Support

Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography

18 Sep 2023 | BioXFEL Publications | Contributor(s): Alexander M. Wolff, Eriko Nango, Iris Diane Young, Aaron S. Brewster, Minoru Kubo, Takashi Nomura, Michihiro Sugahara, Shigeki Owada, Benjamin A. Barad, Kazutaka Ito, Asmit Bhowmick, Sergio Carbajo, Tomoya Hino, James Holton, Dohyun Im, Lee J. O’Riordan, Tomoyuki Tanaka, Rie Tanaka, Raymond G. Sierra, Fumiaki Yumoto, Kensuke Tono, So Iwata, Nicholas K. Sauter, James Fraser, Michael Thompson

http://dx.doi.org/10.1038/s41557-023-01329-4 AbstractUnderstanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric …

Synthesis of Novel Heterocyclic Ferrocenyl Chalcones and Their Biological Evaluation

11 Sep 2023 | BioXFEL Publications | Contributor(s): Ámbar M. Alsina-Sánchez, Sebastián Montalvo-Vázquez, Nilmary Grafals-Ruiz, Carmen Acosta, Emily M. Ormé, Israel Rodriguez, Sara M. Delgado-Rivera, Arthur Tinoco, Suranganie Dharmawardhane, Ingrid C. Montes-González

http://dx.doi.org/10.1021/acsomega.3c01830 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Alsina-Sánchez, Á. M., Montalvo-Vázquez, S., Grafals-Ruiz, N., Acosta, C., Ormé, E. M., Rodríguez, I., Delgado-Rivera, S. M., Tinoco, A. D., Dharmawardhane, S., & Montes-González, I. C. …

Detection of a Geminate Photoproduct of Bovine Cytochrome c Oxidase by Time-Resolved Serial Femtosecond Crystallography

11 Sep 2023 | BioXFEL Publications | Contributor(s): Izumi Ishigami, Sergio Carbajo, Nadia Zatsepin, Masahide Hikita, Chelsie E Conrad, Garrett Charles Nelson, Jesse David Coe, Shibom Basu, Thomas Grant, Matthew H. Seaberg, Raymond G. Sierra, Mark S. Hunter, Petra Fromme, Raimund Fromme, Denis L. Rousseau, Syun-Ru Yeh

http://dx.doi.org/10.1021/jacs.3c07803 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Ishigami, I., Carbajo, S., Zatsepin, N., Hikita, M., Conrad, C. E., Nelson, G., Coe, J., Basu, S., Grant, T., Seaberg, M. H., Sierra, R. G., Hunter, M. S., Fromme, P., Fromme, R., Rousseau, D. …

Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam

07 Sep 2023 | BioXFEL Publications | Contributor(s): Tek Narsingh Malla, Kara Zielinski, Luis Aldama, Sasa Bajt, Denisse Feliz, Brendon Hayes, Mark S. Hunter, Christopher Kupitz, Stella Lisova, Juraj Knoska, Jose Manuel Martin-Garcia, Valerio Mariani, Suraj Pandey, Ishwor Poudyal, Raymond G. Sierra, Alexandra Tolstikova, Oleksandr Yefanov, Chung Hong Yoon, Abbas Ourmazd, Petra Fromme, Peter Schwander, Anton Barty, Henry Chapman, Emina Stojkovic, Alexander Batyuk, Sébastien Boutet, George Phillips, Lois Pollack, Marius Schmidt

http://dx.doi.org/10.1038/s41467-023-41246-1 AbstractFor decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free …

A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo

31 Aug 2023 | BioXFEL Publications | Contributor(s): Taha Y. Taha, Rahul K. Suryawanshi, Irene P. Chen, Galen J. Correy, Maria McCavitt-Malvido, Patrick C. O’Leary, Manasi P. Jogalekar, Morgan E. Diolaiti, Gabriella R. Kimmerly, Chia-Lin Tsou, Ronnie Gascon, Mauricio Montano, Luis Martinez-Sobrido, Nevan J. Krogan, Alan Ashworth, James Fraser, Melanie Ott

http://dx.doi.org/10.1371/journal.ppat.1011614 Despite unprecedented efforts, our therapeutic arsenal against SARS-CoV-2 remains limited. The conserved macrodomain 1 (Mac1) in NSP3 is an enzyme exhibiting ADP-ribosylhydrolase activity and a possible drug target. To determine the role of Mac1 …

Numerical modeling reveals improved organelle separation for dielectrophoretic ratchet migration

25 Aug 2023 | BioXFEL Publications | Contributor(s): Domin Koh, Mukul Sonker, Edgar A. Arriaga, Alexandra Ros

http://dx.doi.org/10.1002/elps.202300091 AbstractOrganelle size varies with normal and abnormal cell function. Thus, size‐based particle separation techniques are key to assessing the properties of organelle subpopulations differing in size. Recently, insulator‐based dielectrophoresis (iDEP) …

Practical considerations for the analysis of time-resolved x-ray data

16 Aug 2023 | BioXFEL Publications | Contributor(s): Marius Schmidt

http://dx.doi.org/10.1063/4.0000196 The field of time-resolved macromolecular crystallography has been expanding rapidly after free electron lasers for hard x rays (XFELs) became available. Techniques to collect and process data from XFELs spread to synchrotron light sources. Although time-scales …

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

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 …

Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data

27 Jul 2023 | BioXFEL Publications | Contributor(s): Siyuan Du, Stephanie A. Wankowicz, Filip Yabukarski, Tzanko Doukov, Daniel Herschlag, James Fraser

http://dx.doi.org/10.1016/bs.mie.2023.06.009 book-chapter Du, S., Wankowicz, S. A., Yabukarski, F., Doukov, T., Herschlag, D., & Fraser, J. S. (2023). Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data. Methods in Enzymology. …

A deep learning solution for crystallographic structure determination

25 May 2023 | BioXFEL Publications | Contributor(s): Tom Pan, Shikai Jin, Mitchell Miller, Anastasios Kyrillidis, George Phillips

http://dx.doi.org/10.1107/s2052252523004293 The general de novo solution of the crystallographic phase problem is difficult and only possible under certain conditions. This paper develops an initial pathway to a deep learning neural network approach for the phase problem in protein crystallography, …

Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source

19 May 2023 | BioXFEL Publications | Contributor(s): Mehmet Gul, Esra Ayan, Ebru Destan, J. Austin Johnson, Alaleh Shafiei, Abdullah Kepceoğlu, Merve Yilmaz, Fatma Betül Ertem, İlkin Yapici, Bilge Tosun, Nilüfer Baldir, Nurettin Tokay, Zeliş Nergiz, Gözde Karakadioğlu, Seyide Seda Paydos, Cahine Kulakman, Cengiz Kaan Ferah, Ömür Güven, Necati Atalay, Enver Kamil Akcan, Haluk Cetinok, Nazlı Eylül Arslan, Kardelen Şabanoğlu, Bengisu Aşci, Serra Tavli, Helin Gümüsboğa, Sevde Altuntaş, Masami Otsuka, Mikako Fujita, Şaban Teki̇n, Halilibrahim Çi̇ftçi̇, Serdar Durdaği, Ezgi Karaca, Burcu Kaplan Türköz, Burak Veli Kabasakal, Ahmet Kati, Hasan DeMi̇rci̇

http://dx.doi.org/10.1038/s41598-023-33989-0 AbstractHigh-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample …

Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering

02 May 2023 | BioXFEL Publications | Contributor(s): Kara Zielinski, Andrea Katz, George Douglas Calvey, Suzette A. Pabit, Shawn K. Milano, Cody Aplin, Josue San Emeterio, Richard A. Cerione, Lois Pollack

http://dx.doi.org/10.1107/s2052252523003482 Advances in time-resolved structural techniques, mainly in macromolecular crystallography and small-angle X-ray scattering (SAXS), allow for a detailed view of the dynamics of biological macromolecules and reactions between binding partners. Of particular …

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

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 …

Inter-Bragg crystallographic phase retrieval from shape transforms, stacking faults and substitutional disorder

31 Mar 2023 | BioXFEL Publications | Contributor(s): J.P.J. Chen, K. Pande, J.J. Donatelli, A.V. Martin, K. Ayyer, H.N. Chapman, R. Bean, K.E. Schmidt, R.A. Kirian

http://dx.doi.org/10.1016/j.ultramic.2023.113728 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Chen, J. P. J., Pande, K., Donatelli, J. J., Martin, A. V., Ayyer, K., Chapman, H. N., Bean, R., Schmidt, K. E., & Kirian, R. A. (2023). Inter-Bragg crystallographic phase retrieval …

Randomness in time-resolved serial crystallography data: alternatives to the binning and averaging approach

17 Mar 2023 | BioXFEL Publications | Contributor(s): C. Casadei, A. Hosseinizadeh, G. Schertler, A. Ourmazd, R. Santra

http://dx.doi.org/10.1107/s2053273322095742 journal-article Casadei, C., Hosseinizadeh, A., Schertler, G., Ourmazd, A., & Santra, R. (2022). Randomness in time-resolved serial crystallography data: alternatives to the binning and averaging approach. Acta Crystallographica Section A Foundations …

Polymer-based microfluidic device for on-chip counter-diffusive crystallization and in situ X-ray crystallography at room temperature

13 Mar 2023 | BioXFEL Publications | Contributor(s): Sarthak Saha, Can Özden, Alfred Samkutty, Silvia Russi, Aina Cohen, Margaret M. Stratton, Sarah Perry

http://dx.doi.org/10.1039/d2lc01194h Here we have reported novel polymeric devices to control fluid flow using surface forces and capillary action to facilitate counter-diffusive, on-chip protein crystallization. journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Saha, S., Özden, C., …

20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening

27 Feb 2023 | BioXFEL Publications | Contributor(s): Miranda Lynch, M. Elizabeth Snell, Stephen A. Potter, Edward Snell, Sarah EJ Bowman

http://dx.doi.org/10.1107/s2059798323001274 Diffraction-based structural methods contribute a large fraction of the biomolecular structural models available, providing a critical understanding of macromolecular architecture. These methods require crystallization of the target molecule, which …

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 …

Biological function investigated by time-resolved structure determination

21 Feb 2023 | BioXFEL Publications | Contributor(s): Marius Schmidt

http://dx.doi.org/10.1063/4.0000177 Inspired by recent progress in time-resolved x-ray crystallography and the adoption of time-resolution by cryo-electronmicroscopy, this article enumerates several approaches developed to become bigger/smaller, faster, and better to gain new insight into the …

Data assimilation in operator algebras

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 …

Reaction coordinate dependent fibrillar formation of human glutamine synthetase tunes activity

10 Feb 2023 | BioXFEL Publications | Contributor(s): Eric R. Greene, Richard Muniz, Angelika Arada, D. John Lee, Daphne Chen, Erin Thompson, Hiroki Yamamura, Justin M. Kollman, James Fraser

http://dx.doi.org/10.1016/j.bpj.2022.11.2541 journal-article Greene, E. R., Muniz, R., Arada, A., Lee, D. J., Chen, D., Thompson, E., Yamamura, H., Kollman, J. M., & Fraser, J. (2023). Reaction coordinate dependent fibrillar formation of human glutamine synthetase tunes activity. Biophysical …

X-ray scattering exhibits time-resolved view of rhodopsin activation

10 Feb 2023 | BioXFEL Publications | Contributor(s): C. Swathi K. Menon, Konstantinos Karpos, Thomas D. Grant, Andrey V. Struts, Steven D.E. Fried, Suchithranga M.D.C. Perera, Irina V. Kosheleva, Leslie Salas-Estrada, Alan Grossfield, Petra Fromme, Richard Kirian, Michael F. Brown

http://dx.doi.org/10.1016/j.bpj.2022.11.1170 journal-article Menon, C. S. K., Karpos, K., Grant, T. D., Struts, A. V., Fried, S. D. E., Perera, S. M. D. C., Kosheleva, I. V., Salas-Estrada, L., Grossfield, A., Fromme, P., Kirian, R. A., & Brown, M. F. (2023). X-ray scattering exhibits …

Large language models generate functional protein sequences across diverse families

26 Jan 2023 | BioXFEL Publications | Contributor(s): Ali Madani, Ben Krause, Eric R. Greene, Subu Subramanian, Benjamin P. Mohr, James Holton, Jose Luis Olmos, Caiming Xiong, Zachary Z. Sun, Richard Socher, James Fraser, Nikhil Naik

http://dx.doi.org/10.1038/s41587-022-01618-2 journal-article Madani, A., Krause, B., Greene, E. R., Subramanian, S., Mohr, B. P., Holton, J. M., Olmos, J. L., Xiong, C., Sun, Z. Z., Socher, R., Fraser, J. S., & Naik, N. (2023). Large language models generate functional protein sequences across …

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 …

Poster Template PPT

19 Jan 2023 | Downloads | Contributor(s): Nicole Terranova

…

Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser

10 Jan 2023 | BioXFEL Publications | Contributor(s): Rebecca Jeanne Jernigan, Dhenugen Logeswaran, Diandra Doppler, Nirupa Nagaratnam, Mukul Sonker, Jay-How Yang, Gihan Kaushylal Ketawala, Jose M. Martin-Garcia, Megan Shelby, Thomas D. Grant, Valerio Mariani, Alexandra Tolstikova, Michelle Z. Sheikh, Mimi Cho Yung, Matthew Coleman, Sahba Zaare, Emily K. Kaschner, Mohammad Towshif Rabbani, Reza Nazari, Michele A. Zacks, Brandon Hayes, Raymond G. Sierra, Mark S. Hunter, Stella Lisova, Alexander Batyuk, Christopher Kupitz, Sebastien Boutet, Debra T. Hansen, Richard Kirian, Marius Schmidt, Raimund Fromme, Matthias Frank, Alexandra Ros, Julian J.-L. Chen, Sabine Botha, Petra Fromme

http://dx.doi.org/10.1016/j.str.2022.12.009 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Jernigan, R. J., Logeswaran, D., Doppler, D., Nagaratnam, N., Sonker, M., Yang, J.-H., Ketawala, G., Martin-Garcia, J. M., Shelby, M. L., Grant, T. D., Mariani, V., Tolstikova, A., Sheikh, …

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2

04 Jan 2023 | BioXFEL Publications | Contributor(s): Stefan Gahbauer, Galen J. Correy, Marion Schuller, Matteo P. Ferla, Yagmur Umay Doruk, Moira Rachman, Taiasean Wu, Morgan Diolaiti, Siyi Wang, R. Jeffrey Neitz, Daren Fearon, Dmytro S. Radchenko, Yurii S. Moroz, John J. Irwin, Adam R. Renslo, Jenny C. Taylor, Jason E. Gestwicki, Frank Von Delft, Alan Ashworth, Ivan Ahel, Brian K. Shoichet, James Fraser

http://dx.doi.org/10.1073/pnas.2212931120 The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors of Mac1 have great …

The crystal structure of Vibrio cholerae (6-4) photolyase reveals interactions with cofactors and a DNA-binding region

14 Dec 2022 | BioXFEL Publications | Contributor(s): Baris Cakilkaya, Ibrahim Halil Kavakli, Hasan Demirci

http://dx.doi.org/10.1016/j.jbc.2022.102794 journal-article Cakilkaya, B., Kavakli, I. H., & DeMirci, H. (2023). The crystal structure of Vibrio cholerae (6-4) photolyase reveals interactions with cofactors and a DNA-binding region. Journal of Biological Chemistry, 299(1), 102794. …

Regulation of light energy conversion between linear and cyclic electron flow within photosystem II controlled by the plastoquinone/quinol redox poise

27 Nov 2022 | BioXFEL Publications | Contributor(s): Colin Gates, Gennady Ananyev, Shatabdi Roy-Chowdhury, Petra Fromme, G. Charles Dismukes

http://dx.doi.org/10.1007/s11120-022-00985-w journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Gates, C., Ananyev, G., Roy-Chowdhury, S., Fromme, P., & Dismukes, G. C. (2022). Regulation of light energy conversion between linear and cyclic electron flow within photosystem II …

Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins

14 Oct 2022 | BioXFEL Publications | Contributor(s): Sebastian Westenhoff, Petra Meszaros, Marius Schmidt

http://dx.doi.org/10.1016/j.sbi.2022.102481 journal-article Westenhoff, S., Meszaros, P., & Schmidt, M. (2022). Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins. Current Opinion in Structural Biology, 77, 102481. …

Identification of New L-Heptanoylphosphatidyl Inositol Pentakisphosphate Derivatives Targeting the Interaction with HIV-1 Gag by Molecular Modelling Studies

12 Oct 2022 | BioXFEL Publications | Contributor(s): Halilibrahim Ciftci, Belgin Sever, Esra Ayan, Mustafa Can, Hasan Demirci, Masami Otsuka, Amaç Fatih TuYuN, Hiroshi Tateishi, Mikako Fujita

http://dx.doi.org/10.3390/ph15101255 The HIV-1 Gag protein binds to the host cell membrane and assembles into immature particles. Then, in the course of immature virion budding, activated protease cleaves Gag into its main components: MA, CA, NC, and p6 proteins. The highly basic residues of MA …

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., …

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 …

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

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 …

Determining the structural ensembles of disordered RNA and proteins using an integrated approach

15 Sep 2022 | BioXFEL Publications | Contributor(s): Tong Wang, Suzette Pabit, Anja Henning-Knechtel, Weiwei He, Serdal Kirmizaltin, Lois Pollack

http://dx.doi.org/10.1107/s205327332209831x journal-article Wang, T., Pabit, S., Henning-Knechtel, A., He, W., Kirmizaltin, S., & Pollack, L. (2022). Determining the structural ensembles of disordered RNA and proteins using an integrated approach. Acta Crystallographica Section A Foundations and …

Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering

15 Sep 2022 | BioXFEL Publications | Contributor(s): Kara Zielinski, Andrea Katz, George Douglas Calvey, Suzette Pabit, Josue San Emeterio, Lois Pollack

http://dx.doi.org/10.1107/s2053273322099715 journal-article Zielinski, K., Katz, A., Calvey, G., Pabit, S., San Emeterio, J., & Pollack, L. (2022). Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering. …

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. …

GPCR Agonist-to-Antagonist Conversion: Enabling the Design of Nucleoside Functional Switches for the A2A Adenosine Receptor

17 Aug 2022 | BioXFEL Publications | Contributor(s): Anna Shiriaeva, Daejin Park, Gyudong Kim, Yoonji Lee, Xiyan Hou, Dnyandev B. Jarhad, Gibae Kim, Jinha Yu, Young Eum Hyun, Woomi Kim, Zhan-Guo Gao, Kenneth A. Jacobson, Gye Won Han, Raymond C. Stevens, Lak Shin Jeong, Sun Choi, Vadim Cherezov

http://dx.doi.org/10.1021/acs.jmedchem.2c00462 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Shiriaeva, A., Park, D., Kim, G., Lee, Y., Hou, X., Jarhad, D. B., Kim, G., Yu, J., Hyun, Y. E., Kim, W., Gao, Z.-G., Jacobson, K. A., Han, G. W., Stevens, R. C., Jeong, L. S., Choi, S., …

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 …

Structural basis for receptor selectivity and inverse agonism in S1P5 receptors

12 Aug 2022 | BioXFEL Publications | Contributor(s): Elizaveta Lyapina, Egor Marin, Anastasiia Gusach, Philipp Orekhov, Andrey Gerasimov, Aleksandra Luginina, Daniil Vakhrameev, Margarita Ergasheva, Margarita Kovaleva, Georgii Khusainov, Polina Khorn, Mikhail Shevtsov, Kirill Kovalev, Sergey Bukhdruker, Ivan Okhrimenko, Petr Popov, Hao Hu, Uwe Weierstall, Wei Liu, Yunje Cho, Ivan Gushchin, Andrey Rogachev, Gleb Bourenkov, Sehan Park, Gisu Park, Hyo Jung Hyun, Jaehyun Park, Valentin Gordeliy, Valentin Borshchevskiy, Alexey Mishin, Vadim Cherezov

http://dx.doi.org/10.1038/s41467-022-32447-1 AbstractThe bioactive lysophospholipid sphingosine-1-phosphate (S1P) acts via five different subtypes of S1P receptors (S1PRs) - S1P1-5. S1P5 is predominantly expressed in nervous and immune systems, regulating the egress of natural killer cells from …

Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers

11 Aug 2022 | BioXFEL Publications | Contributor(s): Susannah Holmes, Henry J. Kirkwood, Richard Bean, Klaus Giewekemeyer, Andrew V. Martin, Marjan Hadian-Jazi, Max Oliver Wiedorn, Dominik Oberthür, Hugh Marman, Luigi Adriano, Nasser Al-Qudami, Saša Bajt, Imrich Barák, Sadia Bari, Johan Bielecki, Sandor Brockhauser, Mathew A. Coleman, Francisco Cruz-Mazo, Cyril Danilevski, Katerina Dörner, Alfonso M. Gañán-Calvo, Rita Graceffa, Hans Fanghor, Michael Heymann, Matthias Frank, Alexander Kaukher, Yoonhee Kim, Bostjan Kobe, Juraj Knoška, Torsten Laurus, Romain Letrun, Luis Maia, Marc Messerschmidt, Markus Metz, Thomas Michelat, Grant Mills, Serguei Molodtsov, Diana Monteiro, Andrew J. Morgan, Astrid Münnich, Gisel E. Peña Murillo, Gianpietro Previtali, Adam Round, Tokushi Sato, Robin Schubert, Joachim Schulz, Megan Shelby, Carolin Seuring, Jonas A. Sellberg, Marcin Sikorski, Alessandro Silenzi, Stephan Stern, Jola Sztuk-Dambietz, Janusz Szuba, Martin Trebbin, Patrick Vagovic, Thomas Ve, Britta Weinhausen, Krzysztof Wrona, Paul Lourdu Xavier, Chen Xu, Oleksandr Yefanov, Keith A. Nugent, Henry Chapman, Adrian P. Mancuso, Anton Barty, Brian Abbey, Connie Darmanin

http://dx.doi.org/10.1038/s41467-022-32434-6 AbstractThe European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work …

Structural and biophysical properties of FopA, a major outer membrane protein of Francisella tularensis

01 Aug 2022 | BioXFEL Publications | Contributor(s): Nirupa Nagaratnam, Jose M. Martin-Garcia, Jay-How Yang, Matthew R. Goode, Gihan Kaushylal Ketawala, Felicia M. Craciunescu, James D Zook, Manashi Sonowal, Dewight Williams, Thomas D. Grant, Raimund Fromme, Debra T. Hansen, Petra Fromme

http://dx.doi.org/10.1371/journal.pone.0267370 Francisella tularensis is an extremely infectious pathogen and a category A bioterrorism agent. It causes the highly contagious zoonosis, Tularemia. Currently, FDA approved vaccines against tularemia are unavailable. F. tularensis outer membrane …

Structure Determination from Multiple-Scattering Electron Crystallography

22 Jul 2022 | BioXFEL Publications | Contributor(s): Jeffrey Donatelli, John Spence

http://dx.doi.org/10.1017/s1431927622010418 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Donatelli, J., & Spence, J. (2022). Structure Determination from Multiple-Scattering Electron Crystallography. Microscopy and Microanalysis, 28(S1), 2766–2767. …

Pump–probe capabilities at the SPB/SFX instrument of the European XFEL

21 Jul 2022 | BioXFEL Publications | Contributor(s): Jayanath C. P. Koliyadu, Romain Letrun, Henry J. Kirkwood, Jia Liu, Man Jiang, Moritz Emons, Richard Bean, Valerio Bellucci, Johan Bielecki, Sarlota Birnsteinova, Raphael De Wijn, Thomas Dietze, Juncheng E, Jan Grünert, Daniel Kane, Chan Kim, Yoonhee Kim, Max Lederer, Bradley Manning, Grant Mills, Luis L. Morillo, Nadja Reimers, Dimitrios Rompotis, Adam Round, Marcin Sikorski, Cedric M. S. Takem, Patrik Vagovič, Sandhya Venkatesan, Jinxiong Wang, Ulrike Wegner, Adrian P. Mancuso, Tokushi Sato

http://dx.doi.org/10.1107/s1600577522006701 Pump–probe experiments at X-ray free-electron laser (XFEL) facilities are a powerful tool for studying dynamics at ultrafast and longer timescales. Observing the dynamics in diverse scientific cases requires optical laser systems with a wide range of …

Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations

11 Jul 2022 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Weiwei He, Serdal Kirmizialtin, Lois Pollack

http://dx.doi.org/10.1016/j.xcrp.2022.100971 journal-article Chen, Y.-L., He, W., Kirmizialtin, S., & Pollack, L. (2022). Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations. Cell Reports Physical Science, 3(7), 100971. …

A Brief Atlas of Insulin

13 Jun 2022 | BioXFEL Publications | Contributor(s): Hasan Demirci, Esra Ayan

http://dx.doi.org/10.2174/1573399819666220610150342 Abstract: Insulin is an essential factor for mammalian organisms: a regulator of glucose metabolism and other key signaling pathways. Insulin is also a multifunctional hormone whose absence can cause many diseases. Recombinant insulin is widely …

The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature

27 May 2022 | BioXFEL Publications | Contributor(s): Galen J. Correy, Daniel W. Kneller, Gwyndalyn Phillips, Swati Pant, Silvia Russi, Aina E. Cohen, George Meigs, James Holton, Stefan Gahbauer, Michael Thompson, Alan Ashworth, Leighton Coates, Andrey Kovalevsky, Flora Meilleur, James Fraser

http://dx.doi.org/10.1126/sciadv.abo5083 The nonstructural protein 3 (NSP3) macrodomain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Mac1) removes adenosine diphosphate (ADP) ribosylation posttranslational modifications, playing a key role in the immune evasion capabilities of …

The Gamification of XFEL Education Using XFEL Crystal Blaster

06 May 2022 | BioXFEL Publications | Contributor(s): Fiacre Kabayiza, Sarah Woodruff, William J. Bauer

http://dx.doi.org/10.3390/cryst12050671 Novel groundbreaking techniques, such as serial femtosecond crystallography (SFX), which utilizes X-ray free-electron lasers (XFELs), have led to impressive advances in the field of structural biology. However, educating the next generation of scientists on …

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 …

From Alignment Laser to 3D Structures: Determining Structures of GPCRs in a Compact X‐ray Light Source

03 May 2022 | BioXFEL Publications | Contributor(s): Gabriela Diaz‐Figueroa, Marc Messerschimdt, Jong Woo‐Kim, Tien Olson

http://dx.doi.org/10.1096/fasebj.2022.36.s1.r3457 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Diaz‐Figueroa, G., Messerschimdt, M., Woo‐Kim, J., & Olson, T. (2022). From Alignment Laser to 3D Structures: Determining Structures of GPCRs in a Compact X‐ray Light Source. The …

Intersubunit Coupling Enables Fast CO2-Fixation by Reductive Carboxylases

25 Apr 2022 | BioXFEL Publications | Contributor(s): Hasan Demirci, Yashas Rao, Gabriele M. Stoffel, Bastian Vögeli, Kristina Schell, Aharon Gomez, Alexander Batyuk, Cornelius Gati, Raymond G. Sierra, Mark S. Hunter, E. Han Dao, Halil I. Ciftci, Brandon Hayes, Fredric Poitevin, Po-Nan Li, Manat Kaur, Kensuke Tono, David Adrian Saez, Samuel Deutsch, Yasuo Yoshikuni, Helmut Grubmüller, Tobias J. Erb, Esteban Vöhringer-Martinez, Soichi Wakatsuki

http://dx.doi.org/10.1021/acscentsci.2c00057 journal-article DeMirci, H., Rao, Y., Stoffel, G. M., Vögeli, B., Schell, K., Gomez, A., Batyuk, A., Gati, C., Sierra, R. G., Hunter, M. S., Dao, E. H., Ciftci, H. I., Hayes, B., Poitevin, F., Li, P.-N., Kaur, M., Tono, K., Saez, D. A., Deutsch, S., …

Transient state measurements on proteins by time-resolved crystallography

22 Apr 2022 | BioXFEL Publications | Contributor(s): Tek Narsingh Malla, Marius Schmidt

http://dx.doi.org/10.1016/j.sbi.2022.102376 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Malla, T. N., & Schmidt, M. (2022). Transient state measurements on proteins by time-resolved crystallography. Current Opinion in Structural Biology, 74, 102376. …

Optical Funnel to Guide and Focus Virus Particles for X-Ray Diffractive Imaging

22 Apr 2022 | BioXFEL Publications | Contributor(s): Salah Awel, Sebastian Lavin-Varela, Nils Roth, Daniel A. Horke, Andrei V. Rode, Richard Kirian, Jochen Küpper, Henry Chapman

http://dx.doi.org/10.1103/physrevapplied.17.044044 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Awel, S., Lavin-Varela, S., Roth, N., Horke, D. A., Rode, A. V., Kirian, R. A., Küpper, J., & Chapman, H. N. (2022). Optical Funnel to Guide and Focus Virus Particles for X-Ray …

MIMAS: microfluidic platform in tandem with MALDI mass spectrometry for protein quantification from small cell ensembles

06 Apr 2022 | BioXFEL Publications | Contributor(s): Jorvani Cruz Villarreal, Rory Kruithoff, Ana Egatz-Gomez, Paul D. Coleman, Robert Ros, Todd R. Sandrin, Alexandra Ros

http://dx.doi.org/10.1007/s00216-022-04038-y journal-article Cruz Villarreal, J., Kruithoff, R., Egatz-Gomez, A., Coleman, P. D., Ros, R., Sandrin, T. R., & Ros, A. (2022). MIMAS: microfluidic platform in tandem with MALDI mass spectrometry for protein quantification from small cell ensembles. …

Serial macromolecular crystallography at ALBA Synchrotron Light Source

04 Apr 2022 | BioXFEL Publications | Contributor(s): Jose M. Martin-Garcia, Sabine Botha, Hao Hu, Rebecca Jeanne Jernigan, Albert Castellví, Stella Lisova, Fernando Gil, Barbara Calisto, Isidro Crespo, Shatabdi Roy-Chowdhury, Alice Grieco, Gihan Kaushylal Ketawala, Uwe Weierstall, John Spence, Petra Fromme, Nadia Zatsepin, Dirk Roeland Boer, Xavi Carpena

http://dx.doi.org/10.1107/s1600577522002508 The increase in successful adaptations of serial crystallography at synchrotron radiation sources continues. To date, the number of serial synchrotron crystallography (SSX) experiments has grown exponentially, with over 40 experiments reported so far. In …

A Metropolis Monte Carlo algorithm for merging single-particle diffraction intensities

04 Apr 2022 | BioXFEL Publications | Contributor(s): B. R. Mobley, K. E. Schmidt, J. P. J. Chen, R. A. Kirian

http://dx.doi.org/10.1107/s2053273322001395 Single-particle imaging with X-ray free-electron lasers depends crucially on algorithms that merge large numbers of weak diffraction patterns despite missing measurements of parameters such as particle orientations. The expand–maximize–compress (EMC) …

Observations of phase changes in monoolein during high viscous injection

21 Mar 2022 | BioXFEL Publications | Contributor(s): Daniel J. Wells, Peter Berntsen, Eugeniu Balaur, Cameron M. Kewish, Patrick Adams, Andrew Aquila, Jack Binns, Sébastien Boutet, Hayden Broomhall, Carl Caleman, Andrew Christofferson, Charlotte E. Conn, Caroline Dahlqvist, Leonie Flueckiger, Francisco Gian Roque, Tamar L. Greaves, Majid Hejazian, Mark S. Hunter, Marjan Hadian Jazi, H. Olof Jönsson, Sachini Kadaoluwa Pathirannahalage, Richard Kirian, Alex Kozlov, Ruslan P. Kurta, Hugh Marman, Derek Mendez, Andrew Morgan, Keith Nugent, Dominik Oberthuer, Harry Quiney, Juliane Reinhardt, Saumitra Saha, Jonas A. Sellberg, Raymond Sierra, Max Oliver Wiedorn, Brian Abbey, Andrew V. Martin, Connie Darmanin

http://dx.doi.org/10.1107/s1600577522001862 Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and …

Ligand binding remodels protein side-chain conformational heterogeneity

21 Mar 2022 | BioXFEL Publications | Contributor(s): Stephanie A Wankowicz, Saulo H De Oliveira, Daniel W Hogan, Henry Van Den Bedem, James Fraser

http://dx.doi.org/10.7554/elife.74114 While protein conformational heterogeneity plays an important role in many aspects of biological function, including ligand binding, its impact has been difficult to quantify. Macromolecular X-ray diffraction is commonly interpreted with a static structure, but …

Amyloid‐β analysis from brain cells using microfluidics and mass spectrometry

15 Mar 2022 | BioXFEL Publications | Contributor(s): Jorvani Cruz Villarreal, Ana Egatz‐Gomez, Jiawei Liu, Robert Ros, George T. Noutsios, Todd R. Sandrin, Paul D. Coleman, Alexandra Ros

http://dx.doi.org/10.1002/alz.054274 journal-article Villarreal, J. C., Egatz‐Gomez, A., Liu, J., Ros, R., Noutsios, G. T., Sandrin, T. R., Coleman, P. D., & Ros, A. (2021). Amyloid‐β analysis from brain cells using microfluidics and mass spectrometry. Alzheimer’s & Dementia, 17(S3). …

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. …

Accurate positioning of functional residues with robotics-inspired computational protein design

07 Mar 2022 | BioXFEL Publications | Contributor(s): Cody Krivacic, Kale Kundert, Xingjie Pan, Roland A. Pache, Lin Liu, Shane O Conchúir, Jeliazko R. Jeliazkov, Jeffrey J. Gray, Michael Thompson, James Fraser, Tanja Kortemme

http://dx.doi.org/10.1073/pnas.2115480119 Significance Computational protein design promises to advance applications in medicine and biotechnology by creating proteins with many new and useful functions. However, new functions require the design of specific and often irregular atom-level …

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

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 …

Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics

14 Feb 2022 | BioXFEL Publications | Contributor(s): Kaitlyn Tsai, Vanja Stojković, D. John Lee, Iris Diane Young, Teresa Szal, Dorota Klepacki, Nora Vázquez-Laslop, Alexander S. Mankin, James Fraser, Danica Galonić Fujimori

http://dx.doi.org/10.1038/s41594-022-00723-9 journal-article Tsai, K., Stojković, V., Lee, D. J., Young, I. D., Szal, T., Klepacki, D., Vázquez-Laslop, N., Mankin, A. S., Fraser, J. S., & Fujimori, D. G. (2022). Structural basis for context-specific inhibition of translation by oxazolidinone …

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

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

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

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. …

Integration of software tools for integrative modeling of biomolecular systems

11 Feb 2022 | BioXFEL Publications | Contributor(s): Matthew Hancock, Thomas-Otavio Peulen, Benjamin Webb, James Fraser, Paul D. Adams, Andrej Sali

http://dx.doi.org/10.1016/j.bpj.2021.11.2555 journal-article Hancock, M., Peulen, T.-O., Webb, B., Fraser, J. S., Adams, P. D., & Sali, A. (2022). Integration of software tools for integrative modeling of biomolecular systems. Biophysical Journal, 121(3), 31a. …

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 …

Time-resolved functional expansion of visual rhodopsin detected by x-ray scattering

11 Feb 2022 | BioXFEL Publications | Contributor(s): C. Swathi K. Menon, Konstantinos Karpos, Thomas D. Grant, Andrey V. Struts, Steven D.E. Fried, Roberto C. Alvarez, Suchithranga M.D.C. Perera, Irina V. Kosheleva, Alan Grossfield, Petra Fromme, Richard Kirian, Michael F. Brown

http://dx.doi.org/10.1016/j.bpj.2021.11.1313 journal-article Menon, C. S. K., Karpos, K., Grant, T. D., Struts, A. V., Fried, S. D. E., Alvarez, R. C., Perera, S. M. D. C., Kosheleva, I. V., Grossfield, A., Fromme, P., Kirian, R. A., & Brown, M. F. (2022). Time-resolved functional expansion of …

Connecting glutamine synthetase biophysics to the cellular environment

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 …

Using deep mutational scanning to identify the determinants of antibiotic resistance

11 Feb 2022 | BioXFEL Publications | Contributor(s): Christian B. Macdonald, Alexis Kelley, Jenna Pellegrino, Willow Coyote-Maestas, James Fraser

http://dx.doi.org/10.1016/j.bpj.2021.11.665 journal-article Macdonald, C. B., Kelley, A., Pellegrino, J., Coyote-Maestas, W., & Fraser, J. (2022). Using deep mutational scanning to identify the determinants of antibiotic resistance. Biophysical Journal, 121(3), 422a. …

Integration of software tools for integrative modeling of biomolecular systems

08 Feb 2022 | BioXFEL Publications | Contributor(s): Matthew Hancock, Thomas-Otavio Peulen, Benjamin Webb, Billy Poon, James Fraser, Paul Adams, Andrej Sali

http://dx.doi.org/10.1016/j.jsb.2022.107841 journal-article Hancock, M., Peulen, T.-O., Webb, B., Poon, B., Fraser, J. S., Adams, P., & Sali, A. (2022). Integration of software tools for integrative modeling of biomolecular systems. Journal of Structural Biology, 214(1), 107841. …

From Protein Design to the Energy Landscape of a Cold Unfolding Protein

07 Feb 2022 | BioXFEL Publications | Contributor(s): Surya V. S. R. K Pulavarti, Jack B. Maguire, Shirley Yuen, Joseph S. Harrison, Jermel Griffin, Lakshmanane Premkumar, Edward A. Esposito, George I. Makhatadze, Angel E. Garcia, Thomas M. Weiss, Edward Snell, Brian Kuhlman, Thomas Szyperski

http://dx.doi.org/10.1021/acs.jpcb.1c10750 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Pulavarti, S. V. S. R. K., Maguire, J. B., Yuen, S., Harrison, J. S., Griffin, J., Premkumar, L., Esposito, E. A., Makhatadze, G. I., Garcia, A. E., Weiss, T. M., Snell, E. H., Kuhlman, B., & …

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 …

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

24 Jan 2022 | BioXFEL Publications | Contributor(s): Dameli Assalauova, Young Yong Kim, Sergey Bobkov, Ruslan Khubbutdinov, Max Rose, Roberto Alvarez, Jakob Andreasson, Eugeniu Balaur, Alice Contreras, Hasan Demirci, Luca Gelisio, Janos Hajdu, Mark S. Hunter, Ruslan P. Kurta, Haoyuan Li, Matthew McFadden, Reza Nazari, Peter Schwander, Anton Teslyuk, Peter Walter, P. Lourdu Xavier, Chun Hong Yoon, Sahba Zaare, Viacheslav A. Ilyin, Richard Kirian, Brenda Hogue, Andrew Aquila, Ivan A. Vartanyants

http://dx.doi.org/10.1107/s2052252522000501 An error in Fig. 3(c) of the article by Assalauova et al. [IUCrJ (2020), 7, 1102–1113] is corrected. journal-article Assalauova, D., Kim, Y. Y., Bobkov, S., Khubbutdinov, R., Rose, M., Alvarez, R., Andreasson, J., Balaur, E., Contreras, A., DeMirci, …

Protocol for Structure Determination of SARS-CoV-2 Main Protease at Near-physiological-temperature by Serial Femtosecond Crystallography

24 Jan 2022 | BioXFEL Publications | Contributor(s): Fatma Betul Ertem, Omur Guven, Cengizhan Buyukdag, Oktay Gocenler, Esra Ayan, Busra Yuksel, Mehmet Gul, Gozde Usta, Barıs Cakılkaya, J. Austin Johnson, E. Han Dao, Zhen Su, Frederic Poitevin, Chun Hong Yoon, Christopher Kupitz, Brandon Hayes, Mengning Liang, Mark S. Hunter, Alexander Batyuk, Raymond G. Sierra, Gihan Kaushylal Ketawala, Sabine Botha, Çağdaş Dağ, Hasan Demirci

http://dx.doi.org/10.1016/j.xpro.2022.101158 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Ertem, F. B., Guven, O., Buyukdag, C., Gocenler, O., Ayan, E., Yuksel, B., Gul, M., Usta, G., Cakılkaya, B., Johnson, J. A., Dao, E. H., Su, Z., Poitevin, F., Yoon, C. H., Kupitz, C., …

In Vitro and In Silico Study of Analogs of Plant Product Plastoquinone to Be Effective in Colorectal Cancer Treatment

23 Jan 2022 | BioXFEL Publications | Contributor(s): Halilibrahim Ciftci, Belgin Sever, Firdevs Ocak, Nilüfer Bayrak, Mahmut Yıldız, Hatice Yıldırım, Hasan Demirci, Hiroshi Tateishi, Masami Otsuka, Mikako Fujita, Amaç Fatih TuYuN

http://dx.doi.org/10.3390/molecules27030693 Plants have paved the way for the attainment of molecules with a wide-range of biological activities. However, plant products occasionally show low biological activities and/or poor pharmacokinetic properties. In that case, development of their …

Innate Type 2 Immunity Controls Hair Follicle Commensalism by <i>Demodex</i> Mites

21 Jan 2022 | BioXFEL Publications | Contributor(s): Roberto Ricardo-Gonzalez, Maya E. Kotas, Claire E. O'Leary, Iliana Tenvooren, Diana M. Marquez, Katelyn Singh, William Damsky, Andrew W. Schroeder, Jarish N. Cohen, Marlys Fassett, Jinwoo Lee, Scott G. Daniel, Kyle Bittinger, Roberto Efraín Díaz, James Fraser, Mark Ansel, Matthew Spitzer, Hong-Erh Liang, Richard M. Locksley

http://dx.doi.org/10.2139/ssrn.4013912 journal-article Ricardo-Gonzalez, R., Kotas, M. E., O'Leary, C. E., Tenvooren, I., Marquez, D. M., Singh, K., Damsky, W., Schroeder, A. W., Cohen, J. N., Fassett, M., Lee, J., Daniel, S. G., Bittinger, K., Díaz, R. E., Fraser, J. S., Ansel, M., …

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

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 …

Structural biology is solved — now what?

11 Jan 2022 | BioXFEL Publications | Contributor(s): Abbas Ourmazd, Keith Moffat, Eaton E Lattman

http://dx.doi.org/10.1038/s41592-021-01357-3 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Ourmazd, A., Moffat, K., & Lattman, E. E. (2022). Structural biology is solved — now what? Nature Methods, 19(1), 24–26. https://doi.org/10.1038/s41592-021-01357-3 Abbas Ourmazd and …

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, …

RNA Triplex Structures Revealed by WAXS-Driven MD Simulations

10 Jan 2022 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Weiwei He, Serdal Kirmizialtin, Lois Pollack

http://dx.doi.org/10.2139/ssrn.4000889 journal-article Chen, Y.-L., He, W., Kirmizialtin, S., & Pollack, L. (2022). RNA Triplex Structures Revealed by WAXS-Driven MD Simulations. SSRN Electronic Journal. https://doi.org/10.2139/ssrn.4000889 Yen-Lin Chen and Weiwei He and Serdal Kirmizialtin and …

Integral equation models for solvent in macromolecular crystals

04 Jan 2022 | BioXFEL Publications | Contributor(s): Jonathon G. Gray, George M. Giambaşu, David Case, Tyler Luchko

http://dx.doi.org/10.1063/5.0070869 journal-article Gray, J. G., Giambaşu, G. M., Case, D. A., & Luchko, T. (2022). Integral equation models for solvent in macromolecular crystals. The Journal of Chemical Physics, 156(1), 014801. https://doi.org/10.1063/5.0070869 Jonathon G. Gray and George M. …

Continuous organelle separation in an insulator‐based dielectrophoretic device

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. …

A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis

20 Dec 2021 | BioXFEL Publications | Contributor(s): Vijay Jayaraman, D. John Lee, Nadav Elad, Shay Vimer, Michal Sharon, James Fraser, Dan S. Tawfik

http://dx.doi.org/10.1038/s41589-021-00919-y journal-article Jayaraman, V., Lee, D. J., Elad, N., Vimer, S., Sharon, M., Fraser, J. S., & Tawfik, D. S. (2021). A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Nature Chemical Biology, 18(2), 161–170. …

Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography

19 Dec 2021 | BioXFEL Publications | Contributor(s): Omur Guven, Mehmet Gul, Esra Ayan, J Austin Johnson, Baris Cakilkaya, Gozde Usta, Fatma Betul Ertem, Nurettin Tokay, Busra Yuksel, Oktay Gocenler, Cengizhan Buyukdag, Sabine Botha, Gihan Kaushylal Ketawala, Zhen Su, Brandon Hayes, Frederic Poitevin, Alexander Batyuk, Chun Hong Yoon, Christopher Kupitz, Serdar Durdagi, Raymond G. Sierra, Hasan Demirci

http://dx.doi.org/10.3390/cryst11121579 Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial …

Co-flow injection for serial crystallography at X-ray free-electron lasers

16 Dec 2021 | BioXFEL Publications | Contributor(s): Diandra Doppler, Mohammad T. Rabbani, Romain Letrun, Jorvani Cruz Villarreal, Dai Hyun Kim, Sahir Ilyas Gandhi, Ana Egatz-Gomez, Mukul Sonker, Joe Chen, Faisal Hammad Mekky Koua, Jayhow Yang, Mohamed Youssef, Victoria Mazalova, Saša Bajt, Megan Shelby, Matt A. Coleman, Max Oliver Wiedorn, Juraj Knoska, Silvan Schön, Tokushi Sato, Mark S. Hunter, Ahmad Hosseinizadeh, Christopher Kuptiz, Reza Nazari, Roberto C. Alvarez, Konstantinos Karpos, Sahba Zaare, Zachary Dobson, Erin Discianno, Shangji Zhang, James D Zook, Johan Bielecki, Raphael De Wijn, Adam R. Round, Patrik Vagovic, Marco Kloos, Mohammad Vakili, Gihan Kaushylal Ketawala, Natasha Stander, Tien L. Olson, Katherine Morin, Jyotirmory Mondal, Jonathan Nguyen, José Domingo Meza-Aguilar, Gerdenis Kodis, Sara Vaiana, Jose M. Martin-Garcia, Valerio Mariani, Peter Schwander, Marius Schmidt, Marc Messerschmidt, Abbas Ourmazd, Nadia Zatsepin, Uwe Weierstall, Barry D. Bruce, Adrian P. Mancuso, Thomas Grant, Anton Barty, Henry Chapman, Matthias Frank, Raimund Fromme, John Spence, Sabine Botha, Petra Fromme, Richard Kirian, Alexandra Ros

http://dx.doi.org/10.1107/s1600576721011079 Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macromolecules at room temperature. Despite the impressive exposition of structural details with this novel …

The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina

16 Dec 2021 | BioXFEL Publications | Contributor(s): Abigael Kosgei, Mitchell Miller, Minakshi Bhardwaj, Weijun Xu, Jon S. Thorson, Steven G. Van Lanen, George Phillips

http://dx.doi.org/10.1107/s2053230x21012322 Dynemicin is an enediyne natural product from Micromonospora chersina ATCC53710. Access to the biosynthetic gene cluster of dynemicin has enabled the in vitro study of gene products within the cluster to decipher their roles in assembling this unique …

Abstract 13747: Targeting Urokinase-Type Plasminogen Activator (uPA) and the uPA Receptor, Reduces Vascular Inflammation and Lung Hemorrhage in Systemic Lupus and SARS CoV2 Infection in Mouse Models of Respiratory Distress Syndromes

16 Dec 2021 | BioXFEL Publications | Contributor(s): Liqiang Zhang, Jordan R Yaron, Lauren Schutz, Emily Aliskevich, Kyle Browder, Nicholas Saldevar, Isabela R Zanetti, Nora Elmadbouly, Honor Glenn, Yize Li, Karen Kibler, Brenda Hogue, Grant McFadden, Alexandra R Lucas

http://dx.doi.org/10.1161/circ.144.suppl_2.13747 Introduction: Acute respiratory distress syndromes with vascular inflammation and alveolar hemorrhage have high mortality and limited treatment. Autoimmune disease and severe viral infection cause vascular inflammation and …

2022 Conference

07 Dec 2021 | Downloads

…

Structural insights into bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus

24 Nov 2021 | BioXFEL Publications | Contributor(s): Ebru Destan, Busra Yuksel, Bradley B. Tolar, Esra Ayan, Sam Deutsch, Yasuo Yoshikuni, Soichi Wakatsuki, Christopher A. Francis, Hasan Demirci

http://dx.doi.org/10.1038/s41598-021-02180-8 AbstractThe ammonia-oxidizing thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle is one of the most energy-efficient CO2 fixation cycles discovered thus far. The protein encoded by Nmar_1308 (from Nitrosopumilus maritimus SCM1) is a …

Few-fs resolution of a photoactive protein traversing a conical intersection

03 Nov 2021 | BioXFEL Publications | Contributor(s): A. Hosseinizadeh, N. Breckwoldt, R. Fung, R. Sepehr, M. Schmidt, P. Schwander, R. Santra, A. Ourmazd

http://dx.doi.org/10.1038/s41586-021-04050-9 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Hosseinizadeh, A. et al., 2021. Few-fs resolution of a photoactive protein traversing a conical intersection. Nature, 599(7886), pp.697–701. Available at: …

Macromolecular movies, storybooks written by nature

03 Nov 2021 | BioXFEL Publications | Contributor(s): Marius Schmidt

http://dx.doi.org/10.1007/s12551-021-00846-1 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Schmidt, M., 2021. Macromolecular movies, storybooks written by nature. Biophysical Reviews. Available at: http://dx.doi.org/10.1007/s12551-021-00846-1. Marius Schmidt

Characterizing and Tuning the Properties of Polydiacetylene Films for Sensing Applications

26 Oct 2021 | BioXFEL Publications | Contributor(s): Tanner J. Finney, Sanjai J. Parikh, Amir Berman, Darryl Y. Sasaki, Tonya L. Kuhl

http://dx.doi.org/10.1021/acs.langmuir.1c02004 journal-article Finney, T. J., Parikh, S. J., Berman, A., Sasaki, D. Y., & Kuhl, T. L. (2021). Characterizing and Tuning the Properties of Polydiacetylene Films for Sensing Applications. Langmuir, 37(44), 12940–12951. …

The neutralization effect of montelukast on SARS-CoV-2 is shown by multiscale in silico simulations and combined in vitro studies

22 Oct 2021 | BioXFEL Publications | Contributor(s): Serdar Durdagi, Timucin Avsar, Muge Didem Orhan, Muge Serhatli, Bertan Koray Balcioglu, Hasan Umit Ozturk, Alisan Kayabolen, Yuksel Cetin, Seyma Aydinlik, Tugba Bagci-Onder, Saban Tekin, Hasan Demirci, Mustafa Guzel, Atilla Akdemir, Seyma Calis, Lalehan Oktay, Ilayda Tolu, Yasar Enes Butun, Ece Erdemoglu, Alpsu Olkan, Nurettin Tokay, Şeyma Işık, Aysenur Ozcan, Elif Acar, Sehriban Buyukkilic, Yesim Yumak

http://dx.doi.org/10.1016/j.ymthe.2021.10.014 journal-article Durdagi, S., Avsar, T., Orhan, M. D., Serhatli, M., Balcioglu, B. K., Ozturk, H. U., Kayabolen, A., Cetin, Y., Aydinlik, S., Bagci-Onder, T., Tekin, S., Demirci, H., Guzel, M., Akdemir, A., Calis, S., Oktay, L., Tolu, I., Butun, Y. E., …

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

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), …

Visualization of biomolecular structures by WAXS and MD

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

http://dx.doi.org/10.1107/s0108767321098755 journal-article He, W., Chen, Y.-L., Kirmizialtin, S., & Pollack, L. (2021). Visualization of biomolecular structures by WAXS and MD. Acta Crystallographica Section A Foundations and Advances, 77(a1), a124–a124. …

What it takes for a successful mix-and-inject serial crystallography experiment: from a sample preparation and sample delivery perspective

21 Oct 2021 | BioXFEL Publications | Contributor(s): Kara Zielinski, Lois Pollack

http://dx.doi.org/10.1107/s0108767321099219 journal-article Zielinski, K., & Pollack, L. (2021). What it takes for a successful mix-and-inject serial crystallography experiment: from a sample preparation and sample delivery perspective. Acta Crystallographica Section A Foundations and Advances, …

Turning up the heat on molecular machines with multi-temperature and temperature-jump X-ray scattering experiments

21 Oct 2021 | BioXFEL Publications | Contributor(s): Michael Thompson, Alexander Wolff, Benjamin Barad, Wilson Nieves Vasquez, Nathaniel Brown, Hyun Sun Cho, Friedrich Schotte, Valentyn Stadnytskyi, Philip Anfinrud, James Fraser

http://dx.doi.org/10.1107/s0108767321097841 journal-article Thompson, M., Wolff, A., Barad, B., Vasquez, W. N., Brown, N., Cho, H. S., Schotte, F., Stadnytskyi, V., Anfinrud, P., & Fraser, J. (2021). Turning up the heat on molecular machines with multi-temperature and temperature-jump X-ray …

Pushing the boundaries in crystallization screening: making automated user-accessible crystallization work

21 Oct 2021 | BioXFEL Publications | Contributor(s): Sarah EJ Bowman, Miranda Lynch, Angela Lauricella, Edward Snell

http://dx.doi.org/10.1107/s0108767321098470 journal-article Bowman, S., Lynch, M., Lauricella, A., & Snell, E. (2021). Pushing the boundaries in crystallization screening: making automated user-accessible crystallization work. Acta Crystallographica Section A Foundations and Advances, 77(a1), …

The ideal crystal for structural biology

21 Oct 2021 | BioXFEL Publications | Contributor(s): Edward Snell, Diana Monteiro, Sarah EJ Bowman

http://dx.doi.org/10.1107/s0108767321098901 journal-article Snell, E., Monteiro, D., & Bowman, S. (2021). The ideal crystal for structural biology. Acta Crystallographica Section A Foundations and Advances, 77(a1), a109–a109. https://doi.org/10.1107/s0108767321098901 Edward Snell and Diana …