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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 …

Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles

23 Dec 2020 | BioXFEL Publications | Contributor(s): Filip Yabukarski, Justin T. Biel, Margaux M. Pinney, Tzanko Doukov, Alexander S. Powers, James Fraser, Daniel Herschlag

http://dx.doi.org/10.1073/pnas.2011350117 How enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes …

Genetic interaction mapping informs integrative structure determination of protein complexes

10 Dec 2020 | BioXFEL Publications | Contributor(s): Hannes Braberg, Ignacia Echeverria, Stefan Bohn, Peter Cimermancic, Anthony Shiver, Richard Alexander, Jiewei Xu, Michael Shales, Raghuvar Dronamraju, Shuangying Jiang, Gajendradhar Dwivedi, Derek Bogdanoff, Kaitlin K. Chaung, Ruth Hüttenhain, Shuyi Wang, David Mavor, Riccardo Pellarin, Dina Schneidman, Joel S. Bader, James Fraser, John Morris, James E. Haber, Brian D. Strahl, Carol A. Gross, Junbiao Dai, Jef D. Boeke, Andrej Sali, Nevan J. Krogan

http://dx.doi.org/10.1126/science.aaz4910 Determining structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo measurements of genetic interactions. We construct phenotypic profiles for …

Friction measurements of model saliva-wine solutions between polydimethylsiloxane surfaces

09 Dec 2020 | BioXFEL Publications | Contributor(s): Ryan S. Edmonds, Tanner J. Finney, Michael R. Bull, Aude A. Watrelot, Tonya L. Kuhl

http://dx.doi.org/10.1016/j.foodhyd.2020.106522 journal-article Edmonds, R.S. et al., 2021. Friction measurements of model saliva-wine solutions between polydimethylsiloxane surfaces. Food Hydrocolloids, 113, p.106522. Available at: http://dx.doi.org/10.1016/j.foodhyd.2020.106522. Ryan S. …

8th BioXFEL International Conference

09 Dec 2020 | Downloads

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Macromolecular phasing using diffraction from multiple crystal forms

08 Dec 2020 | BioXFEL Publications | Contributor(s): Markus Metz, Romain D. Arnal, Wolfgang Brehm, Henry Chapman, Andrew J. Morgan, Rick P. Millane

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 XBI BioLab for life science experiments at the European XFEL

02 Dec 2020 | BioXFEL Publications | Contributor(s): Huijong Han, Ekaterina Round, Robin Schubert, Yasmin Gül, Jana Makroczyová, Domingo Meza, Philipp Heuser, Martin Aepfelbacher, Imrich Barák, Christian Betzel, Petra Fromme, Inari Kursula, Poul Nissen, Elena Tereschenko, Joachim Schulz, Charlotte Uetrecht, Jozef Uličný, Matthias Wilmanns, Janos Hajdu, Victor S. Lamzin, Kristina Lorenzen

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 …

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

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

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

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

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

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

3D diffractive imaging of nanoparticle ensembles using an x-ray laser

20 Nov 2020 | BioXFEL Publications | Contributor(s): Kartik Ayyer, P. Lourdu Xavier, Johan Bielecki, Zhou Shen, Benedikt J. Daurer, Amit K. Samanta, Salah Awel, Richard Bean, Anton Barty, Martin Bergemann, Tomas Ekeberg, Armando D. Estillore, Hans Fangohr, Klaus Giewekemeyer, Mark S. Hunter, Mikhail Karnevskiy, Richard Kirian, Henry Kirkwood, Yoonhee Kim, Jayanath Koliyadu, Holger Lange, Romain Letrun, Jannik Lübke, Thomas Michelat, Andrew J. Morgan, Nils Roth, Tokushi Sato, Marcin Sikorski, Florian Schulz, John Spence, Patrik Vagovic, Tamme Wollweber, Lena Worbs, Oleksandr Yefanov, Yulong Zhuang, Filipe R. N. C. Maia, Daniel A. Horke, Jochen Küpper, N. Duane Loh, Adrian P. Mancuso, Henry Chapman

http://dx.doi.org/10.1364/optica.410851 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Ayyer, K. et al., 2020. 3D diffractive imaging of nanoparticle ensembles using an x-ray laser. Optica, 8(1), p.15. Available at: http://dx.doi.org/10.1364/optica.410851. Kartik Ayyer and P. …

How directed evolution reshapes the energy landscape in an enzyme to boost catalysis

19 Nov 2020 | BioXFEL Publications | Contributor(s): Renee Otten, Ricardo A. P. Pádua, H. Adrian Bunzel, Vy Nguyen, Warintra Pitsawong, MacKenzie Patterson, Shuo Sui, Sarah Perry, Aina E. Cohen, Donald Hilvert, Dorothee Kern

http://dx.doi.org/10.1126/science.abd3623 The advent of biocatalysts designed computationally and optimized by laboratory evolution provides an opportunity to explore molecular strategies for augmenting catalytic function. Applying a suite of NMR, crystallographic, and stopped-flow techniques to an …

Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source

19 Nov 2020 | BioXFEL Publications | Contributor(s): Haoyuan Li, Reza Nazari, Brian Abbey, Roberto Alvarez, Andrew Aquila, Kartik Ayyer, Anton Barty, Peter Berntsen, Johan Bielecki, Alberto Pietrini, Maximilian Bucher, Gabriella Carini, Henry Chapman, Alice Contreras, Benedikt J. Daurer, Hasan Demirci, Leonie Flűckiger, Matthias Frank, Janos Hajdu, Max F. Hantke, Brenda Hogue, Ahmad Hosseinizadeh, Mark S. Hunter, H. Olof Jönsson, Richard Kirian, Ruslan P. Kurta, Duane Loh, Filipe R. N. C. Maia, Adrian P. Mancuso, Andrew J. Morgan, Matthew McFadden, Kerstin Muehlig, Anna Munke, Hemanth Kumar Narayana Reddy, Carl Nettelblad, Abbas Ourmazd, Max Rose, Peter Schwander, M. Marvin Seibert, Jonas A. Sellberg, Raymond G. Sierra, Zhibin Sun, Martin Svenda, Ivan A. Vartanyants, Peter Walter, Daniel Westphal, Garth Williams, P. Lourdu Xavier, Chun Hong Yoon, Sahba Zaare

http://dx.doi.org/10.1038/s41597-020-00745-2 AbstractSingle Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 …

qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps

18 Nov 2020 | BioXFEL Publications | Contributor(s): Blake T. Riley, Stephanie A. Wankowicz, Saulo H. P. Oliveira, Gydo C. P. Zundert, Daniel W. Hogan, James Fraser, Daniel A. Keedy, Henry Bedem

http://dx.doi.org/10.1002/pro.4001 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Riley, B.T. et al., 2020. qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps. Protein …

SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique

17 Nov 2020 | BioXFEL Publications | Contributor(s): Timothy R. Stachowski, Mary E. Snell, Edward Snell

http://dx.doi.org/10.1371/journal.pone.0239702 A significant problem in biological X-ray crystallography is the radiation chemistry caused by the incident X-ray beam. This produces both global and site-specific damage. Site specific damage can misdirect the biological interpretation of the …

Single-femtosecond atomic-resolution observation of a protein traversing a conical intersection

15 Nov 2020 | BioXFEL Publications | Contributor(s): A. Hosseinizadeh, N. Breckwoldt, R. Fung, R. Sepehr, M. Schmidt, P. Schwander, R. Santra, A. Ourmazd

http://dx.doi.org/10.1101/2020.11.13.382218 The structural dynamics of a molecule are determined by the underlying potential energy landscape. Conical intersections are funnels connecting otherwise separate energy surfaces. Posited almost a century ago 1, conical intersections remain the subject of …

Elucidating the Role of Microprocessor Protein DGCR8 in Bending RNA Structures

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

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

Discovery of allosteric binding sites by crystallographic fragment screening

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

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

Methods for Crystallization and Structural Determination of M-T7 Protein from Myxoma Virus

27 Oct 2020 | BioXFEL Publications | Contributor(s): Christopher James Gisriel, Petra Fromme, Jose M. Martin-Garcia

http://dx.doi.org/10.1007/978-1-0716-1012-1_8 book-chapter Gisriel, C., Fromme, P. & Martin-Garcia, J.M., 2020. Methods for Crystallization and Structural Determination of M-T7 Protein from Myxoma Virus. Viruses as Therapeutics, pp.125–162. Available at: …

Molecular-replacement phasing using predicted protein structures from AWSEM-Suite

26 Oct 2020 | BioXFEL Publications | Contributor(s): Shikai Jin, Mitchell Miller, Mingchen Chen, Nicholas P. Schafer, Xingcheng Lin, Xun Chen, George Phillips, Peter G. Wolynes

http://dx.doi.org/10.1107/s2052252520013494 The phase problem in X-ray crystallography arises from the fact that only the intensities, and not the phases, of the diffracting electromagnetic waves are measured directly. Molecular replacement can often estimate the relative phases of reflections …

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

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

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

High intensity x-ray interaction with a model bio-molecule system: double-core-hole states and fragmentation of formamide

15 Oct 2020 | BioXFEL Publications | Contributor(s): D Koulentianos, A E A Fouda, S H Southworth, J D Bozek, J Küpper, R Santra, N V Kryzhevoi, L S Cederbaum, C Bostedt, M Messerschmidt, N Berrah, L Fang, B Murphy, T Osipov, J P Cryan, J Glownia, S Ghimire, P J Ho, B Krässig, D Ray, Y Li, E P Kanter, L Young, G Doumy

http://dx.doi.org/10.1088/1361-6455/abc183 journal-article Koulentianos, D. et al., 2020. High intensity x-ray interaction with a model bio-molecule system: double-core-hole states and fragmentation of formamide. Journal of Physics B: Atomic, Molecular and Optical Physics, 53(24), p.244005. …

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

15 Oct 2020 | 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/s2052252520012798 An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent …

Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase

15 Oct 2020 | BioXFEL Publications | Contributor(s): Ming-Yue Lee, James Geiger, Andrii Ishchenko, Gye Won Han, Anton Barty, Thomas A. White, Cornelius Gati, Alexander Batyuk, Mark S. Hunter, Andrew Aquila, Sébastien Boutet, Uwe Weierstall, Vadim Cherezov, Wei Liu

http://dx.doi.org/10.1107/s2052252520012701 Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has …

Biomechanical Analysis of Retrograde Superior Ramus Screw Fixation Constructs

08 Oct 2020 | BioXFEL Publications | Contributor(s): Justin F. Lucas, Milton L. Chip Routt, Jonathan G. Eastman

http://dx.doi.org/10.1097/bot.0000000000001951 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Justin F. Lucas and Milton L. Chip Routt and Jonathan G. Eastman

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

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

http://dx.doi.org/10.3390/cryst10100886 Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins …

Synthetic group A streptogramin antibiotics that overcome Vat resistance

23 Sep 2020 | BioXFEL Publications | Contributor(s): Qi Li, Jenna Pellegrino, D. John Lee, Arthur A. Tran, Hector Chaires, Ruoxi Wang, Jesslyn E. Park, Kaijie Ji, David Chow, Na Zhang, Axel F. Brilot, Justin T. Biel, Gydo Van Zundert, Kenneth Borrelli, Dean Shinabarger, Cindy Wolfe, Beverly Murray, Matthew P. Jacobson, Estelle Mühle, Olivier Chesneau, James Fraser, Ian B. Seiple

http://dx.doi.org/10.1038/s41586-020-2761-3 journal-article Li, Q. et al., 2020. Synthetic group A streptogramin antibiotics that overcome Vat resistance. Nature, 586(7827), pp.145–150. Available at: http://dx.doi.org/10.1038/s41586-020-2761-3. Qi Li and Jenna Pellegrino and D. John Lee and …

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

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

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

Subthreshold Erosion of an Organic Polymer Induced by Multiple Shots of an X-Ray Free-Electron Laser

22 Sep 2020 | BioXFEL Publications | Contributor(s): T. Burian, J. Chalupský, V. Hájková, M. Toufarová, V. Vorlíček, S. Hau-Riege, J. Krzywinski, J.D. Bozek, C. Bostedt, A.T. Graf, U.F. Jastrow, S. Kreis, R.A. London, M. Messerschmidt, S. Moeller, R. Sobierajski, K. Tiedtke, M. De Grazia, T. Auguste, B. Carré, S. Guizard, H. Merdji, N. Medvedev, L. Juha

http://dx.doi.org/10.1103/physrevapplied.14.034057 journal-article Burian, T. et al., 2020. Subthreshold Erosion of an Organic Polymer Induced by Multiple Shots of an X-Ray Free-Electron Laser. Physical Review Applied, 14(3). Available at: http://dx.doi.org/10.1103/physrevapplied.14.034057. T. …

Characterizing Enzyme Reactions in Microcrystals for Effective Mix-and-Inject Experiments using X-ray Free-Electron Lasers

21 Sep 2020 | BioXFEL Publications | Contributor(s): George Douglas Calvey, Andrea Katz, Kara Zielinski, Boris Dzikovski, Lois Pollack

http://dx.doi.org/10.1021/acs.analchem.0c02569 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Calvey, G.D. et al., 2020. Characterizing Enzyme Reactions in Microcrystals for Effective Mix-and-Inject Experiments using X-ray Free-Electron Lasers. Analytical Chemistry, 92(20), …

Retrieving functional pathways of biomolecules from single-particle snapshots

18 Sep 2020 | BioXFEL Publications | Contributor(s): Ali Dashti, Ghoncheh Mashayekhi, Mrinal Shekhar, Danya Ben Hail, Salah Salah, Peter Schwander, Amedee Des Georges, Abhishek Singharoy, Joachim Frank, Abbas Ourmazd

http://dx.doi.org/10.1038/s41467-020-18403-x Abstract A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining …

High-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle

17 Sep 2020 | 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, Michal 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/10.1101/2020.09.16.298463 AbstractPhytochromes are red/far-red light photoreceptors in bacteria to plants, which elicit a variety of important physiological responses. They display a reversible photocycle between the resting (dark) Pr state and the light activated Pfr state, in …

Segmented flow generator for serial crystallography at the European X-ray free electron laser

10 Sep 2020 | BioXFEL Publications | Contributor(s): Austin Echelmeier, Jorvani Cruz Villarreal, Marc Messerschmidt, Daihyun Kim, Jesse David Coe, Darren Gary Thifault, Sabine Botha, Ana Egatz-Gomez, Sahir Ilyas Gandhi, Gerrit Brehm, Chelsie E Conrad, Debra T. Hansen, Caleb Alexander Madsen, Saša Bajt, J. Domingo Meza-Aguilar, Dominik Oberthür, Max Oliver Wiedorn, Holger Fleckenstein, Derek Mendez, Juraj Knoška, Jose M. Martin-Garcia, Hao Hu, Stella Lisova, Aschkan Allahgholi, Yaroslav Gevorkov, Kartik Ayyer, Steve Aplin, Helen Mary Ginn, Heinz Graafsma, Andrew J. Morgan, Dominic Greiffenberg, Alexander Klujev, Torsten Laurus, Jennifer Poehlsen, Ulrich Trunk, Davide Mezza, Bernd Schmidt, Manuela Kuhn, Raimund Fromme, Jolanta Sztuk-Dambietz, Natascha Raab, Steffen Hauf, Alessandro Silenzi, Thomas Michelat, Chen Xu, Cyril Danilevski, Andrea Parenti, Leonce Mekinda, Britta Weinhausen, Grant Mills, Patrik Vagovic, Yoonhee Kim, Henry Kirkwood, Richard Bean, Johan Bielecki, Stephan Stern, Klaus Giewekemeyer, Adam R. Round, Joachim Schulz, Katerina Dörner, Thomas D. Grant, Valerio Mariani, Anton Barty, Adrian P. Mancuso, Uwe Weierstall, John Spence, Henry Chapman, Nadia Zatsepin, Petra Fromme, Richard Kirian, Alexandra Ros

http://dx.doi.org/10.1038/s41467-020-18156-7 Abstract Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal …

Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing

10 Sep 2020 | BioXFEL Publications | Contributor(s): Serdar Durdagi, Cagdas Dag, Berna Dogan, Merve Yigin, Timucin Avsar, Cengizhan Buyukdag, Ismail Erol, 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/10.1101/2020.09.09.287987 AbstractThe COVID19 pandemic has resulted in 25+ million reported infections and nearly 850.000 deaths. Research to identify effective therapies for COVID19 includes: i) designing a vaccine as future protection; ii) structure-based drug design; and iii) …

Exploring Serum Transferrin Regulation of Nonferric Metal Therapeutic Function and Toxicity

30 Aug 2020 | BioXFEL Publications | Contributor(s): Josué A. Benjamín-Rivera, Andrés E. Cardona-Rivera, Ángel L. Vázquez-Maldonado, Christian Y. Dones-Lassalle, Héctor L. Pabón-Colon, Héctor M. Rodríguez-Rivera, Israel Rodriguez, Jean C. González-Espiet, Jessika Pazol, Jobaniel D. Pérez-Ríos, José F. Catala-Torres, Marielie Carrasquillo Rivera, Michael G. De Jesus-Soto, Nicolle A. Cordero-Virella, Paola M. Cruz-Maldonado, Patricia González-Pagan, Raul Hernández-Ríos, Kavita Gaur, Sergio A. Loza-Rosas, Arthur Tinoco

http://dx.doi.org/10.3390/inorganics8090048 Serum transferrin (sTf) plays a pivotal role in regulating iron biodistribution and homeostasis within the body. The molecular details of sTf Fe(III) binding blood transport, and cellular delivery through transferrin receptor-mediated endocytosis are …

The crystal structure ofAbsH3: A putative flavin adenine dinucleotide‐dependent reductase in the abyssomicin biosynthesis pathway

27 Aug 2020 | BioXFEL Publications | Contributor(s): Jonathan Clinger, Xiachang Wang, Wenlong Cai, Yanyan Zhu, Mitchell Miller, Chang‐Guo Zhan, Steven G. Van Lanen, Jon S. Thorson, George Phillips

http://dx.doi.org/10.1002/prot.25994 journal-article Clinger, J.A. et al., 2020. The crystal structure ofAbsH3: A putative flavin adenine dinucleotide‐dependent reductase in the abyssomicin biosynthesis pathway. Proteins: Structure, Function, and Bioinformatics, 89(1), pp.132–137. Available …

Biophysical characterization dataset of native nicotinic acetylcholine receptor in lipid-like detergent complexes

26 Aug 2020 | BioXFEL Publications | Contributor(s): Rafael Maldonado-Hernandez, Orestes Quesada, José A. Lasalde-Dominicci

http://dx.doi.org/10.1016/j.dib.2020.106230 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Maldonado-Hernández, R., Quesada, O. & Lasalde-Dominicci, J.A., 2020. Biophysical characterization dataset of native nicotinic acetylcholine receptor in lipid-like detergent complexes. Data …

Covalent Capture of Collagen Triple Helices Using Lysine–Aspartate and Lysine–Glutamate Pairs

21 Aug 2020 | BioXFEL Publications | Contributor(s): Sarah A. H. Hulgan, Abhishek A. Jalan, I-Che Li, Douglas R. Walker, Mitchell Miller, Abigael Kosgei, Weijun Xu, George Phillips, Jeffrey D. Hartgerink

http://dx.doi.org/10.1021/acs.biomac.0c00878 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Hulgan, S.A.H. et al., 2020. Covalent Capture of Collagen Triple Helices Using Lysine–Aspartate and Lysine–Glutamate Pairs. Biomacromolecules, 21(9), pp.3772–3781. Available at: …

Need for Speed: Examining Protein Behavior during CryoEM Grid Preparation at Different Timescales

18 Aug 2020 | BioXFEL Publications | Contributor(s): David P. Klebl, Molly S.C. Gravett, Dimitrios Kontziampasis, David J. Wright, Robin S. Bon, Diana Monteiro, Martin Trebbin, Frank Sobott, Howard D. White, Michele C. Darrow, Rebecca F. Thompson, Stephen P. Muench

http://dx.doi.org/10.1016/j.str.2020.07.018 journal-article Klebl, D.P. et al., 2020. Need for Speed: Examining Protein Behavior during CryoEM Grid Preparation at Different Timescales. Structure, 28(11), pp.1238–1248.e4. Available at: http://dx.doi.org/10.1016/j.str.2020.07.018. David P. Klebl …

Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering

11 Aug 2020 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Lois Pollack

http://dx.doi.org/10.1107/s2052252520008830 Macromolecular structures can be determined from solution X-ray scattering. Small-angle X-ray scattering (SAXS) provides global structural information on length scales of 10s to 100s of Ångstroms, and many algorithms are available to convert SAXS data …

Microfluidic polyimide gas dynamic virtual nozzles for serial crystallography

07 Aug 2020 | BioXFEL Publications | Contributor(s): Mohammad Vakili, Ramakrishna Vasireddi, Paul V. Gwozdz, Diana Monteiro, Michael Heymann, Robert H. Blick, Martin Trebbin

http://dx.doi.org/10.1063/5.0012806 journal-article Vakili, M. et al., 2020. Microfluidic polyimide gas dynamic virtual nozzles for serial crystallography. Review of Scientific Instruments, 91(8), p.085108. Available at: http://dx.doi.org/10.1063/5.0012806. Mohammad Vakili and Ramakrishna …

Construction of gateway-compatible baculovirus expression vectors for high-throughput protein expression and in vivo microcrystal screening

07 Aug 2020 | BioXFEL Publications | Contributor(s): Yanyang Tang, Justin Saul, Nirupa Nagaratnam, Jose M. Martin-Garcia, Petra Fromme, Ji Qiu, Joshua LaBaer

http://dx.doi.org/10.1038/s41598-020-70163-2 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Tang, Y. et al., 2020. Construction of gateway-compatible baculovirus expression vectors for high-throughput protein expression and in vivo microcrystal screening. Scientific Reports, …

Inversion of Many-Beam Bragg Intensities for Phasing by Iterated Projections: Removal of Multiple Scattering Artifacts from Diffraction Data

06 Aug 2020 | BioXFEL Publications | Contributor(s): Jeffrey J. Donatelli, John Spence

http://dx.doi.org/10.1103/physrevlett.125.065502 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Donatelli, J.J. & Spence, J.C.H., 2020. Inversion of Many-Beam Bragg Intensities for Phasing by Iterated Projections: Removal of Multiple Scattering Artifacts from Diffraction Data. …

Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED

30 Jul 2020 | BioXFEL Publications | Contributor(s): Lan Zhu, Guanhong Bu, Liang Jing, Dan Shi, Ming-Yue Lee, Tamir Gonen, Wei Liu, Brent L. Nannenga

http://dx.doi.org/10.1016/j.str.2020.07.006 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Zhu, L. et al., 2020. Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED. Structure, 28(10), pp.1149–1159.e4. Available at: …

From Static Structures to Continuous Conformational Changes on the Energy Landscapes

30 Jul 2020 | BioXFEL Publications | Contributor(s): Ghoncheh Mashayekhi, Ali Dashti, Peter Schwander, Abbas Ourmazd

http://dx.doi.org/10.1017/s1431927620018723 journal-article Mashayekhi, G. et al., 2020. From Static Structures to Continuous Conformational Changes on the Energy Landscapes. Microscopy and Microanalysis, 26(S2), pp.1614–1615. Available at: http://dx.doi.org/10.1017/s1431927620018723. Ghoncheh …

Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers

22 Jul 2020 | BioXFEL Publications | Contributor(s): Suraj Pandey, Ishwor Poudyal, Tek Narsingh Malla

http://dx.doi.org/10.3390/cryst10070628 With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating the structure of transient states along the reaction coordinate. X-ray free electron lasers (XFELs) have enabled TRX …

Ptychographic X-ray speckle tracking with multi-layer Laue lens systems

08 Jul 2020 | BioXFEL Publications | Contributor(s): Andrew J. Morgan, Kevin T. Murray, Mauro Prasciolu, Holger Fleckenstein, Oleksandr Yefanov, Pablo Villanueva-Perez, Valerio Mariani, Martin Domaracky, Manuela Kuhn, Steve Aplin, Istvan Mohacsi, Marc Messerschmidt, Karolina Stachnik, Yang Du, Anja Burkhart, Alke Meents, Evgeny Nazaretski, Hanfei Yan, Xiaojing Huang, Yong S. Chu, Henry Chapman, Saša Bajt

http://dx.doi.org/10.1107/s1600576720006925 The ever-increasing brightness of synchrotron radiation sources demands improved X-ray optics to utilize their capability for imaging and probing biological cells, nano-devices and functional matter on the nanometre scale with chemical sensitivity. Hard …

Advances in methods for atomic resolution macromolecular structure determination

02 Jul 2020 | BioXFEL Publications | Contributor(s): Michael Thompson, Todd O. Yeates, Jose A. Rodriguez

http://dx.doi.org/10.12688/f1000research.25097.1 Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. …

3D printing of gas-dynamic virtual nozzles and optical characterization of high-speed microjets

26 Jun 2020 | BioXFEL Publications | Contributor(s): Reza Nazari, Sahba Zaare, Roberto C. Alvarez, Konstantinos Karpos, Trent Engelman, Caleb Alexander Madsen, Garrett Charles Nelson, John Spence, Uwe Weierstall, Ronald J. Adrian, Richard Kirian

http://dx.doi.org/10.1364/oe.390131 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Nazari, R. et al., 2020. 3D printing of gas-dynamic virtual nozzles and optical characterization of high-speed microjets. Optics Express, 28(15), p.21749. Available at: …

Diffusion in multilayers, studied by quantitative chemical mapping at the atomic level

18 Jun 2020 | BioXFEL Publications | Contributor(s): Y. Kim, A. Ourmazd

http://dx.doi.org/10.1017/s0424820100174904 Using chemical lattice imaging in combination with vector pattern recognition, we study diffusion and interdiffusion at single interfaces in mulilayered semiconductors quantitatively with atomic plane resolution. 20 periods of 50Å C-doped GaAs/50Å …

Pyridine-2,6-Dithiocarboxylic Acid and Its Metal Complexes: New Inhibitors of New Delhi Metallo β-Lactamase-1

02 Jun 2020 | BioXFEL Publications | Contributor(s): Chris S. Thomas, Doug R. Braun, Jose Luis Olmos, Scott R. Rajski, George Phillips, David Andes, Tim S. Bugni

http://dx.doi.org/10.3390/md18060295 Keywords: NDM-1 inhibitors; marine-derived Streptomyces sp.; carbapenem-resistant Enterobacteriaceae; metal chelators journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Thomas, C.S. et al., 2020. Pyridine-2,6-Dithiocarboxylic Acid and Its Metal …

Carbon nanotube dielectrophoresis: Theory and applications

31 May 2020 | BioXFEL Publications | Contributor(s): Mohammad Towshif Rabbani, Mukul Sonker, Alexandra Ros

http://dx.doi.org/10.1002/elps.202000049 journal-article Rabbani, M.T., Sonker, M. & Ros, A., 2020. Carbon nanotube dielectrophoresis: Theory and applications. ELECTROPHORESIS. Available at: http://dx.doi.org/10.1002/elps.202000049. Mohammad Towshif Rabbani and Mukul Sonker and Alexandra Ros

Enhanced X-ray diffraction of in vivo-grown μNS crystals by viscous jets at XFELs

29 May 2020 | BioXFEL Publications | Contributor(s): Nirupa Nagaratnam, Yanyang Tang, Sabine Botha, Justin Saul, Chufeng Li, Hao Hu, Sahba Zaare, Mark S. Hunter, David Lowry, Uwe Weierstall, Nadia Zatsepin, John Spence, Ji Qiu, Joshua LaBaer, Petra Fromme, Jose M. Martin-Garcia

http://dx.doi.org/10.1107/s2053230x20006172 μNS is a 70 kDa major nonstructural protein of avian reoviruses, which cause significant economic losses in the poultry industry. They replicate inside viral factories in host cells, and the μNS protein has been suggested to be the minimal viral …

Megahertz single-particle imaging at the European XFEL

29 May 2020 | BioXFEL Publications | Contributor(s): Egor Sobolev, Sergei Zolotarev, Klaus Giewekemeyer, Johan Bielecki, Kenta Okamoto, Hemanth K. N. Reddy, Jakob Andreasson, Kartik Ayyer, Imrich Barak, Sadia Bari, Anton Barty, Richard Bean, Sergey Bobkov, Henry Chapman, Grzegorz Chojnowski, Benedikt J. Daurer, Katerina Dörner, Tomas Ekeberg, Leonie Flückiger, Oxana Galzitskaya, Luca Gelisio, Steffen Hauf, Brenda Hogue, Daniel A. Horke, Ahmad Hosseinizadeh, Vyacheslav Ilyin, Chulho Jung, Chan Kim, Yoonhee Kim, Richard Kirian, Henry Kirkwood, Olena Kulyk, Jochen Küpper, Romain Letrun, N. Duane Loh, Kristina Lorenzen, Marc Messerschmidt, Kerstin Mühlig, Abbas Ourmazd, Natascha Raab, Andrei V. Rode, Max Rose, Adam Round, Takushi Sato, Robin Schubert, Peter Schwander, Jonas A. Sellberg, Marcin Sikorski, Alessandro Silenzi, Changyong Song, John Spence, Stephan Stern, Jolanta Sztuk-Dambietz, Anthon Teslyuk, Nicusor Timneanu, Martin Trebbin, Charlotte Uetrecht, Britta Weinhausen, Garth J. Williams, P. Lourdu Xavier, Chen Xu, Ivan A. Vartanyants, Victor S. Lamzin, Adrian Mancuso, Filipe R. N. C. Maia

http://dx.doi.org/10.1038/s42005-020-0362-y AbstractThe emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL is …

Targeted DNA sequencing analysis to reveal genetic diversity and androgen-receptor alteration in advanced EGFR mutant lung adenocarcinoma.

25 May 2020 | BioXFEL Publications | Contributor(s): Wei Wu, Ross A. Okimoto, Collin Michael Blakely, James Fraser, Trever G. Bivona

http://dx.doi.org/10.1200/jco.2020.38.15_suppl.9526 9526 Background: Lung cancer remains the leading cause of death from cancer around the world. Several oncogenic drivers have been identified from large cancer genome projects focused mainly on profiling early-stage lung cancers. Targeted …

First Experiments in Structural Biology at the European X-ray Free-Electron Laser

25 May 2020 | BioXFEL Publications | Contributor(s): Grant Mills, Richard Bean, Adrian P. Mancuso

http://dx.doi.org/10.3390/app10103642 Ultrabright pulses produced in X-ray free-electron lasers (XFELs) offer new possibilities for industry and research, particularly for biochemistry and pharmaceuticals. The unprecedented brilliance of these next-generation sources enables structure determination …

Length-Selective Dielectrophoretic Manipulation of Single-Walled Carbon Nanotubes

25 May 2020 | BioXFEL Publications | Contributor(s): Mohammad T. Rabbani, Christoph F. Schmidt, Alexandra Ros

http://dx.doi.org/10.1021/acs.analchem.0c00794 journal-article Rabbani, M.T., Schmidt, C.F. & Ros, A., 2020. Length-Selective Dielectrophoretic Manipulation of Single-Walled Carbon Nanotubes. Analytical Chemistry. Available at: http://dx.doi.org/10.1021/acs.analchem.0c00794. Mohammad T. Rabbani …

Science in the age of machine learning

21 May 2020 | BioXFEL Publications | Contributor(s): Abbas Ourmazd

http://dx.doi.org/10.1038/s42254-020-0191-7 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Ourmazd, A., 2020. Science in the age of machine learning. Nature Reviews Physics. Available at: http://dx.doi.org/10.1038/s42254-020-0191-7. Abbas Ourmazd

Prochlorococcus phage ferredoxin: Structural characterization and electron transfer to cyanobacterial sulfite reductases

20 May 2020 | BioXFEL Publications | Contributor(s): Ian J. Campbell, Jose Luis Olmos, Weijun Xu, Dimithree Kahanda, Joshua T. Atkinson, Othneil Noble Sparks, Mitchell Miller, George Phillips, George N. Bennett, Jonathan J. Silberg

http://dx.doi.org/10.1074/jbc.ra120.013501 Marine cyanobacteria are infected by phages whose genomes encode ferredoxin (Fd) electron carriers. These Fds are thought to redirect the energy harvested from light to phage-encoded oxidoreductases that enhance viral fitness, but it is  unclear how the …

Femtosecond timing synchronization at megahertz repetition rates for an x-ray free-electron laser

18 May 2020 | BioXFEL Publications | Contributor(s): Tokushi Sato, Romain Letrun, Henry J. Kirkwood, Jia Liu, Patrik Vagovič, Grant Mills, Yoonhee Kim, Cedric M. S. Takem, Marc Planas, Moritz Emons, Tomasz Jezynski, Guido Palmer, Max Lederer, Sebastian Schulz, Jost Mueller, Holger Schlarb, Alessandro Silenzi, Gabriele Giovanetti, Andrea Parenti, Martin Bergemann, Thomas Michelat, Janusz Szuba, Jan Grünert, Henry Chapman, Adrian P. Mancuso

http://dx.doi.org/10.1364/optica.396728 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Sato, T. et al., 2020. Femtosecond timing synchronization at megahertz repetition rates for an x-ray free-electron laser. Optica, 7(6), p.716. Available at: …

Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser Pulses

04 May 2020 | BioXFEL Publications | Contributor(s): Richard Kirian, Henry Chapman

http://dx.doi.org/10.1007/978-3-030-23201-6_27 book-chapter Kirian, R.A. & Chapman, H.N., 2020. Imaging of Objects by Coherent Diffraction of X-Ray Free-Electron Laser Pulses. Synchrotron Light Sources and Free-Electron Lasers, pp.1337–1397. Available at: …

An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020)

01 May 2020 | BioXFEL Publications | Contributor(s): LaRinda A. Holland, Emily A. Kaelin, Rabia Maqsood, Bereket Estifanos, Lily I. Wu, Arvind Varsani, Rolf U. Halden, Brenda Hogue, Matthew Scotch, Efrem S. Lim

http://dx.doi.org/10.1128/jvi.00711-20 journal-article Holland, L.A. et al., 2020. An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020) T. Gallagher, ed. Journal of Virology, 94(14). Available at: …

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

30 Apr 2020 | BioXFEL Publications | Contributor(s): David E. Gordon, Gwendolyn M. Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Kris M. White, Matthew J. O’Meara, Veronica V. Rezelj, Jeffrey Z. Guo, Danielle L. Swaney, Tia A. Tummino, Ruth Hüttenhain, Robyn M. Kaake, Alicia L. Richards, Beril Tutuncuoglu, Helene Foussard, Jyoti Batra, Kelsey Haas, Maya Modak, Minkyu Kim, Paige Haas, Benjamin J. Polacco, Hannes Braberg, Jacqueline M. Fabius, Manon Eckhardt, Margaret Soucheray, Melanie J. Bennett, Merve Cakir, Michael J. McGregor, Qiongyu Li, Bjoern Meyer, Ferdinand Roesch, Thomas Vallet, Alice Mac Kain, Lisa Miorin, Elena Moreno, Zun Zar Chi Naing, Yuan Zhou, Shiming Peng, Ying Shi, Ziyang Zhang, Wenqi Shen, Ilsa T. Kirby, James E. Melnyk, John S. Chorba, Kevin Lou, Shizhong A. Dai, Inigo Barrio-Hernandez, Danish Memon, Claudia Hernandez-Armenta, Jiankun Lyu, Christopher J. P. Mathy, Tina Perica, Kala Bharath Pilla, Sai J. Ganesan, Daniel J. Saltzberg, Ramachandran Rakesh, Xi Liu, Sara B. Rosenthal, Lorenzo Calviello, Srivats Venkataramanan, Jose Liboy-Lugo, Yizhu Lin, Xi-Ping Huang, YongFeng Liu, Stephanie A. Wankowicz, Markus Bohn, Maliheh Safari, Fatima S. Ugur, Cassandra Koh, Nastaran Sadat Savar, Quang Dinh Tran, Djoshkun Shengjuler, Sabrina J. Fletcher, Michael C. O’Neal, Yiming Cai, Jason C. J. Chang, David J. Broadhurst, Saker Klippsten, Phillip P. Sharp, Nicole A. Wenzell, Duygu Kuzuoglu-Ozturk, Hao-Yuan Wang, Raphael Trenker, Janet M. Young, Devin A. Cavero, Joseph Hiatt, Theodore L. Roth, Ujjwal Rathore, Advait Subramanian, Julia Noack, Mathieu Hubert, Robert Stroud, Alan D. Frankel, Oren S. Rosenberg, Kliment A. Verba, David A. Agard, Melanie Ott, Michael Emerman, Natalia Jura, Mark Von Zastrow, Eric Verdin, Alan Ashworth, Olivier Schwartz, Christophe D’Enfert, Shaeri Mukherjee, Matt Jacobson, Harmit S. Malik, Danica G. Fujimori, Trey Ideker, Charles S. Craik, Stephen N. Floor, James Fraser, John D. Gross, Andrej Sali, Bryan L. Roth, Davide Ruggero, Jack Taunton, Tanja Kortemme, Pedro Beltrao, Marco Vignuzzi, Adolfo García-Sastre, Kevan M. Shokat, Brian K. Shoichet, Nevan J. Krogan

http://dx.doi.org/10.1038/s41586-020-2286-9 journal-article Gordon, D.E. et al., 2020. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature, 583(7816), pp.459–468. Available at: http://dx.doi.org/10.1038/s41586-020-2286-9. David E. Gordon and Gwendolyn M. Jang and …

An 81 base-pair deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)

22 Apr 2020 | BioXFEL Publications | Contributor(s): LaRinda A. Holland, Emily A. Kaelin, Rabia Maqsood, Bereket Estifanos, Lily I. Wu, Arvind Varsani, Rolf U. Halden, Brenda Hogue, Matthew Scotch, Efrem S. Lim

http://dx.doi.org/10.1101/2020.04.17.20069641 On January 26 2020, the first Coronavirus Disease 2019 (COVID-19) case was reported in Arizona of an individual with travel history (3rd case in the US) (1). Here, we report on early SARS-CoV-2 sentinel surveillance in Tempe, Arizona (USA). Genomic …

Dynamics of rare gas solids irradiated by electron beams

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

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

The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

30 Mar 2020 | BioXFEL Publications | Contributor(s): Elin Claesson, Weixiao Yuan Wahlgren, Heikki Takala, Suraj Pandey, Leticia Castillon, Valentyna Kuznetsova, Léocadie Henry, Matthijs Panman, Melissa Carrillo, Joachim Kübel, Rahul Nanekar, Linnéa Isaksson, Amke Nimmrich, Andrea Cellini, Dmitry Morozov, Michał Maj, Moona Kurttila, Robert William Bosman, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, So Iwata, Shigeki Owada, Keith Moffat, Gerrit Groenhof, Emina Stojkovic, Janne A Ihalainen, Marius Schmidt, Sebastian Westenhoff

http://dx.doi.org/10.7554/elife.53514 Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial …

Sample deposition onto cryo-EM grids: from sprays to jets and back

25 Mar 2020 | BioXFEL Publications | Contributor(s): David P. Klebl, Diana Monteiro, Dimitrios Kontziampasis, Florian Kopf, Frank Sobott, Howard D. White, Martin Trebbin, Stephen P. Muench

http://dx.doi.org/10.1107/s2059798320002958 Despite the great strides made in the field of single-particle cryogenic electron microscopy (cryo-EM) in microscope design, direct electron detectors and new processing suites, the area of sample preparation is still far from ideal. Traditionally, sample …

Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding

24 Mar 2020 | BioXFEL Publications | Contributor(s): Suvrajit Maji, Hstau Liao, Ali Dashti, Ghoncheh Mashayekhi, Abbas Ourmazd, Joachim Frank

http://dx.doi.org/10.1021/acs.jcim.9b01115 journal-article Maji, S. et al., 2020. Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding. Journal of Chemical Information and Modeling. Available at: …

Using Machine Learning to Achieve Accurate Estimates of Fetal Gestational Age and Personalized Predictions of Fetal Growth

24 Mar 2020 | BioXFEL Publications | Contributor(s): Russell Fung, Jose Villar, Ali Dashti, Leila Cheikh Ismail, Eleonora Staines-Urias, Eric O. Ohuma, Laurent J. Salomon, Cesar G. Victora, Fernando C. Barros, Ann Lambert, Maria Carvalho, Yasmin A. Jaffer, Alison J. Noble, Michael G. Gravett, Manorama Purwar, Ruyan Pang, Enrico Bertino, Shama Munim, Aung Myat Min, Rose McGready, Shane A. Norris, Zulfiqar A Bhutta, Stephen H. Kennedy, Aris T. Papageorghiou, Abbas Ourmazd, International Fetal And Newborn Gro Group

http://dx.doi.org/10.2139/ssrn.3471997 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Fung, R. et al., 2019. Using Machine Learning to Achieve Accurate Estimates of Fetal Gestational Age and Personalized Predictions of Fetal Growth. SSRN Electronic Journal. Available at: …

Single-particle imaging by x-ray free-electron lasers—How many snapshots are needed?

20 Mar 2020 | BioXFEL Publications | Contributor(s): I. Poudyal, M. Schmidt, P. Schwander

http://dx.doi.org/10.1063/1.5144516 journal-article Poudyal, I., Schmidt, M. & Schwander, P., 2020. Single-particle imaging by x-ray free-electron lasers—How many snapshots are needed? Structural Dynamics, 7(2), p.024102. Available at: http://dx.doi.org/10.1063/1.5144516. I. Poudyal and M. …

XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia

09 Mar 2020 | BioXFEL Publications | Contributor(s): James D Zook, Mrinal Shekhar, Debra Hansen, Chelsie E Conrad, Thomas Grant, Chitrak Gupta, Thomas White, Anton Barty, Shibom Basu, Yun Zhao, Nadia Zatsepin, Andrii Ishchenko, Alex Batyuk, Cornelius Gati, Chufeng Li, Lorenzo Galli, Jesse David Coe, Mark S. Hunter, Meng Liang, Uwe Weierstall, Garret Nelson, Daniel James, Benjamin Stauch, Felicia Craciunescu, Darren Gary Thifault, Wei Liu, Vadim Cherezov, Abhishek Singharoy, Petra Fromme

http://dx.doi.org/10.1016/j.str.2020.02.005 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Zook, J. et al., 2020. XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia. Structure. Available at: …

Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility

07 Mar 2020 | BioXFEL Publications | Contributor(s): Darya Marchany-Rivera, Clyde A. Smith, Josiris D. Rodriguez-Perez, Juan J Lopez-Garriga

http://dx.doi.org/10.1016/j.jinorgbio.2020.111055 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Marchany-Rivera, D. et al., 2020. Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility. Journal of Inorganic Biochemistry, 207, p.111055. Available at: …

Structure-based discovery of potent and selective melatonin receptor agonists

02 Mar 2020 | BioXFEL Publications | Contributor(s): Nilkanth N Patel, Xi Ping Huang, Jessica M Grandner, Linda C Johansson, Benjamin Stauch, John D McCorvy, Yongfeng Liu, Bryan Roth, Vsevolod Katritch

http://dx.doi.org/10.7554/elife.53779 Melatonin receptors MT1 and MT2 are involved in synchronizing circadian rhythms and are important targets for treating sleep and mood disorders, type-2 diabetes and cancer. Here, we performed large scale structure-based virtual screening for new ligand …

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

25 Feb 2020 | BioXFEL Publications | Contributor(s): Alexander M. Wolff, Iris Diane Young, Raymond G. Sierra, Aaron S. Brewster, Michael W. Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, Justin T. Biel, Sergio Carbajo, Aina E. Cohen, Saul Cortez, Ana Gonzalez, Tomoya Hino, Dohyun Im, Jake D. Koralek, Minoru Kubo, Tomas Lazarou, Takashi Nomura, Shigeki Owada, Avi J. Samelson, Tomoyuki Tanaka, Rie Tanaka, Erin M. Thompson, Henry Van Den Bedem, Rahel Woldeyes, Fumiaki Yumoto, Wei Zhao, Kensuke Tono, Sebastien Boutet, So Iwata, Tamir Gonen, Nicholas K. Sauter, James Fraser, Michael Thompson

http://dx.doi.org/10.1107/s205225252000072x Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods …

Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes

24 Feb 2020 | BioXFEL Publications | Contributor(s): Tyler D. Huber, Jonathan Clinger, Yang Liu, Weijun Xu, Mitchell Miller, George Phillips, Jon S. Thorson

http://dx.doi.org/10.1021/acschembio.9b00943 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Huber, T.D. et al., 2020. Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes. ACS Chemical Biology, 15(3), pp.695–705. Available at: …

Serial Crystallography: Preface

24 Feb 2020 | BioXFEL Publications | Contributor(s): John Spence

http://dx.doi.org/10.3390/cryst10020135 The history of serial crystallography (SC) has its origins in the earliest attempts to merge data from several crystals. This preface provides an overview of some recent work, with a survey of the rapid advances made over the past decade in both sample …

Reaction Initiation in Enzyme Crystals by Diffusion of Substrate

14 Feb 2020 | BioXFEL Publications | Contributor(s): Marius Schmidt

http://dx.doi.org/10.3390/cryst10020116 Ever since the first structure of an enzyme, lysozyme, was solved, scientists have been eager to explore how these molecules perform their catalytic function. There has been an overwhelmingly large body of publications that report the X-ray structures of …

Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

10 Feb 2020 | BioXFEL Publications | Contributor(s): Reed M. Stein, Hye Jin Kang, John D. McCorvy, Grant C. Glatfelter, Anthony J. Jones, Tao Che, Samuel Slocum, Xi-Ping Huang, Olena Savych, Yurii S. Moroz, Benjamin Stauch, Linda C. Johansson, Vadim Cherezov, Terry Kenakin, John J. Irwin, Brian K. Shoichet, Bryan L. Roth, Margarita L. Dubocovich

http://dx.doi.org/10.1038/s41586-020-2027-0 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Stein, R.M. et al., 2020. Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. Nature. Available at: http://dx.doi.org/10.1038/s41586-020-2027-0. Reed M. Stein and …

Prochlorococcusphage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases

08 Feb 2020 | BioXFEL Publications | Contributor(s): Ian J. Campbell, Jose L. Olmos, Weijun Xu, Dimithree Kahanda, Joshua T. Atkinson, Othneil N. Sparks, Mitchell Miller, George Phillips, George N. Bennett, Jonathan J. Silberg

http://dx.doi.org/10.1101/2020.02.07.937771 AbstractMarine cyanobacteria are infected by phage whose genomes encode ferredoxin (Fd) electron carriers. While these Fds are thought to redirect the energy harvested from light to phage-encoded oxidoreductases that enhance viral fitness, it is not clear …

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

07 Feb 2020 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Lois Pollack

http://dx.doi.org/10.1016/j.bpj.2019.11.1706 poster Chen, Y.-L. & Pollack, L., 2020. Convolutional Neural Networks Bridge Molecular Models and Solution X-ray Scattering Experiments. Biophysical Journal, 118(3), p.301a. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.1706. Yen-Lin Chen and …

Rhodopsin's Ultra-Fast Activation Dynamics in Bilayer and Micelle Environments

07 Feb 2020 | BioXFEL Publications | Contributor(s): Leslie A. Salas-Estrada, Thomas D. Grant, Suchithranga M. Perera, Andrey V. Struts, Udeep Chawla, Xiaolin Xu, Steven D. Fried, Nipuna Weerasinghe, D. Mendez, R. Alvarez, K. Karpos, S. Lisova, S. Zaare, R. Nazari, N.A. Zatsepsin, Abhishek Singharoy, S. Boutet, S. Carbajo, M.S. Hunter, M. Liang, M.D. Seaberg, Raimund Fromme, Petra Fromme, Richard Kirian, Michael F. Brown, Alan Grossfield

http://dx.doi.org/10.1016/j.bpj.2019.11.669 journal-article Salas-Estrada, L.A. et al., 2020. Rhodopsin’s Ultra-Fast Activation Dynamics in Bilayer and Micelle Environments. Biophysical Journal, 118(3), p.92a. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.669. Leslie A. Salas-Estrada …

Discovering Design Principles to Re-Engineer Functional RNA Elements

07 Feb 2020 | BioXFEL Publications | Contributor(s): Alex Plumridge, Lois Pollack

http://dx.doi.org/10.1016/j.bpj.2019.11.556 poster Plumridge, A. & Pollack, L., 2020. Discovering Design Principles to Re-Engineer Functional RNA Elements. Biophysical Journal, 118(3), p.70a. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.556. Alex Plumridge and Lois Pollack