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

   BioXFEL Publications 28 May 2021 Contributor(s): James Fraser

   http://dx.doi.org/10.15252/embr.202153256 journal-article Elias, M.… et al., 2021.… EMBO reports. Available at: http://dx.doi.org/10.15252/embr.202153256.

   https://bioxfel.org/resources/2016

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

   BioXFEL Publications 17 Jun 2021 Contributor(s): Hasan Demirci

   http://dx.doi.org/10.1016/j.ijid.2021.… 029 journal-article Tanisali, G. et al., 2021.… International Journal of Infectious Diseases. Available at: http://dx.doi.org/10.1016/j.ijid.2021.

   https://bioxfel.org/resources/2022

3. A new solution to the curved Ewald sphere problem for 3D image reconstruction in electron microscopy

   BioXFEL Publications 22 Feb 2021

   http://dx.doi.org/10.1016/j.ultramic.2021.… P.J. et al., 2021.… Ultramicroscopy, p.113234. Available at: http://dx.doi.org/10.1016/j.ultramic.2021.

   https://bioxfel.org/resources/1958

4. Quantitative agreement between dynamical rocking curves in ultrafast electron diffraction for x-ray lasers

   BioXFEL Publications 5 Feb 2021

   http://dx.doi.org/10.1016/j.ultramic.2021.… E. et al., 2021.… Ultramicroscopy, 223, p.113211. Available at: http://dx.doi.org/10.1016/j.ultramic.2021.

   https://bioxfel.org/resources/1990

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

   BioXFEL Publications 13 Jan 2021 Contributor(s): Wei Liu

   http://dx.doi.org/10.1016/j.bbamem.2021.… et al., 2021.… Biochimica et Biophysica Acta (BBA) - Biomembranes, p.183557. Available at: http://dx.doi.org/10.1016/j.bbamem.2021.

   https://bioxfel.org/resources/1989

6. Microgravity as an environment for macromolecular crystallization – an outlook in the era of space stations and commercial space flight

   BioXFEL Publications 8 Apr 2021

   http://dx.doi.org/10.1080/0889311x.2021.… H. & Helliwell, J.R., 2021.… Crystallography Reviews, pp.1–44. Available at: http://dx.doi.org/10.1080/0889311x.2021.

   https://bioxfel.org/resources/1991

7. High-resolution crystal structures of transient intermediates in the phytochrome photocycle

   BioXFEL Publications 23 Mar 2021 Contributor(s): Melissa Carrillo, suraj pandey, Ishwor Poudyal, Tek Narsingh Malla, Emina Stojkovic, Marius Schmidt

   http://dx.doi.org/10.1016/j.str.2021.… 004 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Carrillo, M. et al., 2021.… Structure. Available at: http://dx.doi.org/10.1016/j.str.2021.

   https://bioxfel.org/resources/1993

8. The ligand-bound state of a G protein-coupled receptor stabilizes the interaction of functional cholesterol molecules

   BioXFEL Publications 26 Feb 2021 Contributor(s): Vadim Cherezov

   http://dx.doi.org/10.1016/j.jlr.2021.… et al., 2021.… Journal of Lipid Research, 62, p.100059. Available at: http://dx.doi.org/10.1016/j.jlr.2021.

   https://bioxfel.org/resources/1970

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

   BioXFEL Publications 22 Sep 2021 Contributor(s): Petra Fromme

   http://dx.doi.org/10.1016/j.matt.2021.… 004 journal-article Shekhar, M., Terashi, G., Gupta, C., Sarkar, D., Debussche, G., Sisco, N. J., Nguyen, J., Mondal, A., Vant, J., Fromme, P., Van Horn, W. D., Tajkhorshid, E., Kihara, D., Dill, K., Perez, A., & Singharoy, A. (2021).… Matter, 4(10), 3195–3216.…

   https://bioxfel.org/resources/2160

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

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

    http://dx.doi.org/10.1016/j.bpj.2021.… 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.

    https://bioxfel.org/resources/2120

11. Connecting glutamine synthetase biophysics to the cellular environment

    BioXFEL Publications 11 Feb 2022 Contributor(s): James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.… 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.

    https://bioxfel.org/resources/2121

12. Using deep mutational scanning to identify the determinants of antibiotic resistance

    BioXFEL Publications 11 Feb 2022 Contributor(s): James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.… 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. https://doi.org/10.1016/j.bpj.2021.

    https://bioxfel.org/resources/2122

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

    BioXFEL Publications 11 Feb 2022 Contributor(s): James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.… 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.

    https://bioxfel.org/resources/2119

14. Integration of software tools for integrative modeling of biomolecular systems

    BioXFEL Publications 11 Feb 2022 Contributor(s): James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.… 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. https://doi.org/10.1016/j.bpj.2021.

    https://bioxfel.org/resources/2125

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

    BioXFEL Publications 11 Feb 2022 Contributor(s): James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.… 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. https://doi.org/10.1016/j.bpj.2021.

    https://bioxfel.org/resources/2118

16. Vitamin C Binds to SARS Coronavirus-2 Main Protease Essential for Viral Replication

    BioXFEL Publications 4 May 2021 Contributor(s): Tek Narsingh Malla, suraj pandey, Ishwor Poudyal, George Phillips, Emina Stojkovic, Marius Schmidt

    http://dx.doi.org/10.1101/2021.… 02.442358 AbstractThere is an urgent need for anti-viral agents that treat and/or prevent Covid-19 caused by SARS-Coronavirus (CoV-2) infections. The replication of the SARS CoV-2 is dependent on the activity of two cysteine proteases, a papain-like protease, PL-pro, and the 3C-like protease known…

    https://bioxfel.org/resources/2041

17. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

    BioXFEL Publications 16 Aug 2021 Contributor(s): Gihan Kaushylal Ketawala, Sabine Botha, Brandon Hayes, Mark S. Hunter, Christopher Kupitz, Edward Snell, Hasan Demirci

    http://dx.doi.org/10.1016/j.str.2021.… 007 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Durdagi, S. et al., 2021.… Structure. Available at: http://dx.doi.org/10.1016/j.str.2021.

    https://bioxfel.org/resources/2071

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

    BioXFEL Publications 11 Feb 2022 Contributor(s): Konstantinos Karpos, Petra Fromme, Richard Kirian

    http://dx.doi.org/10.1016/j.bpj.2021.… 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 visual rhodopsin detected by x-ray…

    https://bioxfel.org/resources/2117

19. Characterization of a Spatially resolved multi-element laser ablation ion source

    BioXFEL Publications 26 Nov 2021

    http://dx.doi.org/10.1016/j.ijms.2021.… , Chambers, C., Chen, D., Feng, Z., Fraser, J., Ito, Y., Lan, Y., Mendez, S., Medina Peregrina, M., Rasiwala, H., Richez, L., Roy, N., Simpson, R., Dilling, J., Fairbank, W., Kwiatkowski, A. A., & Brunner, T. (2022). Characterization of a Spatially resolved multi-element laser ablation ion…

    https://bioxfel.org/resources/2203

20. Molecular Dynamics Analysis of a Flexible Loop at the Binding Interface of the SARS-CoV-2 Spike Protein Receptor-Binding Domain

    BioXFEL Publications 14 Jan 2021 Contributor(s): David Case

    http://dx.doi.org/10.1101/2021.… 08.425965 AbstractSince the identification of the SARS-CoV-2 virus as the causative agent of the current COVID-19 pandemic, considerable effort has been spent characterizing the interaction between the Spike protein receptor-binding domain (RBD) and the human angiotensin converting enzyme 2 (ACE2)…

    https://bioxfel.org/resources/1964

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

    BioXFEL Publications 22 Oct 2021 Contributor(s): Hasan Demirci

    http://dx.doi.org/10.1016/j.ymthe.2021.… 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., Erdemoglu, E., … Yumak, Y.…

    https://bioxfel.org/resources/2108

22. Mediator structure and conformation change

    BioXFEL Publications 10 Feb 2021 Contributor(s): Rayees Mattoo, David Bushnell, Roger Kornberg

    http://dx.doi.org/10.1016/j.molcel.2021.

    https://bioxfel.org/resources/1980

23. Structural insight into host plasma membrane association and assembly of HIV-1 Matrix protein

    BioXFEL Publications 22 Feb 2021 Contributor(s): Hasan Demirci

    http://dx.doi.org/10.1101/2021.… 21.432153 ABSTRACTHIV-1 continues to be a global health concern since AIDS was first recognized by the World Health Organization (WHO). It is estimated that there were 38 million people infected with HIV-1 and 1.5 million deaths in 2019 alone. A better understanding of the details of the HIV…

    https://bioxfel.org/resources/1971

24. Classical molecular dynamics

    BioXFEL Publications 11 Mar 2021 Contributor(s): David Case

    http://dx.doi.org/10.1063/5.0045455 journal-article Brooks, C.L. et al., 2021.

    https://bioxfel.org/resources/1963

25. PEGylated Serp-1 Markedly Reduces Pristane-Induced Experimental Diffuse Alveolar Hemorrhage, Altering uPAR Distribution, and Macrophage Invasion

    BioXFEL Publications 18 Feb 2021 Contributor(s): Ryan Boyd, Petra Fromme

    http://dx.doi.org/10.3389/fcvm.2021.… The prevalence of DAH is reported to range from 1 to 5%, but while DAH is considered a rare complication there is a reported 50–80% mortality. There is at present no proven effective treatment for DAH and the therapeutics that have been tested have significant side effects. There is a clear…

    https://bioxfel.org/resources/1978

26. Visualization of biomolecular structures by WAXS and MD

    BioXFEL Publications 21 Oct 2021 Contributor(s): Lois Pollack

    http://dx.doi.org/10.1107/s0108767321098755 journal-article He, W., Chen, Y.-L., Kirmizialtin, S., & Pollack, L. (2021).

    https://bioxfel.org/resources/2103

27. The ideal crystal for structural biology

    BioXFEL Publications 21 Oct 2021 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).

    https://bioxfel.org/resources/2132

28. Structural biology in the time of COVID-19: perspectives on methods and milestones

    BioXFEL Publications 22 Apr 2021 Contributor(s): Miranda Lynch, Edward Snell, Sarah EJ Bowman

    http://dx.doi.org/10.1107/s2052252521003948 The global COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has wreaked unprecedented havoc on global society, in terms of a huge loss of life and burden of morbidity, economic upheaval and social disruption. Yet the sheer magnitude and uniqueness of this event has…

    https://bioxfel.org/resources/1996

29. Macromolecular movies, storybooks written by nature

    BioXFEL Publications 3 Nov 2021 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.

    https://bioxfel.org/resources/2078

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

    BioXFEL Publications 3 Nov 2021

    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.

    https://bioxfel.org/resources/2077

31. A science education model for large collaborative centers

    BioXFEL Publications 5 Mar 2021 Contributor(s): Sarah Woodruff

    http://dx.doi.org/10.1063/4.0000081 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Bauer, W.J. & Woodruff, S.B., 2021.

    https://bioxfel.org/resources/1987

32. Selecting XFEL single-particle snapshots by geometric machine learning

    BioXFEL Publications 18 Feb 2021 Contributor(s): Ahmad Hosseinizadeh, Ghoncheh Mashayekhi, Russell Fung, Abbas Ourmazd, Peter Schwander

    http://dx.doi.org/10.1063/4.0000060 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Cruz-Chú, E.R. et al., 2021.

    https://bioxfel.org/resources/1955

33. Sodium Binding in Cysteinyl Leukotriene G Protein-Coupled Receptors

    BioXFEL Publications 12 Feb 2021 Contributor(s): Vadim Cherezov

    http://dx.doi.org/10.1016/j.bpj.2020.11.987 journal-article Shaulskaia, V. et al., 2021.

    https://bioxfel.org/resources/1969

34. SAXS structure of homodimeric oxyHemoglobin III from bivalve Lucina pectinata

    BioXFEL Publications 1 Apr 2021

    http://dx.doi.org/10.1002/bip.23427 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Marchany‐Rivera, D. et al., 2021.

    https://bioxfel.org/resources/1984

35. ORACLE reveals a bright future to fight bacteria

    BioXFEL Publications 15 Apr 2021 Contributor(s): James Fraser

    http://dx.doi.org/10.7554/elife.68277 A new way to alter the genome of bacteriophages helps produce large libraries of variants, allowing these bacteria-killing viruses to be designed to target species harmful to human health. journal-article Coyote-Maestas, W., & Fraser, J. S. (2021).

    https://bioxfel.org/resources/2123

36. Friction measurements of model saliva-wine solutions between polydimethylsiloxane surfaces

    BioXFEL Publications 10 Dec 2020

    http://dx.doi.org/10.1016/j.foodhyd.2020.106522 journal-article Edmonds, R.S. et al., 2021.

    https://bioxfel.org/resources/1981

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

    BioXFEL Publications 15 Mar 2022 Contributor(s): 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).

    https://bioxfel.org/resources/2134

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

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

    http://dx.doi.org/10.1107/s0108767321099219 journal-article Zielinski, K., & Pollack, L. (2021).

    https://bioxfel.org/resources/2104

39. Molecular Dynamics Simulations Unravel the Mysteries of Hemoglobin Diseases

    BioXFEL Publications 12 Feb 2021 Contributor(s): David Case

    http://dx.doi.org/10.1016/j.bpj.2020.11.1905 journal-article Samuel, P.P. & Case, D.A., 2021.

    https://bioxfel.org/resources/1962

40. Reply to: Limitations of the iterative electron density reconstruction algorithm from solution scattering data

    BioXFEL Publications 1 Mar 2021

    http://dx.doi.org/10.1038/s41592-021-01083-w journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Grant, T.D., 2021.

    https://bioxfel.org/resources/1973

41. Characterizing and Tuning the Properties of Polydiacetylene Films for Sensing Applications

    BioXFEL Publications 26 Oct 2021

    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).

    https://bioxfel.org/resources/2106

42. Breaking the Boundary between Solution X-Ray Scattering and Molecular Dynamics Simulations of Structured Nucleic Acids

    BioXFEL Publications 12 Feb 2021 Contributor(s): Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2020.11.1995 journal-article Chen, Y.-L. et al., 2021.

    https://bioxfel.org/resources/1956

43. Functional Expansion of G-Protein-Coupled Receptor Shown by Time-Resolved X-Ray Scattering

    BioXFEL Publications 12 Feb 2021 Contributor(s): Konstantinos Karpos, Petra Fromme, Richard Kirian

    http://dx.doi.org/10.1016/j.bpj.2020.11.1003 journal-article Menon, C.S.K. et al., 2021.

    https://bioxfel.org/resources/1957

44. A glycan gate controls opening of the SARS-CoV-2 spike protein

    BioXFEL Publications 19 Aug 2021 Contributor(s): Ghoncheh Mashayekhi, Abbas Ourmazd

    http://dx.doi.org/10.1038/s41557-021-00758-3 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Sztain, T. et al., 2021.

    https://bioxfel.org/resources/2072

45. Surface coatings for microfluidic biomedical devices

    BioXFEL Publications 16 Aug 2021

    http://dx.doi.org/10.1016/b978-0-12-819971-8.00003-2 book-chapter Sonker, M., Abdallah, B.G. & Ros, A., 2021.

    https://bioxfel.org/resources/2073

46. A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis

    BioXFEL Publications 20 Dec 2021 Contributor(s): James Fraser

    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).

    https://bioxfel.org/resources/2110

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

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

    http://dx.doi.org/10.1107/s0108767321098470 journal-article Bowman, S., Lynch, M., Lauricella, A., & Snell, E. (2021).

    https://bioxfel.org/resources/2131

48. Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV ‐2 spike protein receptor‐binding domain

    BioXFEL Publications 10 Aug 2021 Contributor(s): David Case

    http://dx.doi.org/10.1002/prot.26208 journal-article Williams, J.K. et al., 2021.

    https://bioxfel.org/resources/2075

49. Quantitative Approach for Protein Analysis in Small Cell Ensembles by an Integrated Microfluidic Chip with MALDI Mass Spectrometry

    BioXFEL Publications 5 Apr 2021 Contributor(s): Alexandra Ros

    http://dx.doi.org/10.1021/acs.analchem.0c04112 journal-article Yang, M. et al., 2021.

    https://bioxfel.org/resources/2034

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

    BioXFEL Publications 21 Oct 2021 Contributor(s): Lois Pollack

    http://dx.doi.org/10.1107/s0108767321098731 journal-article Chen, Y.-L., & Pollack, L. (2021).

    https://bioxfel.org/resources/2102

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

    BioXFEL Publications 24 Nov 2020 Contributor(s): Petra Fromme

    http://dx.doi.org/10.1016/j.jmmm.2020.167574 journal-article Abdellatif-Youssef, M. et al., 2021.

    https://bioxfel.org/resources/1976

52. Femtosecond Single-Particle Diffractive Imaging of 3D DNA-Origami Molecular Scaffolds with XFEL Pulses

    BioXFEL Publications 12 Feb 2021 Contributor(s): David Bushnell, Roger Kornberg, Henry Chapman

    http://dx.doi.org/10.1016/j.bpj.2020.11.1697 journal-article Xavier, P.L. et al., 2021.

    https://bioxfel.org/resources/1965

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

    BioXFEL Publications 12 Feb 2021 Contributor(s): Nadia Zatsepin, Derek Mendez, Petra Fromme, Richard Kirian

    http://dx.doi.org/10.1016/j.bpj.2020.11.1006 journal-article Grant, T.D. et al., 2021.

    https://bioxfel.org/resources/1975

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

    BioXFEL Publications 21 Oct 2021 Contributor(s): Michael Thompson, 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).

    https://bioxfel.org/resources/2105

55. Macromolecular phasing using diffraction from multiple crystal forms

    BioXFEL Publications 8 Dec 2020 Contributor(s): Henry Chapman

    http://dx.doi.org/10.1107/s2053273320013650 A phasing algorithm for macromolecular crystallography is proposed that utilizes diffraction data from multiple crystal forms – crystals of the same molecule with different unit-cell packings (different unit-cell parameters or space-group symmetries). The approach is based on the method of iterated…

    https://bioxfel.org/resources/1967

56. The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

    BioXFEL Publications 23 Apr 2021 Contributor(s): Lois Pollack

    http://dx.doi.org/10.1126/sciadv.abf6106 Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental…

    https://bioxfel.org/resources/2013

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

    BioXFEL Publications 24 Nov 2021 Contributor(s): 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 promiscuous enzyme that catalyzes two essential…

    https://bioxfel.org/resources/2107

58. Polo: an open-source graphical user interface for crystallization screening

    BioXFEL Publications 19 Feb 2021 Contributor(s): Ethan T Holleman, Sarah EJ Bowman

    http://dx.doi.org/10.1107/s1600576721000108 Polo is a Python-based graphical user interface designed to streamline viewing and analysis of images to monitor crystal growth, with a specific target to enable users of the High-Throughput Crystallization Screening Center at Hauptman-Woodward Medical Research Institute (HWI) to…

    https://bioxfel.org/resources/1986

59. State of the structure address on MET receptor activation by HGF

    BioXFEL Publications 17 Apr 2021 Contributor(s): James Fraser

    http://dx.doi.org/10.1042/bst20200394 The MET receptor tyrosine kinase (RTK) and its cognate ligand hepatocyte growth factor (HGF) comprise a signaling axis essential for development, wound healing and tissue homeostasis. Aberrant HGF/MET signaling is a driver of many cancers and contributes to drug resistance to several approved therapeutics…

    https://bioxfel.org/resources/2136

60. C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening

    BioXFEL Publications 26 Jan 2021 Contributor(s): Henry Chapman

    http://dx.doi.org/10.1107/s2059798320016071 The unique crystallization properties of the antenna protein C-phycocyanin (C-PC) from the thermophilic cyanobacterium Thermosynechococcus elongatus are reported and discussed. C-PC crystallizes in hundreds of significantly different conditions within a broad pH range and in the presence of a wide variety…

    https://bioxfel.org/resources/1968

61. The three-dimensional structure of Drosophila melanogaster (6–4) photolyase at room temperature

    BioXFEL Publications 29 Jul 2021 Contributor(s): suraj pandey, Emina Stojkovic, Marius Schmidt

    http://dx.doi.org/10.1107/s2059798321005830 (6–4) photolyases are flavoproteins that belong to the photolyase/cryptochrome family. Their function is to repair DNA lesions using visible light. Here, crystal structures of Drosophila melanogaster (6–4) photolyase [Dm(6–4)photolyase] at room and cryogenic temperatures are reported. The…

    https://bioxfel.org/resources/2069

62. Solution structure(s) of trinucleosomes from contrast variation SAXS

    BioXFEL Publications 12 Apr 2021 Contributor(s): Lois Pollack

    http://dx.doi.org/10.1093/nar/gkab290 Abstract Nucleosomes in all eukaryotic cells are organized into higher order structures that facilitate genome compaction. Visualizing these organized structures is an important step in understanding how genomic DNA is efficiently stored yet remains accessible to information-processing machinery.…

    https://bioxfel.org/resources/2014

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

    BioXFEL Publications 22 Mar 2021 Contributor(s): Chufeng Li, suraj pandey, Mark S. Hunter, Uwe Weierstall, Nadia Zatsepin, John Spence, Marius Schmidt, 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 femtosecond (fs) crystallography using the Linac…

    https://bioxfel.org/resources/1988

64. The XBI BioLab for life science experiments at the European XFEL

    BioXFEL Publications 2 Dec 2020 Contributor(s): Petra Fromme, Jozef Uličný

    http://dx.doi.org/10.1107/s1600576720013989 The science of X-ray free-electron lasers (XFELs) critically depends on the performance of the X-ray laser and on the quality of the samples placed into the X-ray beam. The stability of biological samples is limited and key biomolecular transformations occur on short timescales. Experiments in biology…

    https://bioxfel.org/resources/1977

65. A capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screening

    BioXFEL Publications 14 Jun 2021 Contributor(s): Shuo Sui, Sarah Perry

    http://dx.doi.org/10.1107/s1600576721004155 A novel capillary-based microfluidic strategy to accelerate the process of small-molecule-compound screening by room-temperature X-ray crystallography using protein crystals is reported. The ultra-thin microfluidic devices are composed of a UV-curable polymer, patterned by cleanroom photolithography, and…

    https://bioxfel.org/resources/2021

66. Synchronous RNA conformational changes trigger ordered phase transitions in crystals

    BioXFEL Publications 19 Mar 2021 Contributor(s): Chelsie E Conrad, Max Oliver Wiedorn, Chufeng Li, Mark S. Hunter, Nadia Zatsepin, suraj pandey, Marius Schmidt, John Spence, Henry Chapman

    http://dx.doi.org/10.1038/s41467-021-21838-5 AbstractTime-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed…

    https://bioxfel.org/resources/1966

67. X-ray-Based Techniques to Study the Nano–Bio Interface

    BioXFEL Publications 2 Mar 2021 Contributor(s): Henry Chapman, Marius Schmidt

    http://dx.doi.org/10.1021/acsnano.0c09563 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Sanchez-Cano, C. et al., 2021.

    https://bioxfel.org/resources/1995

68. Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein

    BioXFEL Publications 4 Aug 2021 Contributor(s): Hasan Demirci

    http://dx.doi.org/10.1038/s41598-021-95236-8 AbstractOligomerization of Pr55Gag is a critical step of the late stage of the HIV life cycle. It has been known that the binding of IP6, an abundant endogenous cyclitol molecule at the MA domain, has been linked to the oligomerization of Pr55Gag. However, the exact binding site of IP6 on MA remains…

    https://bioxfel.org/resources/2074

69. Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

    BioXFEL Publications 8 Sep 2021 Contributor(s): suraj pandey, George Douglas Calvey, Andrea Katz, Tek Narsingh Malla, Faisal Hammad Mekky Koua, Ishwor Poudyal, Jay-How Yang, Kara Zielinski, Matthias Frank, Rebecca Jeanne Jernigan, Mitchell Miller, Garrett Charles Nelson, Abbas Ourmazd, John Spence, Peter Schwander, Henry Chapman, Petra Fromme, George Phillips, Lois Pollack, Marius Schmidt

    http://dx.doi.org/10.1107/s2052252521008125 Here, we illustrate what happens inside the catalytic cleft of an enzyme when substrate or ligand binds on single-millisecond timescales. The initial phase of the enzymatic cycle is observed with near-atomic resolution using the most advanced X-ray source currently available: the European XFEL (EuXFEL).…

    https://bioxfel.org/resources/2070

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

    BioXFEL Publications 20 Dec 2021 Contributor(s): Sabine Botha, Gihan Kaushylal Ketawala, Brandon Hayes, Christopher Kupitz, 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 part of this research has been drug repurposing;…

    https://bioxfel.org/resources/2109

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

    BioXFEL Publications 4 Feb 2021 Contributor(s): James Fraser

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

    https://bioxfel.org/resources/1972

72. A SAXS-based approach to rationally evaluate radical scavengers – toward eliminating radiation damage in solution and crystallographic studies

    BioXFEL Publications 10 Aug 2021 Contributor(s): Edward Snell

    http://dx.doi.org/10.1107/s1600577521004045 X-ray-based techniques are a powerful tool in structural biology but the radiation-induced chemistry that results can be detrimental and may mask an accurate structural understanding. In the crystallographic case, cryocooling has been employed as a successful mitigation strategy but also has its…

    https://bioxfel.org/resources/2068

73. A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography

    BioXFEL Publications 25 Sep 2023 Contributor(s): Kevin Gu, Megan Shelby, Sankar Raju Narayanasamy, Sabine Botha, Christopher Kupitz, Matthew Coleman, Matthias Frank

    http://dx.doi.org/10.1107/s2059798323007027 Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and structure determination. A crucial need to continue…

    https://bioxfel.org/resources/2195

74. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

    BioXFEL Publications 14 Apr 2021 Contributor(s): Iris Diane Young, James Holton, Michael Thompson, James Fraser, Ron Morganti

    http://dx.doi.org/10.1126/sciadv.abf8711 The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate–ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we…

    https://bioxfel.org/resources/2046

75. Biological Networks across Scales—The Theoretical and Empirical Foundations for Time-Varying Complex Networks that Connect Structure and Function across Levels of Biological Organization

    BioXFEL Publications 21 May 2021 Contributor(s): Edward Snell

    http://dx.doi.org/10.1093/icb/icab069 Abstract Many biological systems across scales of size and complexity exhibit a time-varying complex network structure that emerges and self-organizes as a result of interactions with the environment. Network interactions optimize some intrinsic cost functions that are unknown and involve for…

    https://bioxfel.org/resources/2133

76. 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

    BioXFEL Publications 16 Dec 2021 Contributor(s): Brenda Hogue

    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 hemorrhage. Serine protease coagulation pathways…

    https://bioxfel.org/resources/2130