peter Schwander, Abbas Ourmazd

http://dx.doi.org/10.1038/s41598-023-28401-w AbstractBiomolecules undergo continuous conformational motions, a subset of which are functionally relevant. Understanding, and ultimately controlling biomolecular function are predicated on the ability to map continuous conformational motions, and …

Enhanced hydrogenation activity and diastereomeric interactions of methyl pyruvate co-adsorbed with R-1-(1-naphthyl)ethylamine on Pd(111)

04 Aug 2016 | BioXFEL Publications | Contributor(s): Mausumi Mahapatra, Luke Burkholder, Michael Garvey, Yun Bai, Dilano Saldin, Wilfred T. Tysoe

http://dx.doi.org/10.1038/ncomms12380 Mausumi Mahapatra and Luke Burkholder and Michael Garvey and Yun Bai and Dilano K. Saldin and Wilfred T. Tysoe Mahapatra, M. et al., 2016. Enhanced hydrogenation activity and diastereomeric interactions of methyl pyruvate co-adsorbed with …

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 …

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

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

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

Enzyme Intermediates Captured "on-the-fly" by Mix-and-Inject Serial Crystallography

13 Oct 2017 | BioXFEL Publications | Contributor(s): Jose Olmos, Suraj Pandey, Jose M. Martin-Garcia, George Douglas Calvey, Andrea Katz, Juray Knoska, Christopher Kupitz, Mark S. Hunter, Mengning Liang, Dominik Oberthuer, Oleksandr Yefanov, Max Oliver Wiedorn, Michael Heymann, Mark Holl, Kanupriya Pande, Anton Barty, Mitchell Miller, Stephan Stern, Shatabdi Roy-Chowdhury, Jesse David Coe, Nirupa Nagaratnam, James D Zook, Jacob Christopher Verburgt, Tyler Norwood, Ishwor Poudyal, David Xu, Jason Koglin, Matt Seaberg, Yun Zhao, Sasa Bajt, Thomas Grant, Valerio Mariani, Garrett Charles Nelson, GANESH SUBRAMANIAN, Euiyoung Bae, Raimund Fromme, Russel Fung, Peter Schwander, Matthias Frank, Thomas White, Uwe Weierstall, Nadia Zatsepin, John Spence, Petra Fromme, Henry Chapman, Lois Pollack, Lee Tremblay, Abbas Ourmazd, George Phillips, Marius Schmidt

http://dx.doi.org/10.1101/202432 Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number …

Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography

30 May 2018 | BioXFEL Publications | Contributor(s): Jose L. Olmos, Suraj Pandey, Jose M. Martin-Garcia, George Douglas Calvey, Andrea Katz, Juraj Knoska, Christopher Kupitz, Mark S. Hunter, Mengning Liang, Dominik Oberthuer, Oleksandr Yefanov, Max Oliver Wiedorn, Michael Heyman, Mark Holl, Kanupriya Pande, Anton Barty, Mitchell Miller, Stephan Stern, Shatabdi Roy-Chowdhury, Jesse David Coe, Nirupa Nagaratnam, James D Zook, Jacob Christopher Verburgt, Tyler Norwood, Ishwor Poudyal, David Xu, Jason Koglin, Matthew H. Seaberg, Yun Zhao, Saša Bajt, Thomas Grant, Valerio Mariani, Garrett Charles Nelson, GANESH SUBRAMANIAN, Euiyoung Bae, Raimund Fromme, Russell Fung, Peter Schwander, Matthias Frank, Thomas A. White, Uwe Weierstall, Nadia Zatsepin, John Spence, Petra Fromme, Henry Chapman, Lois Pollack, Lee Tremblay, Abbas Ourmazd, George Phillips, Marius Schmidt

http://dx.doi.org/10.1186/s12915-018-0524-5 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Olmos, J.L. et al., 2018. Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography. BMC Biology, 16(1). Available at: …

Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer

27 Mar 2014 | BioXFEL Publications | Contributor(s): Marius Schmidt, Dilano Saldin

http://dx.doi.org/10.1063/1.4869472 Marius Schmidt and Dilano K. Saldin Schmidt, M. & Saldin, D.K., 2014. Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer. Structural Dynamics, 1(2), p.024701. Available at: …

Establishing nonlinearity thresholds with ultraintense X-ray pulses

13 Sep 2016 | BioXFEL Publications | Contributor(s): Jakub Szlachetko, Joanna Hoszowska, Jean-Claude Dousse, Maarten Nachtegaal, Wojciech Błachucki, Yves Kayser, Jacinto Sà, Marc Messerschmidt, Sebastien Boutet, Garth J. Williams, Christian David, Grigory Smolentsev, Jeroen A. Van Bokhoven, Bruce D. Patterson, Thomas J. Penfold, Gregor Knopp, Marek Pajek, Rafael Abela, Christopher J. Milne

http://dx.doi.org/10.1038/srep33292 Jakub Szlachetko and Joanna Hoszowska and Jean-Claude Dousse and Maarten Nachtegaal and Wojciech Błachucki and Yves Kayser and Jacinto Sà and Marc Messerschmidt and Sebastien Boutet and Garth J. Williams and Christian David and Grigory Smolentsev and Jeroen A. …

Eukaryotic RNA Polymerase II

22 Oct 2013 | BioXFEL Publications | Contributor(s): David Bushnell, Roger Kornberg

book-chapter http://dx.doi.org/10.1007/978-3-642-39796-7_12 Bushnell, D.A. & Kornberg, R.D., 2013. Eukaryotic RNA Polymerase II. Nucleic Acids and Molecular Biology, pp.277–287. Available at: http://dx.doi.org/10.1007/978-3-642-39796-7_12. David A. Bushnell and Roger D. Kornberg

European XFEL Users Meeting

28 Oct 2014 | Downloads

EuXFEL Workshop

30 Nov 2017 | Downloads

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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 …

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

01 Mar 2019 | BioXFEL Publications

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 …

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

01 Mar 2019 | BioXFEL Publications

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 …

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. …

Evidence that specific interactions play a role in the cholesterol sensitivity of G protein-coupled receptors

12 Jan 2021 | BioXFEL Publications | Contributor(s): James Geiger, Rick Sexton, Zina Al-Sahouri, Ming-Yue Lee, Eugene Chun, Kaleeckal G. Harikumar, Laurence J. Miller, Oliver Beckstein, Wei Liu

http://dx.doi.org/10.1016/j.bbamem.2021.183557 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Geiger, J. et al., 2021. Evidence that specific interactions play a role in the cholesterol sensitivity of G protein-coupled receptors. Biochimica et Biophysica Acta (BBA) - Biomembranes, …

Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases

06 Aug 2014 | BioXFEL Publications | Contributor(s): Adam J Book, Ragothaman M Yennamalli, Taichi E Takasuka, Cameron R Currie, George Phillips, Brian G Fox

http://dx.doi.org/10.1186/1754-6834-7-109 journal-article Book, A.J. et al., 2014. Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases. Biotechnology for Biofuels, 7(1), p.109. Available at: http://dx.doi.org/10.1186/1754-6834-7-109. Adam J Book and …

Evolving Experimental Techniques for Structure-Based Drug Design

27 Aug 2022 | BioXFEL Publications | Contributor(s): Cody Aplin, Shawn K. Milano, Kara Zielinski, Lois Pollack, Richard A. Cerione

http://dx.doi.org/10.1021/acs.jpcb.2c04344 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Aplin, C., Milano, S. K., Zielinski, K. A., Pollack, L., & Cerione, R. A. (2022). Evolving Experimental Techniques for Structure-Based Drug Design. The Journal of Physical Chemistry B. …

Examples of Biological Small Angle Scattering

20 Sep 2018 | BioXFEL Publications | Contributor(s): Eaton E Lattman, Thomas D. Grant, Edward Snell

http://dx.doi.org/10.1093/oso/9780199670871.003.0012 In this chapter we illustrate the biological applications of small angle scattering. We cover examples of contrast matching has been used in the neutron case and with SAXS,. time-resolved studies that have helped reveal mechanism and how SAXS or …

Expanding the eukaryotic genetic code with a biosynthesized 21st amino acid

28 Sep 2022 | BioXFEL Publications | Contributor(s): Kuan‐Lin Wu, Joshua A. Moore, Mitchell Miller, Yuda Chen, Catherine Lee, Weijun Xu, Zane Peng, Qinghui Duan, George Phillips, Rosa A. Uribe, Han Xiao

http://dx.doi.org/10.1002/pro.4443 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Wu, K., Moore, J. A., Miller, M. D., Chen, Y., Lee, C., Xu, W., Peng, Z., Duan, Q., Phillips, G. N., Uribe, R. A., & Xiao, H. (2022). Expanding the eukaryotic genetic code with a biosynthesized 21st …

Expanding the space of protein geometries by computational design of de novo fold families

16 Oct 2020 | BioXFEL Publications | Contributor(s): Xingjie Pan, Michael Thompson, Yang Zhang, Lin Liu, James Fraser, Mark J. S. Kelly, Tanja Kortemme

http://dx.doi.org/10.1126/science.abc0881 Naturally occurring proteins vary the precise geometries of structural elements to create distinct shapes optimal for function. We present a computational design method, loop-helix-loop unit combinatorial sampling (LUCS), that mimics nature’s ability to …

Experience with the CSPAD during dedicated detector runs at LCLS

31 Mar 2014 | BioXFEL Publications | Contributor(s): G A Carini, S Boutet, M Chollet, A Dragone, G Haller, P A Hart, S C Herrmann, C J Kenney, J Koglin, M Messerschmidt, S Nelson, J Pines, A Robert, S Song, J B Thayer, G J Williams, D Zhu

http://dx.doi.org/10.1088/1742-6596/493/1/012011 journal-article Carini, G.A. et al., 2014. Experience with the CSPAD during dedicated detector runs at LCLS. Journal of Physics: Conference Series, 493, p.012011. Available at: http://dx.doi.org/10.1088/1742-6596/493/1/012011. G A Carini and S …

Experimental Phasing

08 Apr 2015 | Teaching Materials

Tom Terwilliger introduces experimental phasing techniques for X-ray crystallography and describes recent developments in SAD phasing using the Phenix software package.

Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses

07 Apr 2017 | BioXFEL Publications | Contributor(s): Benedikt J. Daurer, Kenta Okamoto, Johan Bielecki, Filipe R. N. C. Maia, Kerstin Mühlig, M. Marvin Seibert, Max F. Hantke, Carl Nettelblad, W. Henry Benner, Martin Svenda, Nicuşor Tîmneanu, Tomas Ekeberg, N. Duane Loh, Alberto Pietrini, Alessandro Zani, Asawari D. Rath, Daniel Westphal, Richard Kirian, Salah Awel, Max Oliver Wiedorn, Gijs Van Der Schot, Gunilla H. Carlsson, Dirk Hasse, Jonas A. Sellberg, Anton Barty, Jakob Andreasson, Sébastien Boutet, Garth Williams, Jason Koglin, Inger Andersson, Janos Hajdu, Daniel S. D. Larsson

http://dx.doi.org/10.1107/s2052252517003591 This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. AerosolizedOmono River …

Exploring Adsorption and Reactivity of NH3on Reduced Graphene Oxide

28 Apr 2013 | BioXFEL Publications | Contributor(s): Eric C. Mattson, Kanupriya Pande, Miriam Unger, Shumao Cui, Ganhua Lu, M. Gajdardziska-Josifovska, Michael Weinert, Junhong Chen, Carol J. Hirschmugl

journal-article http://dx.doi.org/10.1021/jp3122853 Mattson, E.C. et al., 2013. Exploring Adsorption and Reactivity of NH3on Reduced Graphene Oxide. The Journal of Physical Chemistry C, 117(20), pp.10698–10707. Available at: http://dx.doi.org/10.1021/jp3122853. Eric C. Mattson and Kanupriya …

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 …

Exploring Titanium(IV) Complexes as Potential Antimicrobial Compounds

26 Jan 2022 | BioXFEL Publications | Contributor(s): Israel Rodriguez, Lauren Fernández-Vega, Andrea N. Maser-Figueroa, Branlee Sang, Patricia González-Pagán, Arthur Tinoco

http://dx.doi.org/10.3390/antibiotics11020158 Due to the rapid mutation of pathogenic microorganisms, drug-resistant superbugs have evolved. Antimicrobial-resistant germs may share their resistance genes with other germs, making them untreatable. The search for more combative antibiotic compounds …

Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

05 May 2015 | BioXFEL Publications | Contributor(s): Daniel A Keedy, James Fraser, Henry Van Den Bedem

Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated …

Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

27 Oct 2015 | BioXFEL Publications | Contributor(s): Daniel A. Keedy, James Fraser, Henry Van Den Bedem

http://dx.doi.org/10.1371/journal.pcbi.1004507 Daniel A. Keedy and James S. Fraser and Henry van den Bedem Keedy, D.A., Fraser, J.S. & van den Bedem, H., 2015. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit A. Shehu, ed. PLoS Comput Biol, 11(10), p.e1004507. …

Expression and Association of the Yersinia pestis Translocon Proteins, YopB and YopD, Are Facilitated by Nanolipoprotein Particles

25 Mar 2016 | BioXFEL Publications | Contributor(s): Matthew Coleman, Jenny A. Cappuccio, Craig D. Blanchette, Tingjuan Gao, Erin S. Arroyo, Angela K. Hinz, Feliza A. Bourguet, Brent W. Segelke, Paul D. Hoeprich, Thomas Huser, Ted A. Laurence, Vladimir L. Motin, Brett A. Chromy

http://dx.doi.org/10.1371/journal.pone.0150166 Matthew A. Coleman and Jenny A. Cappuccio and Craig D. Blanchette and Tingjuan Gao and Erin S. Arroyo and Angela K. Hinz and Feliza A. Bourguet and Brent Segelke and Paul D. Hoeprich and Thomas Huser and Ted A. Laurence and Vladimir L. Motin and Brett …

Expression and purification of an engineered human endothelin receptor B in a monomeric form

19 May 2016 | BioXFEL Publications | Contributor(s): A. V. Mishin, A. P. Luginina, A. P. Potapenko, V. I. Borshchevskiy, V. Katritch, E. Edelweiss, I. S. Okhrimenko, V. I. Gordeliy, V. G. Cherezov

journal-article http://dx.doi.org/10.1134/s1607672916020216 Mishin, A.V. et al., 2016. Expression and purification of an engineered human endothelin receptor B in a monomeric form. Doklady Biochemistry and Biophysics, 467(1), pp.157–161. Available at: …

Expression platforms for producing eukaryotic proteins: a comparison of E. coli cell-based and wheat germ cell-free synthesis, affinity and solubility tags, and cloning strategies

08 Apr 2015 | BioXFEL Publications | Contributor(s): David J. Aceti, Craig A. Bingman, Russell L. Wrobel, Ronnie O. Frederick, Shin-ichi Makino, Karl W. Nichols, Sarata C. Sahu, Lai F. Bergeman, Paul G. Blommel, Claudia C. Cornilescu, Katarzyna A. Gromek, Kory D. Seder, Soyoon Hwang, John G. Primm, Grzegorz Sabat, Frank C. Vojtik, Brian F. Volkman, Zsolt Zolnai, George Phillips, John L. Markley, Brian G. Fox

http://dx.doi.org/10.1007/s10969-015-9198-1 David J. Aceti and Craig A. Bingman and Russell L. Wrobel and Ronnie O. Frederick and Shin-ichi Makino and Karl W. Nichols and Sarata C. Sahu and Lai F. Bergeman and Paul G. Blommel and Claudia C. Cornilescu and Katarzyna A. Gromek and Kory D. Seder and …

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

19 Aug 2014 | BioXFEL Publications | Contributor(s): Ho-Hsien Lee, Irene Cherni, HongQi Yu, Raimund Fromme, Jeffrey D. Doran, Ingo Grotjohann, Michele Mittman, Shibom Basu, Arpan Deb, Katerina Dörner, Andrew Aquila, Anton Barty, Sébastien Boutet, Henry Chapman, R. Bruce Doak, Mark S. Hunter, Daniel James, Richard Kirian, Christopher Kupitz, Robert M Lawrence, Haiguang Liu, Karol Nass, Ilme Schlichting, Kevin E. Schmidt, M. Marvin Seibert, Robert L. Shoeman, John Spence, Francesco Stellato, Uwe Weierstall, Garth J. Williams, Chunhong Yoon, Dingjie Wang, Nadia Zatsepin, Brenda Hogue, Nobuyuki Matoba, Petra Fromme, Tsafrir S. Mor

CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein ofHuman immunodeficiency virus 1(HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral …

Extended asymmetric-cut multilayer X-ray gratings

01 Jun 2015 | BioXFEL Publications | Contributor(s): Mauro Prasciolu, Anton Haase, Frank Scholze, Henry Chapman, Saša Bajt

http://dx.doi.org/10.1364/oe.23.015195 Mauro Prasciolu and Anton Haase and Frank Scholze and Henry N. Chapman and Saša Bajt Prasciolu, M. et al., 2015. Extended asymmetric-cut multilayer X-ray gratings. Optics Express, 23(12), p.15195. Available at: http://dx.doi.org/10.1364/oe.23.015195. …

Extended properties of magnetic spins of zinc ferrite nanoparticles in the THz frequency range

23 Nov 2020 | BioXFEL Publications | Contributor(s): Mohamed Abdellatif-Youssef, Martin Etter, Petra Fromme, Marco Salerno

http://dx.doi.org/10.1016/j.jmmm.2020.167574 journal-article Abdellatif-Youssef, M. et al., 2021. Extended properties of magnetic spins of zinc ferrite nanoparticles in the THz frequency range. Journal of Magnetism and Magnetic Materials, 525, p.167574. Available at: …

Extracting conformational heterogeneity from 2D and 3D cryo-EM data

08 Feb 2024 | BioXFEL Publications | Contributor(s): Samuel Hoff, Massimiliano Bonomi, James Fraser, Eric Greene

http://dx.doi.org/10.1016/j.bpj.2023.11.376 journal-article Hoff, S., Bonomi, M., Fraser, J., & Greene, E. (2024). Extracting conformational heterogeneity from 2D and 3D cryo-EM data. Biophysical Journal, 123(3), 50a–51a. https://doi.org/10.1016/j.bpj.2023.11.376 Samuel Hoff and Massimiliano …

Extracting water and ion distributions from solution x-ray scattering experiments

03 Jun 2016 | BioXFEL Publications | Contributor(s): Hung T. Nguyen, Suzette A. Pabit, Lois Pollack, David Case

http://dx.doi.org/10.1063/1.4953037 journal-article Nguyen, H.T. et al., 2016. Extracting water and ion distributions from solution x-ray scattering experiments. The Journal of Chemical Physics, 144(21), p.214105. Available at: http://dx.doi.org/10.1063/1.4953037. Hung T. Nguyen and Suzette A. …

Extraction of fast changes in the structure of a disordered ensemble of photoexcited biomolecules

13 Oct 2015 | Teaching Materials

Using pump-probe experiments of varying time intervals between pump and probe, the method of time-resolved crystallography has given many insights into the fast time variations of crystallized molecules as a result of photoexcitation. We show here that quantities extractable from multiple …

Fabrication of wedged multilayer Laue lenses

12 Mar 2015 | BioXFEL Publications | Contributor(s): M. Prasciolu, A. F. G. Leontowich, J. Krzywinski, A. Andrejczuk, H. N. Chapman, S. Bajt

http://dx.doi.org/10.1364/ome.5.000748 M. Prasciolu and A. F. G. Leontowich and J. Krzywinski and A. Andrejczuk and H. N. Chapman and S. Bajt Prasciolu, M. et al., 2015. Fabrication of wedged multilayer Laue lenses. Opt. Mater. Express, 5(4), p.748. Available at: …