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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

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

26 Nov 2021 | BioXFEL Publications | Contributor(s): K. Murray, C. Chambers, D. Chen, Z. Feng, J. Fraser, Y. Ito, Y. Lan, S. Mendez, M. Medina Peregrina, H. Rasiwala, L. Richez, N. Roy, R. Simpson, J. Dilling, W. Fairbank, A.A. Kwiatkowski, T. Brunner

http://dx.doi.org/10.1016/j.ijms.2021.116763 journal-article Murray, K., 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). …

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 …

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

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

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

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

08 Sep 2021 | BioXFEL Publications | Contributor(s): Suraj Pandey, George Douglas Calvey, Andrea Katz, Tek Narsingh Malla, Faisal Hammad Mekky Koua, Jose M. Martin-Garcia, Ishwor Poudyal, Jay-How Yang, Mohammad Vakili, Oleksandr Yefanov, Kara Zielinski, Sasa Bajt, Salah Awel, Katarina Doerner, Matthias Frank, Luca Gelisio, Rebecca Jeanne Jernigan, Henry Kirkwood, Marco Kloos, Jayanath Koliyadu, Valerio Mariani, Mitchell Miller, Grant Mills, Garrett Charles Nelson, Jose L. Olmos, Alireza Sadri, Tokushi Sato, Alexandra Tolstikova, Weijun Xu, Abbas Ourmazd, John Spence, Peter Schwander, Anton Barty, Henry Chapman, Petra Fromme, Adrian P. Mancuso, George Phillips, Richard Bean, Lois Pollack, Marius Schmidt

http://dx.doi.org/10.1107/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 …

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

19 Aug 2021 | BioXFEL Publications | Contributor(s): Terra Sztain, Surl-Hee Ahn, Anthony T. Bogetti, Lorenzo Casalino, Jory A. Goldsmith, Evan Seitz, Ryan S. McCool, Fiona L. Kearns, Francisco Acosta-Reyes, Suvrajit Maji, Ghoncheh Mashayekhi, J. Andrew McCammon, Abbas Ourmazd, Joachim Frank, Jason S. McLellan, Lillian T. Chong, Rommie E. Amaro

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. A glycan gate controls opening of the SARS-CoV-2 spike protein. Nature Chemistry. Available at: http://dx.doi.org/10.1038/s41557-021-00758-3. Terra Sztain and …

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

16 Aug 2021 | BioXFEL Publications | Contributor(s): Serdar Durdagi, Çağdaş Dağ, Berna Dogan, Merve Yigin, Timucin Avsar, Cengizhan Buyukdag, Ismail Erol, Fatma Betul Ertem, Seyma Calis, Gunseli Yildirim, Muge D. Orhan, Omur Guven, Busecan Aksoydan, Ebru Destan, Kader Sahin, Sabri O. Besler, Lalehan Oktay, Alaleh Shafiei, Ilayda Tolu, Esra Ayan, Busra Yuksel, Ayse B. Peksen, Oktay Gocenler, Ali D. Yucel, Ozgur Can, Serena Ozabrahamyan, Alpsu Olkan, Ece Erdemoglu, Fulya Aksit, Gokhan Tanisali, Oleksandr M. Yefanov, Anton Barty, Alexandra Tolstikova, Gihan Kaushylal Ketawala, Sabine Botha, E. Han Dao, Brandon Hayes, Mengning Liang, Matthew H. Seaberg, Mark S. Hunter, Alex Batyuk, Valerio Mariani, Zhen Su, Frederic Poitevin, Chun Hong Yoon, Christopher Kupitz, Raymond G. Sierra, Edward Snell, Hasan Demirci

http://dx.doi.org/10.1016/j.str.2021.07.007 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Durdagi, S. et al., 2021. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing. Structure. …

Surface coatings for microfluidic biomedical devices

16 Aug 2021 | BioXFEL Publications | Contributor(s): M. Sonker, B.G. Abdallah, A. Ros

http://dx.doi.org/10.1016/b978-0-12-819971-8.00003-2 book-chapter Sonker, M., Abdallah, B.G. & Ros, A., 2021. Surface coatings for microfluidic biomedical devices. Microfluidic Devices for Biomedical Applications, pp.79–123. Available at: http://dx.doi.org/10.1016/b978-0-12-819971-8.00003-2. …

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

10 Aug 2021 | BioXFEL Publications | Contributor(s): Jonathan K. Williams, Baifan Wang, Andrew Sam, Cody L. Hoop, David Case, Jean Baum

http://dx.doi.org/10.1002/prot.26208 journal-article Williams, J.K. et al., 2021. Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV ‐2 spike protein receptor‐binding domain. Proteins: Structure, Function, …

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

10 Aug 2021 | BioXFEL Publications | Contributor(s): Timothy R. Stachowski, Mary E. Snell, 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 …

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

04 Aug 2021 | BioXFEL Publications | Contributor(s): Halilibrahim Ciftci, Hiroshi Tateishi, Kotaro Koiwai, Ryoko Koga, Kensaku Anraku, Kazuaki Monde, Çağdaş Dağ, Ebru Destan, Busra Yuksel, Esra Ayan, Gunseli Yildirim, Merve Yigin, F. Betul Ertem, Alaleh Shafiei, Omur Guven, Sabri O. Besler, Raymond G. Sierra, Chun Hong Yoon, Zhen Su, Mengling Liang, Burcin Acar, Turkan Haliloglu, Masami Otsuka, Fumiaki Yumoto, Mikako Fujita, Toshiya Senda, 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. …

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

29 Jul 2021 | BioXFEL Publications | Contributor(s): Andrea Cellini, Weixiao Yuan Wahlgren, Léocadie Henry, Suraj Pandey, Swagatha Ghosh, Leticia Castillon, Elin Claesson, Heikki Takala, Joachim Kübel, Amke Nimmrich, Valentyna Kuznetsova, Eriko Nango, So Iwata, Shigeki Owada, Emina Stojkovic, Marius Schmidt, Janne A. Ihalainen, Sebastian Westenhoff

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 …

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

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

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

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

14 Jun 2021 | BioXFEL Publications | Contributor(s): Shuo Sui, Anne Mulichak, Raviraj Kulathila, Joshua McGee, Danny Filiatreault, Sarthak Saha, Aina Cohen, Jinhu Song, Holly Hung, Jonathan Selway, Christina Kirby, Om K. Shrestha, Wilhelm Weihofen, Michelle Fodor, Mei Xu, Rajiv Chopra, 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 …

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

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

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

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

21 May 2021 | BioXFEL Publications | Contributor(s): Paul Bogdan, Gustavo Caetano-Anollés, Anna Jolles, Hyunju Kim, James Morris, Cheryl A Murphy, Catherine Royer, Edward Snell, Adam Steinbrenner, Nicholas Strausfeld

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 …

Applications of microfluidic mixers for time-resolved SAXS and crystallography experiments

11 May 2021 | BioXFEL Publications | Contributor(s): Kara Zielinski, Lois Pollack

http://dx.doi.org/10.1107/s0108767320099663 journal-article Zielinski, K. & Pollack, L., 2020. Applications of microfluidic mixers for time-resolved SAXS and crystallography experiments. Acta Crystallographica Section A Foundations and Advances, 76(a1), pp.a33–a33. Available at: …

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

04 May 2021 | BioXFEL Publications | Contributor(s): Tek Narsingh Malla, Suraj Pandey, Luis Aldama, Dennisse Feliz, Moraima Noda, Ishwor Poudyal, George Phillips, Emina Stojkovic, Marius Schmidt

http://dx.doi.org/10.1101/2021.05.02.442358 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, …

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

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

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 …

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

22 Apr 2021 | BioXFEL Publications | 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 …

State of the structure address on MET receptor activation by HGF

17 Apr 2021 | BioXFEL Publications | Contributor(s): Edmond M. Linossi, Gabriella O. Estevam, Masaya Oshima, James Fraser, Eric A. Collisson, Natalia Jura

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 …

ORACLE reveals a bright future to fight bacteria

15 Apr 2021 | BioXFEL Publications | Contributor(s): Willow Coyote-Maestas, 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). ORACLE …

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

14 Apr 2021 | BioXFEL Publications | Contributor(s): Marion Schuller, Galen J. Correy, Stefan Gahbauer, Daren Fearon, Taiasean Wu, Roberto Efraín Díaz, Iris Diane Young, Luan Carvalho Martins, Dominique H. Smith, Ursula Schulze-Gahmen, Tristan W. Owens, Ishan Deshpande, Gregory E. Merz, Aye C. Thwin, Justin T. Biel, Jessica K. Peters, Michelle Moritz, Nadia Herrera, Huong T. Kratochvil, Anthony Aimon, James M. Bennett, Jose Brandao Neto, Aina E. Cohen, Alexandre Dias, Alice Douangamath, Louise Dunnett, Oleg Fedorov, Matteo P. Ferla, Martin R. Fuchs, Tyler J. Gorrie-Stone, James Holton, Michael G. Johnson, Tobias Krojer, George Meigs, Ailsa J. Powell, Johannes Gregor Matthias Rack, Victor L. Rangel, Silvia Russi, Rachael E. Skyner, Clyde A. Smith, Alexei S. Soares, Jennifer L. Wierman, Kang Zhu, Peter O’Brien, Natalia Jura, Alan Ashworth, John J. Irwin, Michael Thompson, Jason E. Gestwicki, Frank Von Delft, Brian K. Shoichet, James Fraser, Ivan Ahel, 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 …

Solution structure(s) of trinucleosomes from contrast variation SAXS

12 Apr 2021 | BioXFEL Publications | Contributor(s): Alexander W Mauney, Uma M Muthurajan, Karolin Luger, 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 …

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

08 Apr 2021 | BioXFEL Publications | Contributor(s): E. H. Snell, J. R. Helliwell

http://dx.doi.org/10.1080/0889311x.2021.1900833 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Snell, E.H. & Helliwell, J.R., 2021. Microgravity as an environment for macromolecular crystallization – an outlook in the era of space stations and commercial space flight. …

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

05 Apr 2021 | BioXFEL Publications | Contributor(s): Mian Yang, Jorvani Cruz Villarreal, Nethmi Ariyasinghe, Rory Kruithoff, Robert Ros, Alexandra Ros

http://dx.doi.org/10.1021/acs.analchem.0c04112 journal-article Yang, M. et al., 2021. Quantitative Approach for Protein Analysis in Small Cell Ensembles by an Integrated Microfluidic Chip with MALDI Mass Spectrometry. Analytical Chemistry, 93(15), pp.6053–6061. Available at: …

SAXS structure of homodimeric oxyHemoglobin III from bivalve Lucina pectinata

01 Apr 2021 | BioXFEL Publications | Contributor(s): Darya Marchany‐Rivera, Rafael A. Estremera‐Andújar, Carlos Nieves‐Marrero, Carlos R. Ruiz‐Martínez, William Bauer, Juan López‐Garriga

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. SAXS structure of homodimeric oxyHemoglobin III from bivalve Lucina pectinata. Biopolymers. …

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

23 Mar 2021 | BioXFEL Publications | Contributor(s): Melissa Carrillo, Suraj Pandey, Juan Sanchez, Moraima Noda, Ishwor Poudyal, Luis Aldama, Tek Narsingh Malla, Elin Claesson, Weixiao Yuan Wahlgren, Denisse Feliz, Vukica Šrajer, Michał Maj, Leticia Castillon, So Iwata, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, Kensuke Tono, Shigeki Owada, Sebastian Westenhoff, Emina Stojkovic, Marius Schmidt

http://dx.doi.org/10.1016/j.str.2021.03.004 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Carrillo, M. et al., 2021. High-resolution crystal structures of transient intermediates in the phytochrome photocycle. Structure. Available at: http://dx.doi.org/10.1016/j.str.2021.03.004. …

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

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

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

Synchronous RNA conformational changes trigger ordered phase transitions in crystals

19 Mar 2021 | BioXFEL Publications | Contributor(s): Saminathan Ramakrishnan, Jason R. Stagno, Chelsie E Conrad, Jienyu Ding, Ping Yu, Yuba R. Bhandari, Yun-Tzai Lee, Gary Pauly, Oleksandr Yefanov, Max Oliver Wiedorn, Juraj Knoska, Dominik Oberthür, Thomas A. White, Anton Barty, Valerio Mariani, Chufeng Li, Wolfgang Brehm, William F. Heinz, Valentin Magidson, Stephen Lockett, Mark S. Hunter, Sébastien Boutet, Nadia Zatsepin, Xiaobing Zuo, Thomas D. Grant, Suraj Pandey, Marius Schmidt, John Spence, Henry Chapman, Yun-Xing Wang

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 …

Classical molecular dynamics

11 Mar 2021 | BioXFEL Publications | Contributor(s): Charles L. Brooks, David Case, Steve Plimpton, Benoît Roux, David Van Der Spoel, Emad Tajkhorshid

http://dx.doi.org/10.1063/5.0045455 journal-article Brooks, C.L. et al., 2021. Classical molecular dynamics. The Journal of Chemical Physics, 154(10), p.100401. Available at: http://dx.doi.org/10.1063/5.0045455. Charles L. Brooks and David A. Case and Steve Plimpton and Benoît Roux and David …

A science education model for large collaborative centers

05 Mar 2021 | BioXFEL Publications | Contributor(s): William J. Bauer, 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. A science education model for large collaborative centers. Structural Dynamics, 8(2), p.020402. Available at: http://dx.doi.org/10.1063/4.0000081. William J. …

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

02 Mar 2021 | BioXFEL Publications | Contributor(s): Carlos Sanchez-Cano, Ramon A. Alvarez-Puebla, John M. Abendroth, Tobias Beck, Robert Blick, Yuan Cao, Frank Caruso, Indranath Chakraborty, Henry Chapman, Chunying Chen, Bruce E. Cohen, Andre L. C. Conceição, David P. Cormode, Daxiang Cui, Kenneth A. Dawson, Gerald Falkenberg, Chunhai Fan, Neus Feliu, Mingyuan Gao, Elisabetta Gargioni, Claus-C. Glüer, Florian Grüner, Moustapha Hassan, Yong Hu, Yalan Huang, Samuel Huber, Nils Huse, Yanan Kang, Ali Khademhosseini, Thomas F. Keller, Christian Körnig, Nicholas A. Kotov, Dorota Koziej, Xing-Jie Liang, Beibei Liu, Sijin Liu, Yang Liu, Ziyao Liu, Luis M. Liz-Marzán, Xiaowei Ma, Andres Machicote, Wolfgang Maison, Adrian P. Mancuso, Saad Megahed, Bert Nickel, Ferdinand Otto, Cristina Palencia, Sakura Pascarelli, Arwen Pearson, Oula Peñate-Medina, Bing Qi, Joachim Rädler, Joseph J. Richardson, Axel Rosenhahn, Kai Rothkamm, Michael Rübhausen, Milan K. Sanyal, Raymond E. Schaak, Heinz-Peter Schlemmer, Marius Schmidt, Oliver Schmutzler, Theo Schotten, Florian Schulz, A. K. Sood, Kathryn M. Spiers, Theresa Staufer, Dominik M. Stemer, Andreas Stierle, Xing Sun, Gohar Tsakanova, Paul S. Weiss, Horst Weller, Fabian Westermeier, Ming Xu, Huijie Yan, Yuan Zeng, Ying Zhao, Yuliang Zhao, Dingcheng Zhu, Ying Zhu, Wolfgang J. Parak

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. X-ray-Based Techniques to Study the Nano–Bio Interface. ACS Nano, 15(3), pp.3754–3807. Available at: http://dx.doi.org/10.1021/acsnano.0c09563. Carlos …

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

01 Mar 2021 | BioXFEL Publications | Contributor(s): Thomas D. Grant

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. Reply to: Limitations of the iterative electron density reconstruction algorithm from solution scattering data. Nature Methods, 18(3), pp.246–248. Available at: …

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

26 Feb 2021 | BioXFEL Publications | Contributor(s): Laura Lemel, Katarzyna Nieścierowicz, M. Dolores García-Fernández, Leonardo Darré, Thierry Durroux, Marta Busnelli, Mylène Pezet, Fabrice Rébeillé, Juliette Jouhet, Bernard Mouillac, Carmen Domene, Bice Chini, Vadim Cherezov, Christophe J. Moreau

http://dx.doi.org/10.1016/j.jlr.2021.100059 journal-article Lemel, L. et al., 2021. The ligand-bound state of a G protein-coupled receptor stabilizes the interaction of functional cholesterol molecules. Journal of Lipid Research, 62, p.100059. Available at: …

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

22 Feb 2021 | BioXFEL Publications | Contributor(s): J.P.J. Chen, K.E. Schmidt, J.C.H. Spence, R.A. Kirian

http://dx.doi.org/10.1016/j.ultramic.2021.113234 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Chen, J.P.J. et al., 2021. A new solution to the curved Ewald sphere problem for 3D image reconstruction in electron microscopy. Ultramicroscopy, p.113234. Available at: …

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

21 Feb 2021 | BioXFEL Publications | Contributor(s): Halilibrahim Ciftci, Hiroshi Tateishi, Kotaro Koiwai, Ryoko Koga, Kensaku Anraku, Kazuaki Monde, Çağdaş Dağ, Ebru Destan, Busra Yuksel, Esra Ayan, Gunseli Yildirim, Merve Yigin, F. Betul Ertem, Alaleh Shafiei, Omur Guven, Sabri O. Besler, Raymond G. Sierra, Chun Hong Yoon, Zhen Su, Mengling Liang, Burcin Acar, Turkan Haliloglu, Masami Otsuka, Fumiaki Yumoto, Mikako Fujita, Toshiya Senda, Hasan Demirci

http://dx.doi.org/10.1101/2021.02.21.432153 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 …

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

19 Feb 2021 | BioXFEL Publications | Contributor(s): Ethan T Holleman, Erica Duguid, Lisa J. Keefe, 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 …

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

18 Feb 2021 | BioXFEL Publications | Contributor(s): Qiuyun Guo, Jordan R. Yaron, John W. Wallen, Kyle F. Browder, Ryan Boyd, Tien L. Olson, Michelle Burgin, Peaches Ulrich, Emily Aliskevich, Lauren N. Schutz, Petra Fromme, Liqiang Zhang, Alexandra R. Lucas

http://dx.doi.org/10.3389/fcvm.2021.633212 Diffuse alveolar hemorrhage (DAH) is one of the most serious clinical complications of systemic lupus erythematosus (SLE). 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% …

Selecting XFEL single-particle snapshots by geometric machine learning

18 Feb 2021 | BioXFEL Publications | Contributor(s): Eduardo R. Cruz-Chú, 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. Selecting XFEL single-particle snapshots by geometric machine learning. Structural Dynamics, 8(1), p.014701. Available at: http://dx.doi.org/10.1063/4.0000060. Eduardo …

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

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

http://dx.doi.org/10.1016/j.bpj.2020.11.1995 journal-article Chen, Y.-L. et al., 2021. Breaking the Boundary between Solution X-Ray Scattering and Molecular Dynamics Simulations of Structured Nucleic Acids. Biophysical Journal, 120(3), p.315a. Available at: …

Molecular Dynamics Simulations Unravel the Mysteries of Hemoglobin Diseases

12 Feb 2021 | BioXFEL Publications | Contributor(s): Premila P. Samuel, David Case

http://dx.doi.org/10.1016/j.bpj.2020.11.1905 journal-article Samuel, P.P. & Case, D.A., 2021. Molecular Dynamics Simulations Unravel the Mysteries of Hemoglobin Diseases. Biophysical Journal, 120(3), p.298a. Available at: http://dx.doi.org/10.1016/j.bpj.2020.11.1905. Premila P. Samuel and David …

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

12 Feb 2021 | BioXFEL Publications | Contributor(s): P. Lourdu Xavier, Kartik Ayyer, Oleksandr Yefanov, Luca Gelisio, Johan Bielecki, Amit K. Samanta, Saša Bajt, Ruojie Sha, David Bushnell, Roger Kornberg, Yevheniy Ovcharenko, Jochen Kuepper, Michael Meyer, Nadrian C. Seeman, Henry Chapman

http://dx.doi.org/10.1016/j.bpj.2020.11.1697 journal-article Xavier, P.L. et al., 2021. Femtosecond Single-Particle Diffractive Imaging of 3D DNA-Origami Molecular Scaffolds with XFEL Pulses. Biophysical Journal, 120(3), p.265a. Available at: http://dx.doi.org/10.1016/j.bpj.2020.11.1697. P. …

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

12 Feb 2021 | BioXFEL Publications | Contributor(s): Thomas D. Grant, Suchithranga M.D.C. Perera, Leslie A. Salas-Estrada, Andrey V. Struts, Udeep Chawla, Steven D.E. Fried, Nipuna Weerasinghe, Kostantinos Karpos, Domingo Meza, Nadia Zatsepin, Alan Grossfield, Derek Mendez, Petra Fromme, Richard Kirian, Michael F. Brown

http://dx.doi.org/10.1016/j.bpj.2020.11.1006 journal-article Grant, T.D. et al., 2021. Ultrafast Membrane Protein Dynamics Revealed by X-Ray Scattering with a Femtosecond Free-Electron Laser. Biophysical Journal, 120(3), p.133a. Available at: http://dx.doi.org/10.1016/j.bpj.2020.11.1006. Thomas …

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

12 Feb 2021 | 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.2020.11.1003 journal-article Menon, C.S.K. et al., 2021. Functional Expansion of G-Protein-Coupled Receptor Shown by Time-Resolved X-Ray Scattering. Biophysical Journal, 120(3), p.132a. Available at: http://dx.doi.org/10.1016/j.bpj.2020.11.1003. C. Swathi K. Menon …

Sodium Binding in Cysteinyl Leukotriene G Protein-Coupled Receptors

12 Feb 2021 | BioXFEL Publications | Contributor(s): Viktoriia Shaulskaia, Aleksandra Luginina, Polina Khorn, Anastasiia Gusach, Olga Sukhacheva, Ekaterina Smirnova, Valentin Borshchevskiy, Alexey Mishin, Vadim Cherezov

http://dx.doi.org/10.1016/j.bpj.2020.11.987 journal-article Shaulskaia, V. et al., 2021. Sodium Binding in Cysteinyl Leukotriene G Protein-Coupled Receptors. Biophysical Journal, 120(3), p.129a. Available at: http://dx.doi.org/10.1016/j.bpj.2020.11.987. Viktoriia Shaulskaia and Aleksandra …

Mediator structure and conformation change

10 Feb 2021 | BioXFEL Publications | Contributor(s): Heqiao Zhang, Dong-Hua Chen, Rayees Mattoo, David Bushnell, Yannan Wang, Chao Yuan, Lin Wang, Chunnian Wang, Ralph E. Davis, Yan Nie, Roger Kornberg

http://dx.doi.org/10.1016/j.molcel.2021.01.022 journal-article Heqiao Zhang and Dong-Hua Chen and Rayees U.H. Mattoo and David A. Bushnell and Yannan Wang and Chao Yuan and Lin Wang and Chunnian Wang and Ralph E. Davis and Yan Nie and Roger D. Kornberg

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

05 Feb 2021 | BioXFEL Publications | Contributor(s): L.E. Malin, W.S. Graves, M. Holl, J.C.H. Spence, E.A. Nanni, R.K. Li, X. Shen, S. Weathersby

http://dx.doi.org/10.1016/j.ultramic.2021.113211 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Malin, L.E. et al., 2021. Quantitative agreement between dynamical rocking curves in ultrafast electron diffraction for x-ray lasers. Ultramicroscopy, 223, p.113211. Available at: …

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

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

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

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

26 Jan 2021 | BioXFEL Publications | Contributor(s): Iosifina Sarrou, Christian G. Feiler, Sven Falke, Nolan Peard, Oleksandr Yefanov, 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 …

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

14 Jan 2021 | BioXFEL Publications | Contributor(s): Jonathan K. Williams, Baifan Wang, Andrew Sam, Cody L. Hoop, David Case, Jean Baum

http://dx.doi.org/10.1101/2021.01.08.425965 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 …

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

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

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

Using X-ray Diffraction Techniques for Biomimetic Drug Development, Formulation, and Polymorphic Characterization

30 Dec 2020 | BioXFEL Publications | Contributor(s): Israel Rodriguez, Ritika Gautam, Arthur Tinoco

http://dx.doi.org/10.3390/biomimetics6010001 Drug development is a decades-long, multibillion dollar investment that often limits itself. To decrease the time to drug approval, efforts are focused on drug targets and drug formulation for optimal biocompatibility and efficacy. X-ray structural …