Support

Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from arabidopsis thaliana in complex with AMP

28 Apr 2015 | BioXFEL Publications | Contributor(s): Do Jin Kim, Eduard Bitto, Craig A. Bingman, Hyun-Jung Kim, Byung Woo Han, George Phillips

http://dx.doi.org/10.1002/prot.24821 Do Jin Kim and Eduard Bitto and Craig A. Bingman and Hyun-Jung Kim and Byung Woo Han and George N. Phillips Kim, D.J. et al., 2015. Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from arabidopsis thaliana in …

Crystal structure of the protein fromArabidopsis thalianagene At5g06450, a putative DnaQ-like exonuclease domain-containing protein with homohexameric assembly

24 Apr 2013 | BioXFEL Publications | Contributor(s): David W. Smith, Mi Ra Han, Joon Sung Park, Kyung Rok Kim, Taeho Yeom, Ji Yeon Lee, Do Jin Kim, Craig A. Bingman, Hyun-Jung Kim, Kyubong Jo, Byung Woo Han, George Phillips

http://dx.doi.org/10.1002/prot.24315 journal-article Smith, D.W. et al., 2013. Crystal structure of the protein fromArabidopsis thalianagene At5g06450, a putative DnaQ-like exonuclease domain-containing protein with homohexameric assembly. Proteins: Structure, Function, and Bioinformatics, 81(9), …

Crystal Structure of the Zorbamycin-Binding Protein ZbmA, the Primary Self-Resistance Element in Streptomyces flavoviridis ATCC21892

29 Oct 2015 | BioXFEL Publications | Contributor(s): Jeffrey D. Rudolf, Lance Bigelow, Changsoo Chang, Marianne E. Cuff, Jeremy R. Lohman, Chin-Yuan Chang, Ming Ma, Dong Yang, Shonda Clancy, Gyorgy Babnigg, Andrzej Joachimiak, George Phillips, Ben Shen

http://dx.doi.org/10.1021/acs.biochem.5b01008 Jeffrey D. Rudolf and Lance Bigelow and Changsoo Chang and Marianne E. Cuff and Jeremy R. Lohman and Chin-Yuan Chang and Ming Ma and Dong Yang and Shonda Clancy and Gyorgy Babnigg and Andrzej Joachimiak and George N. Phillips and Ben Shen Rudolf, J.D. …

Crystal Structure of α-Xylosidase from Aspergillus niger in Complex with a Hydrolyzed Xyloglucan Product and New Insights in Accurately Predicting Substrate Specificities of GH31 Family Glycosidases

23 Jan 2020 | BioXFEL Publications | Contributor(s): Hongnan Cao, Jonathan D. Walton, Phillip Brumm, George Phillips

http://dx.doi.org/10.1021/acssuschemeng.9b07073 journal-article Cao, H. et al., 2020. Crystal Structure of α-Xylosidase from Aspergillus niger in Complex with a Hydrolyzed Xyloglucan Product and New Insights in Accurately Predicting Substrate Specificities of GH31 Family Glycosidases. ACS …

Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 inStreptomyces globisporus

25 Aug 2016 | BioXFEL Publications | Contributor(s): Chin-Yuan Chang, Jeremy R. Lohman, Hongnan Cao, Kemin Tan, Jeffrey D. Rudolf, Ming Ma, Weijun Xu, Craig A. Bingman, Ragothaman M. Yennamalli, Lance Bigelow, Gyorgy Babnigg, Xiaohui Yan, Andrzej Joachimiak, George Phillips, Ben Shen

http://dx.doi.org/10.1021/acs.biochem.6b00713 Chin-Yuan Chang and Jeremy R. Lohman and Hongnan Cao and Kemin Tan and Jeffrey D. Rudolf and Ming Ma and Weijun Xu and Craig A. Bingman and Ragothaman M. Yennamalli and Lance Bigelow and Gyorgy Babnigg and Xiaohui Yan and Andrzej Joachimiak and George …

Crystallization of a self-assembled three-dimensional DNA nanostructure

30 Jan 2013 | BioXFEL Publications | Contributor(s): Kimberly N. Rendek, Raimund Fromme, Ingo Grotjohann, Petra Fromme

journal-article http://dx.doi.org/10.1107/s1744309112052128 Rendek, K.N. et al., 2013. Crystallization of a self-assembled three-dimensional DNA nanostructure. Acta Crystallographica Section F Structural Biology and Crystallization Communications, 69(2), pp.141–146. Available at: …

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 …

Crystallization of Membrane Proteins: An Overview

01 Jun 2017 | BioXFEL Publications | Contributor(s): Andrii Ishchenko, Enrique E. Abola, Vadim Cherezov

http://dx.doi.org/10.1007/978-1-4939-7000-1_5 book-chapter Ishchenko, A., Abola, E.E. & Cherezov, V., 2017. Crystallization of Membrane Proteins: An Overview. Protein Crystallography, pp.117–141. Available at: http://dx.doi.org/10.1007/978-1-4939-7000-1_5. Andrii Ishchenko and Enrique E. Abola …

Crystallization of Photosystem II for Time-Resolved Structural Studies Using an X-ray Free Electron Laser

18 Apr 2015 | BioXFEL Publications | Contributor(s): Jesse David Coe, Christopher Kupitz, Shibom Basu, Chelsie E Conrad, Shatabdi Roy-Chowdhury, Raimund Fromme, Petra Fromme

http://dx.doi.org/10.1016/bs.mie.2015.01.011 Jesse Coe and Christopher Kupitz and Shibom Basu and Chelsie E. Conrad and Shatabdi Roy-Chowdhury and Raimund Fromme and Petra Fromme Coe, J. et al., 2015. Crystallization of Photosystem II for Time-Resolved Structural Studies Using an X-ray Free …

Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel

05 Nov 2013 | BioXFEL Publications | Contributor(s): Bahige G. Abdallah, Christopher Kupitz, Petra Fromme, Alexandra Ros

http://dx.doi.org/10.1021/nn402515q Bahige G. Abdallah and Christopher Kupitz and Petra Fromme and Alexandra Ros Abdallah, B.G. et al., 2013. Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel. ACS Nano, 7(12), pp.10534–10543. Available at: …

Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel

09 Oct 2015 | Teaching Materials

Traditional macroscale protein crystallization is accomplished nontrivially by exploring a range of protein concentrations and buffers in solution until a suitable combination is attained. This methodology is time-consuming and resource-intensive, hindering protein structure determination. Even …

Crystallization screening: the influence of history on current practice

26 Jun 2014 | BioXFEL Publications | Contributor(s): Joseph Luft, Janet Newman, Edward Snell

While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed. …

Crystallographic data processing for free-electron laser sources

14 Jun 2013 | BioXFEL Publications | Contributor(s): Thomas A. White, Anton Barty, Francesco Stellato, James Holton, Richard Kirian, Nadia Zatsepin, Henry Chapman

A processing pipeline for diffraction data acquired using the `serial crystallography' methodology with a free-electron laser source is described with reference to the crystallographic analysis suiteCrystFELand the pre-processing programCheetah. A detailed analysis of the nature and impact of …

Crystallographic Methods - Crystallographic Symmetry - Part I

20 Oct 2014 | Teaching Materials | Contributor(s): Edward Snell

Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

Crystallographic Methods - Crystallographic Symmetry - Part II

20 Oct 2014 | Teaching Materials

Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

Crystallographic Methods - Crystallographic Symmetry - Part III

22 Oct 2014 | Teaching Materials | Contributor(s): Edward Snell

Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

Crystallographic Methods - Geometrical Crystallography - Part I

19 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing Geometrical crystallography     Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation and the Ewald construction; Reciprocal space and the reciprocal lattice Rupp, ch. 5

Crystallographic Methods - Geometrical Crystallography - Part II

04 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing Geometrical crystallography     Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation and the Ewald construction; Reciprocal space and the reciprocal lattice Rupp, ch. 5

Crystallographic Methods - Introduction and Overview

25 Aug 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing Introduction     Protein structural elements: 1° aa sequence,  2° α-helix, β strand, β sheet, loop, 3° domain fold,  4° domain assembly; Overview of biomacromolecular crystallography

Crystallographic Methods - X-ray Diffraction Physics - Part I

08 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part II

11 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part III

15 Sep 2014 | Teaching Materials

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part IV

18 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part IX

03 Oct 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part V

22 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part VI

25 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part VII

28 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part VIII

01 Oct 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods of Structural Biology

18 Sep 2016 | Courses | Contributor(s): Robert H Blessing, Edward Snell

The goal of the course is that students acquire sufficient knowledge and understanding of the basic principles of biomolecular crystal structure analysis that they will be able to comfortably, and with interest and insight, read and comprehend the articles in Volume F of the International Tables …

Crystallography with an XFEL

21 Jul 2015 | Seminars | Contributor(s): Marc Messerschmidt

Dr. Marc Messerschmidt discusses the design and operation of the X-ray free electron laser at the LCLS. Be sure to grab the attached MP3 audio file to follow along. Topics discussed include: - XFEL fundamentals - LCLS machine capabilities and energy spectrum - Beamlines and instrumentation for …

Crystallography: Sources of inspiration

28 Jan 2014 | BioXFEL Publications | Contributor(s): Sean McSweeney, Petra Fromme

http://dx.doi.org/10.1038/505620a Sean McSweeney and Petra Fromme McSweeney, S. & Fromme, P., 2014. Crystallography: Sources of inspiration. Nature, 505(7485), pp.620–621. Available at: http://dx.doi.org/10.1038/505620a. journal-article

CrystFEL Tutorial

03 Sep 2014 | Teaching Materials

Tom White (CFEL)

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

Cysteine modification can gate non-equilibrium conformational dynamics during enzyme catalysis: Supplemental Information

19 Jan 2019 | BioXFEL Publications | Contributor(s): Medhanjali DasGupta, Dominik Budday, Peter Madzelan, Javier Seravalli, Brandon Hayes, Raymond G. Sierra, Roberto Alonso-Mori, Aaron S. Brewster, Nicholas K. Sauter, Gregory A. Applegate, Virendra Tiwari, David B. Berkowitz, Michael Thompson, James Fraser, Michael E. Wall, Henry Van Den Bedem, Mark A. Wilson

http://dx.doi.org/10.1101/524751 Post-translational modification of cysteine residues can regulate protein function and is essential for catalysis by cysteine-dependent enzymes. Covalent modifications neutralize charge on the reactive cysteine thiolate anion and thus alter the active site …

Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization

30 Jan 2017 | BioXFEL Publications | Contributor(s): Madison B. Adolph, Anjuman Ara, Yuqing Feng, Cristina J. Wittkopp, Michael Emerman, James Fraser, Linda Chelico

journal-article http://dx.doi.org/10.1093/nar/gkx066 Adolph, M.B. et al., 2017. Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization. Nucleic Acids Research, 45(6), pp.3378–3394. Available at: http://dx.doi.org/10.1093/nar/gkx066. …

Damage threshold of amorphous carbon mirror for 177eV FEL radiation

10 Nov 2010 | BioXFEL Publications | Contributor(s): Sh. Dastjani Farahani, Jaromir Chalupsky, T. Burian, Henry Chapman, A.J. Gleeson, V. Hajkoya, L. Juha, M. Jurek, Dorota Klinger, Harald Sinn, R. Sobierajski, M. Störmer, K. Tiedtke, S. Toleikis, Thomas Tschentscher, H. Wabnitz, Jerome Gaudin

http://dx.doi.org/10.1016/j.nima.2010.10.133 journal-article Dastjani Farahani, S. et al., 2011. Damage threshold of amorphous carbon mirror for 177eV FEL radiation. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, …

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 …

Data Analysis and Sample Delivery

29 Aug 2014 | Teaching Materials

John Spence (ASU/LBNL) How XFEL MX differs from MX and why we do it.

Data Analysis Scripts

21 Jul 2015 | Downloads

A repository of useful scripts for the analysis of XFEL data. 

Data assimilation in operator algebras

17 Feb 2023 | BioXFEL Publications | Contributor(s): David Freeman, Dimitrios Giannakis, Brian Mintz, Abbas Ourmazd, Joanna Slawinska

http://dx.doi.org/10.1073/pnas.2211115120 We develop an algebraic framework for sequential data assimilation of partially observed dynamical systems. In this framework, Bayesian data assimilation is embedded in a nonabelian operator algebra, which provides a representation of observables by …

Data publication with the structural biology data grid supports live analysis

07 Mar 2016 | BioXFEL Publications | Contributor(s): Peter A. Meyer, Stephanie Socias, Jason Key, Elizabeth Ransey, Emily C. Tjon, Alejandro Buschiazzo, Ming Lei, Chris Botka, James Withrow, David Neau, Kanagalaghatta Rajashankar, Karen S. Anderson, Richard H. Baxter, Stephen C. Blacklow, Titus J. Boggon, Alexandre M. J. J. Bonvin, Dominika Borek, Tom J. Brett, Amedeo Caflisch, Chung-I Chang, Walter J. Chazin, Kevin D. Corbett, Michael S. Cosgrove, Sean Crosson, Sirano Dhe-Paganon, Enrico Di Cera, Catherine L. Drennan, Michael J. Eck, Brandt F. Eichman, Qing R. Fan, Adrian R. Ferré-D'Amaré, J. Christopher Fromme, K. Christopher Garcia, Rachelle Gaudet, Peng Gong, Stephen C. Harrison, Ekaterina E. Heldwein, Zongchao Jia, Robert J. Keenan, Andrew C. Kruse, Marc Kvansakul, Jason S. McLellan, Yorgo Modis, Yunsun Nam, Zbyszek Otwinowski, Emil F. Pai, Pedro José Barbosa Pereira, Carlo Petosa, C. S. Raman, Tom A. Rapoport, Antonina Roll-Mecak, Michael K. Rosen, Gabby Rudenko, Joseph Schlessinger, Thomas U. Schwartz, Yousif Shamoo, Holger Sondermann, Yizhi J. Tao, Niraj H. Tolia, Oleg V. Tsodikov, Kenneth D. Westover, Hao Wu, Ian Foster, James Fraser, Filipe R. N C. Maia, Tamir Gonen, Tom Kirchhausen, Kay Diederichs, Mercè Crosas, Piotr Sliz

journal-article http://dx.doi.org/10.1038/ncomms10882 Meyer, P.A. et al., 2016. Data publication with the structural biology data grid supports live analysis. Nature Communications, 7, p.10882. Available at: http://dx.doi.org/10.1038/ncomms10882. Peter A. Meyer and Stephanie Socias and Jason Key …

De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure

27 Sep 2016 | BioXFEL Publications | Contributor(s): Jacques-Philippe Colletier, Michael R. Sawaya, Mari Gingery, Jose A. Rodriguez, Duilio Cascio, Aaron S. Brewster, Tara Michels-Clark, Robert H. Hice, Nicolas Coquelle, Sébastien Boutet, Garth J. Williams, Marc Messerschmidt, Daniel P. DePonte, Raymond G. Sierra, Hartawan Laksmono, Jason E. Koglin, Mark S. Hunter, Hyun-Woo Park, Monarin Uervirojnangkoorn, Dennis K. Bideshi, Axel T. Brunger, Brian A. Federici, Nicholas K. Sauter, David S. Eisenberg

http://dx.doi.org/10.1038/nature19825 Jacques-Philippe Colletier and Michael R. Sawaya and Mari Gingery and Jose A. Rodriguez and Duilio Cascio and Aaron S. Brewster and Tara Michels-Clark and Robert H. Hice and Nicolas Coquelle and Sébastien Boutet and Garth J. Williams and Marc Messerschmidt and …

De novo protein crystal structure determination from X-ray free-electron laser data

22 Nov 2013 | BioXFEL Publications | Contributor(s): Thomas R. M. Barends, Lutz Foucar, Sabine Botha, R. Bruce Doak, Robert L. Shoeman, Karol Nass, Jason E. Koglin, Garth J. Williams, Sébastien Boutet, Marc Messerschmidt, Ilme Schlichting

http://dx.doi.org/10.1038/nature12773 journal-article Barends, T.R.M. et al., 2013. De novo protein crystal structure determination from X-ray free-electron laser data. Nature, 505(7482), pp.244–247. Available at: http://dx.doi.org/10.1038/nature12773. Thomas R. M. Barends and Lutz Foucar and …

De novo protein structure determination by heavy-atom soaking in lipidic cubic phase and SIRAS phasing using serial synchrotron crystallography

08 Aug 2018 | BioXFEL Publications | Contributor(s): S. Botha, D. Baitan, K. E. J. Jungnickel, D. Oberthür, C. Schmidt, S. Stern, M. O. Wiedorn, M. Perbandt, H. N. Chapman, C. Betzel

http://dx.doi.org/10.1107/s2052252518009223 During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application …

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), …

Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases

01 Mar 2024 | BioXFEL Publications | Contributor(s): Edwin G. Peña-Martínez, Jose Arcadio Rodriguez-Martinez

http://dx.doi.org/10.31083/j.fbs1601004 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Peña-Martínez, E. G., & Rodríguez-Martínez, J. A. (2024). Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases. Frontiers in …

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. …

Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment

09 Jun 2014 | BioXFEL Publications | Contributor(s): K. Pande, P. Schwander, M. Schmidt, D. K. Saldin

http://dx.doi.org/10.1098/rstb.2013.0332 K. Pande and P. Schwander and M. Schmidt and D. K. Saldin Pande, K. et al., 2014. Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment. Philosophical Transactions of the Royal Society B: …

Deducing fast electron density changes in uncrystallized biomolecules

13 Oct 2015 | Teaching Materials

We propose a method for deducing time-resolved structural changes in uncrystallized biomolecules in solution. The method relies on measuring the angular correlations of the intensities, when averaged over a large number of diffraction patterns from randomly oriented biomolecules in solution in a …

DefNEtTrp: An Iron Dual Chelator Approach for Anticancer Application

04 Dec 2024 | BioXFEL Publications | Contributor(s): Israel Rodriguez, Carmen Acosta, Christopher Nieves-Escobar, Estelle Strangmark, Oscar Claudio-Ares, Adriana I. Vargas Figueroa, Alexandra M. Soto-Millán, Aixa M. Orta-Rivera, Andrei V. Astashkin, Arthur Tinoco

https://doi.org/10.1021/jacsau.4c00774 journal-article Rodríguez, I., Acosta, C., Nieves-Escobar, C., Strangmark, E., Claudio-Ares, O., Vargas Figueroa, A. I., Soto-Millán, A. M., M. Orta-Rivera, A., Astashkin, A. V., & Tinoco, A. D. (2024). DefNEtTrp: An Iron Dual Chelator Approach for …

Demonstration of simultaneous experiments using thin crystal multiplexing at the Linac Coherent Light Source

09 Apr 2015 | BioXFEL Publications | Contributor(s): Y. Feng, R. Alonso-Mori, T. R. M. Barends, V. D. Blank, S. Botha, M. Chollet, D. S. Damiani, R. B. Doak, J. M. Glownia, J. M. Koglin, H. T. Lemke, M. Messerschmidt, K. Nass, S. Nelson, I. Schlichting, R. L. Shoeman, Yu. V. Shvyd'ko, M. Sikorski, S. Song, S. Stoupin, S. Terentyev, G. J. Williams, D. Zhu, A. Robert, S. Boutet

Multiplexing of the Linac Coherent Light Source beam was demonstrated for hard X-rays by spectral division using a near-perfect diamond thin-crystal monochromator operating in the Bragg geometry. The wavefront and coherence properties of both the reflected and transmitted beams were well preserved, …

DENSS: Ab Initio Electron Density Maps from Biological SAXS Data

20 Mar 2019 | Seminars | Contributor(s): Thomas Grant

Small angle scattering is an experimental technique used to analyze the molecular structures of a wide variety of biological and non-biological samples in solution. In contrast to X-ray crystallography and cryo-electron microscopy, where 3D electron density maps are calculated, available methods …

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

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

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

Detection of Protein Nanocrystals Based on the Reversibility of Crystallization

18 Apr 2015 | BioXFEL Publications | Contributor(s): Katerina Dörner, Jose Martin Garcia, Christopher Kupitz, Rebekka M. Wachter, Petra Fromme

http://dx.doi.org/10.1016/j.bpj.2013.11.2597 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Dörner, K. et al., 2014. Detection of Protein Nanocrystals Based on the Reversibility of Crystallization. Biophysical Journal, 106(2), p.458a. Available at: …

Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting

26 Aug 2015 | BioXFEL Publications | Contributor(s): David Mavor, James Fraser, Ron Morganti

http://dx.doi.org/10.1101/025452 Ubiquitination is an essential post-translational regulatory process that can control protein stability, localization, and activity. Ubiquitin is essential for eukaryotic life and is highly conserved, varying in only 3 amino acid positions between yeast and humans. …

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

25 Apr 2016 | BioXFEL Publications | Contributor(s): David Mavor, Kyle Barlow, Samuel Thompson, Benjamin A Barad, Alain R Bonny, Clinton L Cario, Garrett Gaskins, Zairan Liu, Laura Deming, Seth D Axen, Elena Caceres, Weilin Chen, Adolfo Cuesta, Rachel E Gate, Evan M Green, Kaitlin R Hulce, Weiyue Ji, Lillian R Kenner, Bruk Mensa, Leanna S Morinishi, Steven M Moss, Marco Mravic, Ryan K Muir, Stefan Niekamp, Chimno I Nnadi, Eugene Palovcak, Erin M Poss, Tyler D Ross, Eugenia C Salcedo, Stephanie K See, Meena Subramaniam, Allison W Wong, Jennifer Li, Kurt S Thorn, Shane Ó Conchúir, Benjamin P Roscoe, Eric D Chow, Joseph L DeRisi, Tanja Kortemme, Daniel N Bolon, James Fraser

Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced …

Determining the Enzymatic Mechanism of DJ-1 Using a New Approach to Mix-and-Inject Synchrotron Serial Crystallography

10 Apr 2025 | BioXFEL Publications | Contributor(s): Kara Zielinski, Cole Dolamore, Kevin Dalton, Doeke Hekstra, Robert Henning, Vukica Srajer, Mark Wilson, Lois Pollack

https://doi.org/10.1063/4.0000425 Mix-and-inject serial crystallography (MISC) is a well established technique at X-ray Free Electron Lasers (XFELs) to capture snapshots of the progress of a reaction, typically between a protein and a ligand. Key to this method are specialized diffusive mixers …

Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements

16 Jun 2015 | BioXFEL Publications | Contributor(s): Steve P. Meisburger, Suzette A. Pabit, Lois Pollack

http://dx.doi.org/10.1016/j.bpj.2015.05.006 journal-article Meisburger, S.P., Pabit, S.A. & Pollack, L., 2015. Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements. Biophysical Journal, 108(12), pp.2886–2895. Available at: …

Determining the Mechanism of DJ-1 Using Mix-and-Inject Synchrotron Serial Crystallography

10 Apr 2025 | BioXFEL Publications | Contributor(s): Cole Dolamore, Kara Zielinski, Kevin Dalton, Stephen Meisburger, John Termini, Nathan Smith, Robert Henning, Vukica Srajer, Doeke Hekstra, Lois Pollack, Mark Wilson

https://doi.org/10.1063/4.0000378 Determining the molecular basis of enzyme catalytic activity is a central challenge in biochemistry. Time-resolved serial X-ray crystallography using X-ray free electron (XFELs) and synchrotron sources allows enzyme reactions to be observed in real time in a …

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

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

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

Deterministic Absolute Negative Mobility for Micro- and Submicrometer Particles Induced in a Microfluidic Device

05 May 2016 | BioXFEL Publications | Contributor(s): Jinghui Luo, Katherine A. Muratore, Edgar A. Arriaga, Alexandra Ros

http://dx.doi.org/10.1021/acs.analchem.6b00837 Jinghui Luo and Katherine A. Muratore and Edgar A. Arriaga and Alexandra Ros Luo, J. et al., 2016. Deterministic Absolute Negative Mobility for Micro- and Submicrometer Particles Induced in a Microfluidic Device. Analytical Chemistry, 88(11), …

Deterministic Ratchet for Sub-micrometer (Bio)particle Separation

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

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

Developing mix-and-inject serial crystallography at synchrotrons

10 May 2024 | BioXFEL Publications | Contributor(s): K. A. Zielinski, L. Pollack

https://doi.org/10.1107/s2053273323090666 journal-article Zielinski, K. A., & Pollack, L. (2023). Developing mix-and-inject serial crystallography at synchrotrons. Acta Crystallographica Section A Foundations and Advances, 79(a2), C550–C550. https://doi.org/10.1107/s2053273323090666 K. A. …

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

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

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

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

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

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

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

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

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

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

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

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

Dielectrophoresis of lambda-DNA using 3D carbon electrodes

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

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

Dielectrophoresis: From molecular to micrometer scale analytes

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

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

Dielectrophoretic Sorting of Membrane Protein Nanocrystals

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

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

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

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

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

Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates

12 Jan 2020 | BioXFEL Publications | Contributor(s): Benjamin A. Barad, Lin Liu, Roberto E. Diaz, Ralp Basilio, Steven J. Van Dyken, Richard M. Locksley, James Fraser

http://dx.doi.org/10.1002/pro.3822 journal-article Barad, B.A. et al., 2020. Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates. Protein Science. Available at: http://dx.doi.org/10.1002/pro.3822. Benjamin A. Barad and Lin Liu and Roberto E. Diaz …

Diffraction before destruction

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

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

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

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

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

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

11 Apr 2017 | BioXFEL Publications | Contributor(s): Xuanxuan Li, Chun-Ya Chiu, Hsiang-Ju Wang, Stephan Kassemeyer, Sabine Botha, Robert L. Shoeman, Robert M Lawrence, Christopher Kupitz, Richard Kirian, Daniel James, Dingjie Wang, Garrett Charles Nelson, Marc Messerschmidt, Sébastien Boutet, Garth J. Williams, Elisabeth Hartmann, Aliakbar Jafarpour, Lutz M. Foucar, Anton Barty, Henry Chapman, Mengning Liang, Andreas Menzel, Fenglin Wang, Shibom Basu, Raimund Fromme, R. Bruce Doak, Petra Fromme, Uwe Weierstall, Michael H. Huang, John Spence, Ilme Schlichting, Brenda Hogue, Haiguang Liu

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

Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins

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

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

Diffuse X-Ray Scattering to Model Protein Motions

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

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

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

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

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

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

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

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

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

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

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

Direct phasing in femtosecond nanocrystallography. I. Diffraction characteristics

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

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

Direct phasing in femtosecond nanocrystallography. II. Phase retrieval

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

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

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

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

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

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

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

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

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

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

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

Discovering Design Principles to Re-Engineer Functional RNA Elements

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

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

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

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

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

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

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

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

Discovery of allosteric binding sites by crystallographic fragment screening

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

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

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

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

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

Distinct conformational states enable transglutaminase 2 to promote cancer cell survival versus cell death

12 Aug 2024 | BioXFEL Publications | Contributor(s): Cody Aplin, Kara Zielinski, Suzette Pabit, Deborah Ogunribido, William P. Katt, Lois Pollack, Richard A. Cerione, Shawn K. Milano

https://doi.org/10.1038/s42003-024-06672-x AbstractTransglutaminase 2 (TG2) is a GTP-binding, protein-crosslinking enzyme that has been investigated as a therapeutic target for Celiac disease, neurological disorders, and aggressive cancers. TG2 has been suggested to adopt two conformational states …

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

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

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

DNA Sequence and Histone Core Composition Control the Unwrapping of DNA from Nucleosome Core Particles

15 Feb 2019 | BioXFEL Publications | Contributor(s): Alex Mauney, Joshua Tokuda, Yujie Chen, Lois Pollack

http://dx.doi.org/10.1016/j.bpj.2018.11.1179 poster Mauney, A. et al., 2019. DNA Sequence and Histone Core Composition Control the Unwrapping of DNA from Nucleosome Core Particles. Biophysical Journal, 116(3), p.214a. Available at: http://dx.doi.org/10.1016/j.bpj.2018.11.1179. Alex Mauney and …

DNA Sequence and Histone Core Composition Determine the Unwrapping Pathways in Nucleosomes

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

http://dx.doi.org/10.1016/j.bpj.2019.11.2706 poster Mauney, A. & Pollack, L., 2020. DNA Sequence and Histone Core Composition Determine the Unwrapping Pathways in Nucleosomes. Biophysical Journal, 118(3), p.489a. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.2706. Alex Mauney and Lois …

Dose efficient Compton X-ray microscopy

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

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

Double-flow focused liquid injector for efficient serial femtosecond crystallography

16 Mar 2017 | BioXFEL Publications | Contributor(s): Dominik Oberthuer, Juraj Knoška, Max Oliver Wiedorn, Kenneth R. Beyerlein, David Bushnell, Elena G. Kovaleva, Michael Heymann, Lars Gumprecht, Richard Kirian, Anton Barty, Valerio Mariani, Aleksandra Tolstikova, Luigi Adriano, Salah Awel, Miriam Barthelmess, Katerina Dörner, P. Lourdu Xavier, Oleksandr Yefanov, Daniel R. James, Garrett Charles Nelson, Dingjie Wang, George Douglas Calvey, Yujie Chen, Andrea Schmidt, Michael Szczepek, Stefan Frielingsdorf, Oliver Lenz, Edward Snell, Philip J. Robinson, Božidar Šarler, Grega Belšak, Marjan Maček, Fabian Wilde, Andrew Aquila, Sébastien Boutet, Mengning Liang, Mark S. Hunter, Patrick Scheerer, John D. Lipscomb, Uwe Weierstall, Roger Kornberg, John Spence, Lois Pollack, Henry Chapman, Saša Bajt

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

Double-focusing mixing jet for XFEL study of chemical kinetics

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

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

Double-focusing mixing jet for XFEL study of chemical kinetics

13 Oct 2015 | Teaching Materials

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

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

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

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

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

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

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