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  1. Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography

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    14 Aug 2014 | BioXFEL Publications | Contributor(s): Wei Liu, Andrii Ishchenko, Vadim Cherezov

    http://dx.doi.org/10.1038/nprot.2014.141 journal-article Liu, W., Ishchenko, A. & Cherezov, V., 2014. Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography. Nature Protocols, 9(9), pp.2123–2134. Available at: http://dx.doi.org/10.1038/nprot.2014.141. Wei …

  2. Preprints for the life sciences

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    20 May 2016 | BioXFEL Publications | Contributor(s): J. M. Berg, N. Bhalla, P. E. Bourne, M. Chalfie, D. G. Drubin, J. S. Fraser, C. W. Greider, M. Hendricks, C. Jones, R. Kiley, S. King, M. W. Kirschner, H. M. Krumholz, R. Lehmann, M. Leptin, B. Pulverer, B. Rosenzweig, J. E. Spiro, M. Stebbins, C. Strasser, S. Swaminathan, P. Turner, R. D. Vale, K. VijayRaghavan, C. Wolberger

    http://dx.doi.org/10.1126/science.aaf9133 journal-article Berg, J.M. et al., 2016. Preprints for the life sciences. Science, 352(6288), pp.899–901. Available at: http://dx.doi.org/10.1126/science.aaf9133. J. M. Berg and N. Bhalla and P. E. Bourne and M. Chalfie and D. G. Drubin and J. S. …

  3. Prioritizing cardiovascular disease-associated variants altering NKX2-5 and TBX5 binding through an integrative computational approach

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    03 Nov 2023 | BioXFEL Publications | Contributor(s): Edwin G. Peña-Martínez, Diego A. Pomales-Matos, Alejandro Rivera-Madera, Jean L. Messon-Bird, Joshua G. Medina-Feliciano, Leandro Sanabria-Alberto, Adriana C. Barreiro-Rosario, Jeancarlos Rivera-Del Valle, Jessica M. Rodríguez-Ríos, Jose Arcadio Rodriguez-Martinez

    http://dx.doi.org/10.1016/j.jbc.2023.105423 journal-article Peña-Martínez, E. G., Pomales-Matos, D. A., Rivera-Madera, A., Messon-Bird, J. L., Medina-Feliciano, J. G., Sanabria-Alberto, L., Barreiro-Rosario, A. C., Rivera-Del Valle, J., Rodríguez-Ríos, J. M., & Rodríguez-Martínez, J. A. …

  4. Probing Mg2+-Mediated RNA-RNA Interactions in the Presence of Metabolites

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    07 Feb 2020 | BioXFEL Publications | Contributor(s): Derrick R. Lin, Suzette A. Pabit, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2019.11.551 poster Lin, D.R., Pabit, S.A. & Pollack, L., 2020. Probing Mg2+-Mediated RNA-RNA Interactions in the Presence of Metabolites. Biophysical Journal, 118(3), p.69a. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.551. Derrick R. Lin and Suzette A. …

  5. Probing the Nature of Charge Transfer at Nano–Bio Interfaces: Peptides on Metal Oxide Nanoparticles

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    03 Oct 2014 | BioXFEL Publications | Contributor(s): Pilarisetty Tarakeshwar, Julio L. Palma, Gregory P. Holland, Petra Fromme, Jeffery L. Yarger, Vladimiro Mujica

    journal-article http://dx.doi.org/10.1021/jz501854x Tarakeshwar, P. et al., 2014. Probing the Nature of Charge Transfer at Nano–Bio Interfaces: Peptides on Metal Oxide Nanoparticles. The Journal of Physical Chemistry Letters, 5(20), pp.3555–3559. Available at: …

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

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    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 …

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

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    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 …

  8. Product-stabilized filamentation by human glutamine synthetase allosterically tunes activity

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    08 Feb 2024 | BioXFEL Publications | Contributor(s): Eric R. Greene, Richard Muniz, Hiroki Yamamura, Samuel Hoff, Angelika Arada, Priyanka Bajaj, Daphne Chen, John D. Lee, Massimiliano Bonomi, Justin M. Kollman, James Fraser

    http://dx.doi.org/10.1016/j.bpj.2023.11.2135 journal-article Greene, E. R., Muniz, R., Yamamura, H., Hoff, S., Arada, A., Bajaj, P., Chen, D., Lee, J. D., Bonomi, M., Kollman, J. M., & Fraser, J. (2024). Product-stabilized filamentation by human glutamine synthetase allosterically tunes activity. …

  9. Production and Properties of XFEL Radiation

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    13 Nov 2014 | Teaching Materials

    Dr. Pietro Musumeci (UCLA) discusses an introduction to the physics and characteristics of X-ray free electron lasers.

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

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    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: …

  11. Proposal Writing Workshop Agenda

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    08 May 2017 | Downloads | Contributor(s): Bill Bauer

    …

  12. Protein and RNA dynamical fingerprinting

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    04 Mar 2019 | BioXFEL Publications | Contributor(s): Katherine A. Niessen, Mengyang Xu, Deepu K. George, Michael C. Chen, Adrian R. Ferré-D’Amaré, Edward Snell, Vivian Cody, James Pace, Marius Schmidt, Andrea Markelz

    http://dx.doi.org/10.1038/s41467-019-08926-3 journal-article Niessen, K.A. et al., 2019. Protein and RNA dynamical fingerprinting. Nature Communications, 10(1). Available at: http://dx.doi.org/10.1038/s41467-019-08926-3. Katherine A. Niessen and Mengyang Xu and Deepu K. George and Michael C. …

  13. Protein crystal structure obtained at 2.9 A resolution from injecting bacterial cells into an X-ray free-electron laser beam

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    19 Aug 2014 | BioXFEL Publications | Contributor(s): M. R. Sawaya, D. Cascio, M. Gingery, J. Rodriguez, L. Goldschmidt, J.-P. Colletier, M. M. Messerschmidt, S. Boutet, J. E. Koglin, G. J. Williams, A. S. Brewster, K. Nass, J. Hattne, S. Botha, R. B. Doak, R. L. Shoeman, D. P. DePonte, H.-W. Park, B. A. Federici, N. K. Sauter, I. Schlichting, D. S. Eisenberg

    http://dx.doi.org/10.1073/pnas.1413456111 journal-article Sawaya, M.R. et al., 2014. Protein crystal structure obtained at 2.9 A resolution from injecting bacterial cells into an X-ray free-electron laser beam. Proceedings of the National Academy of Sciences, 111(35), pp.12769–12774. Available …

  14. Protein Crystallization in an Actuated Microfluidic Nanowell Device

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    25 Feb 2016 | BioXFEL Publications | Contributor(s): Bahige G. Abdallah, Shatabdi Roy-Chowdhury, Raimund Fromme, Petra Fromme, Alexandra Ros

    http://dx.doi.org/10.1021/acs.cgd.5b01748 Bahige G. Abdallah and Shatabdi Roy-Chowdhury and Raimund Fromme and Petra Fromme and Alexandra Ros Abdallah, B.G. et al., 2016. Protein Crystallization in an Actuated Microfluidic Nanowell Device. Crystal Growth & Design. Available at: …

  15. Protein dielectrophoresis and the link to dielectric properties

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    20 Feb 2015 | BioXFEL Publications | Contributor(s): Fernanda Camacho-Alanis, Alexandra Ros

    http://dx.doi.org/10.4155/bio.14.306 Fernanda Camacho-Alanis and Alexandra Ros Camacho-Alanis, F. & Ros, A., 2015. Protein dielectrophoresis and the link to dielectric properties. Bioanalysis, 7(3), pp.353–371. Available at: http://dx.doi.org/10.4155/bio.14.306. journal-article

  16. Protein dielectrophoresis: Advances, challenges, and applications

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    11 Feb 2013 | BioXFEL Publications | Contributor(s): Asuka Nakano, Alexandra Ros

    http://dx.doi.org/10.1002/elps.201200482 journal-article Nakano, A. & Ros, A., 2013. Protein dielectrophoresis: Advances, challenges, and applications. ELECTROPHORESIS, 34(7), pp.1085–1096. Available at: http://dx.doi.org/10.1002/elps.201200482. Asuka Nakano and Alexandra Ros

  17. Protein energy landscapes determined by five-dimensional crystallography

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    19 Nov 2013 | BioXFEL Publications | Contributor(s): Marius Schmidt, Vukica Srajer, Robert Henning, Hyotcherl Ihee, Namrta Purwar, Jason Tenboer, Shailesh Tripathi

    Free-energy landscapes decisively determine the progress of enzymatically catalyzed reactions [Cornish-Bowden (2012),Fundamentals of Enzyme Kinetics, 4th ed.]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [Moffat (2001),Chem. Rev.101, …

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

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

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

  19. Protein structural ensembles are revealed by redefining X-ray electron density noise

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    21 Dec 2013 | BioXFEL Publications | Contributor(s): P. T. Lang, J. M. Holton, J. S. Fraser, T. Alber

    http://dx.doi.org/10.1073/pnas.1302823110 journal-article Lang, P.T. et al., 2013. Protein structural ensembles are revealed by redefining X-ray electron density noise. Proceedings of the National Academy of Sciences, 111(1), pp.237–242. Available at: http://dx.doi.org/10.1073/pnas.1302823110. …

  20. Protein–DNA and ion–DNA interactions revealed through contrast variation SAXS

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    02 Apr 2016 | BioXFEL Publications | Contributor(s): Joshua M. Tokuda, Suzette A. Pabit, Lois Pollack

    http://dx.doi.org/10.1007/s12551-016-0196-8 journal-article Tokuda, J.M., Pabit, S.A. & Pollack, L., 2016. Protein–DNA and ion–DNA interactions revealed through contrast variation SAXS. Biophysical Reviews, 8(2), pp.139–149. Available at: http://dx.doi.org/10.1007/s12551-016-0196-8. Joshua …

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

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

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

  22. Psana Tutorial

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    03 Sep 2014 | Teaching Materials

    Chris O'Grady (SLAC) Psana is the main analysis tool developed by LCLS, upon which some other tools are based. It uses a combination of C++ and python. I will discuss recent psana developments and future plans. Recent developments include the ability to express complex analysis ideas with simple …

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

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    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 …

  24. Publisher Correction: Structural basis of ligand recognition at the human MT1 melatonin receptor

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    02 May 2019 | BioXFEL Publications | Contributor(s): Benjamin Stauch, Linda C. Johansson, John D. McCorvy, Nilkanth N Patel, Gye Won Han, Xi-Ping Huang, Cornelius Gati, Alexander Batyuk, Samuel T. Slocum, Andrii Ishchenko, Wolfgang Brehm, Thomas A. White, Nairie Michaelian, Caleb Alexander Madsen, Lan Zhu, Thomas D. Grant, Jessica M. Grandner, Anna Shiriaeva, Reid H. J. Olsen, Alexandra R. Tribo, Saïd Yous, Raymond C. Stevens, Uwe Weierstall, Vsevolod Katritch, Bryan L. Roth, Wei Liu, Vadim Cherezov

    http://dx.doi.org/10.1038/s41586-019-1209-0 journal-article Stauch, B. et al., 2019. Publisher Correction: Structural basis of ligand recognition at the human MT1 melatonin receptor. Nature, 569(7756), pp.E6–E6. Available at: http://dx.doi.org/10.1038/s41586-019-1209-0. Benjamin Stauch and …

  25. Publisher's Note: “Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer” [Struct. Dyn. 1, 024701 (2014)]

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    28 Nov 2017 | BioXFEL Publications | Contributor(s): Marius Schmidt, Dilano Saldin

    http://dx.doi.org/10.1063/1.5016802 journal-article Schmidt, M. & Saldin, D.K., 2017. Publisher’s Note: “Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer” [Struct. Dyn. 1, 024701 (2014)]. Structural Dynamics, 4(6), p.069901. …

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

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    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 …

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

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

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

  28. Purification and assembly of thermostable Cy5 labeled γ-PNAs into a 3D DNA nanocage

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    11 Mar 2015 | BioXFEL Publications | Contributor(s): Justin D Flory, Trey Johnson, Chad R Simmons, Su Lin, Giovanna Ghirlanda, Petra Fromme

    http://dx.doi.org/10.4161/1949095x.2014.992181 journal-article Flory, J.D. et al., 2014. Purification and assembly of thermostable Cy5 labeled γ-PNAs into a 3D DNA nanocage. Artificial DNA: PNA & XNA, 5(3), p.e992181. Available at: http://dx.doi.org/10.4161/1949095x.2014.992181. Justin D Flory …

  29. Purification and biochemical characterization of the ATP synthase from Heliobacterium modesticaldum

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    12 May 2015 | BioXFEL Publications | Contributor(s): Jay-How Yang, Iosifina Sarrou, Jose M. Martin-Garcia, Shangji Zhang, Kevin E. Redding, Petra Fromme

    http://dx.doi.org/10.1016/j.pep.2015.05.006 Jay-How Yang and Iosifina Sarrou and Jose M. Martin-Garcia and Shangji Zhang and Kevin E. Redding and Petra Fromme Yang, J.-H. et al., 2015. Purification and biochemical characterization of the ATP synthase from Heliobacterium modesticaldum. Protein …

  30. Purification and Biophysical Characterization of the CapA Membrane Protein FTT0807 fromFrancisella tularensis

    0.0 out of 5 stars 

    04 Mar 2014 | BioXFEL Publications | Contributor(s): Jose M. Martin-Garcia, Debra T. Hansen, James D Zook, Andrey V. Loskutov, Mark D. Robida, Felicia M. Craciunescu, Kathryn F. Sykes, Rebekka M. Wachter, Petra Fromme, James P. Allen

    http://dx.doi.org/10.1021/bi401644s journal-article Martin-Garcia, J.M. et al., 2014. Purification and Biophysical Characterization of the CapA Membrane Protein FTT0807 fromFrancisella tularensis. Biochemistry, 53(12), pp.1958–1970. Available at: http://dx.doi.org/10.1021/bi401644s. Jose M. …

  31. Purification and SAXS Analysis of the Integrin Linked Kinase, PINCH, Parvin (IPP) Heterotrimeric Complex

    0.0 out of 5 stars 

    31 Jan 2013 | BioXFEL Publications | Contributor(s): Amy L. Stiegler, Thomas D. Grant, Joseph Luft, David A. Calderwood, Edward Snell, Titus J. Boggon

    http://dx.doi.org/10.1371/journal.pone.0055591 journal-article Stiegler, A.L. et al., 2013. Purification and SAXS Analysis of the Integrin Linked Kinase, PINCH, Parvin (IPP) Heterotrimeric Complex B. Kobe, ed. PLoS ONE, 8(1), p.e55591. Available at: …

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

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

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

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

    0.0 out of 5 stars 

    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 …

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

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    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 …

  35. qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps

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    26 Jan 2018 | BioXFEL Publications | Contributor(s): Gydo CP Van Zundert, Brandi M Hudson, Daniel A Keedy, Rasmus Fonseca, Amelie Heliou, Pooja Suresh, Kenneth Borrelli, Tyler Day, James Fraser, Henry Van Den Bedem

    http://dx.doi.org/10.1101/253419 Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and enthalpy in lead …

  36. qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps

    0.0 out of 5 stars 

    20 Nov 2018 | BioXFEL Publications | Contributor(s): Gydo C. P. Van Zundert, Brandi M. Hudson, Saulo H. P. De Oliveira, Daniel A. Keedy, Rasmus Fonseca, Amelie Heliou, Pooja Suresh, Kenneth Borrelli, Tyler Day, James Fraser, Henry Van Den Bedem

    http://dx.doi.org/10.1021/acs.jmedchem.8b01292 journal-article Van Zundert, G. et al., 2018. qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps. Journal of Medicinal Chemistry. Available at: …

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

    0.0 out of 5 stars 

    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: …

  38. Quantitative Analysis of Salt-Induced RNA Duplex Variations by Wide-Angle X-ray Scattering (WAXS)

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

    http://dx.doi.org/10.1016/j.bpj.2019.11.548 poster Chen, Y.-L. & Pollack, L., 2020. Quantitative Analysis of Salt-Induced RNA Duplex Variations by Wide-Angle X-ray Scattering (WAXS). Biophysical Journal, 118(3), p.68a. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.548. Yen-Lin Chen and …

  39. Quantitative Analysis of the Electrostatic Potential in Rock-Salt Crystals Using Accurate Electron Diffraction Data

    0.0 out of 5 stars 

    26 Jul 2002 | BioXFEL Publications | Contributor(s): V. G. Tsirelson, A. S. Avilov, G. G. Lepeshov, A. K. Kulygin, J. Stahn, U. Pietsch, J. C. H. Spence

    http://dx.doi.org/10.1021/jp0015729 journal-article Tsirelson, V.G. et al., 2001. Quantitative Analysis of the Electrostatic Potential in Rock-Salt Crystals Using Accurate Electron Diffraction Data. The Journal of Physical Chemistry B, 105(21), pp.5068–5074. Available at: …

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

    0.0 out of 5 stars 

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

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

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

    0.0 out of 5 stars 

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

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

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

    0.0 out of 5 stars 

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

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

  43. Rapid Data Quality Feedback and Online Monitoring using CASS

    0.0 out of 5 stars 

    29 Aug 2014 | Teaching Materials

    Karol Nass (MPI) Description of the layout of CASS software suite and its functionality on the LCLS online and offline data streams. Real time monitoring of the SFX experiment: hit rate, resolution, pixel saturation, 2D powder pattern. Rapid offline processing of the raw LCLS data: crystal hit …

  44. Rapid sample delivery for megahertz serial crystallography at X-ray FELs

    0.0 out of 5 stars 

    27 Jul 2018 | BioXFEL Publications | Contributor(s): Max Oliver Wiedorn, Salah Awel, Andrew J. Morgan, Kartik Ayyer, Yaroslav Gevorkov, Holger Fleckenstein, Nils Roth, Luigi Adriano, Richard Bean, Kenneth R. Beyerlein, Joe Chen, Jesse David Coe, Francisco Cruz-Mazo, Tomas Ekeberg, Rita Graceffa, Michael Heymann, Daniel A. Horke, Juraj Knoška, Valerio Mariani, Reza Nazari, Dominik Oberthür, Amit K. Samanta, Raymond G. Sierra, Claudiu A. Stan, Oleksandr Yefanov, Dimitrios Rompotis, Jonathan Correa, Benjamin Erk, Rolf Treusch, Joachim Schulz, Brenda Hogue, Alfonso M. Gañán-Calvo, Petra Fromme, Jochen Küpper, Andrei V. Rode, Saša Bajt, Richard Kirian, Henry Chapman

    http://dx.doi.org/10.1107/s2052252518008369 Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and …

  45. Rayleigh-scattering microscopy for tracking and sizing nanoparticles in focused aerosol beams

    0.0 out of 5 stars 

    11 Sep 2018 | BioXFEL Publications | Contributor(s): Max F. Hantke, Johan Bielecki, Olena Kulyk, Daniel Westphal, Daniel S. D. Larsson, Martin Svenda, Hemanth K. N. Reddy, Richard Kirian, Jakob Andreasson, Janos Hajdu, Filipe R. N. C. Maia

    http://dx.doi.org/10.1107/s2052252518010837 Ultra-bright femtosecond X-ray pulses generated by X-ray free-electron lasers (XFELs) can be used to image high-resolution structures without the need for crystallization. For this approach, aerosol injection has been a successful method to deliver …

  46. Re-directing bacterial microcompartment systems to enhance recombinant expression of lysis protein E from bacteriophage ϕX174 in Escherichia coli

    0.0 out of 5 stars 

    25 Apr 2017 | BioXFEL Publications | Contributor(s): Mimi C. Yung, Feliza A. Bourguet, Timothy S. Carpenter, Matthew Coleman

    http://dx.doi.org/10.1186/s12934-017-0685-x journal-article Yung, M.C. et al., 2017. Re-directing bacterial microcompartment systems to enhance recombinant expression of lysis protein E from bacteriophage ϕX174 in Escherichia coli. Microbial Cell Factories, 16(1). Available at: …

  47. Reaction coordinate dependent fibrillar formation of human glutamine synthetase tunes activity

    0.0 out of 5 stars 

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

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

  48. Reaction Initiation in Enzyme Crystals by Diffusion of Substrate

    0.0 out of 5 stars 

    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 …

  49. Real-time observation of the initiation of RNA polymerase II transcription

    0.0 out of 5 stars 

    02 Sep 2015 | BioXFEL Publications | Contributor(s): Furqan M. Fazal, Cong A. Meng, Kenji Murakami, Roger Kornberg, Steven M. Block

    journal-article http://dx.doi.org/10.1038/nature14882 Fazal, F.M. et al., 2015. Real-time observation of the initiation of RNA polymerase II transcription. Nature, 525(7568), pp.274–277. Available at: http://dx.doi.org/10.1038/nature14882. Furqan M. Fazal and Cong A. Meng and Kenji Murakami and …

  50. Recent Advances in SFX at BioXFEL

    0.0 out of 5 stars 

    25 Jul 2015 | Teaching Materials | Contributor(s): John Spence

    Dr. John Spence, Scientific Director for BioXFEL, discusses recent advances in the field of serial crystallography.

  51. Recent developments in CrystFEL

    0.0 out of 5 stars 

    29 Mar 2016 | BioXFEL Publications | Contributor(s): Thomas A. White, Valerio Mariani, Wolfgang Brehm, Oleksandr Yefanov, Anton Barty, Kenneth R. Beyerlein, Fedor Chervinskii, Lorenzo Galli, Cornelius Gati, Takanori Nakane, Alexandra Tolstikova, Keitaro Yamashita, Chun Hong Yoon, Kay Diederichs, Henry Chapman

    CrystFELis a suite of programs for processing data from `serial crystallography' experiments, which are usually performed using X-ray free-electron lasers (FELs) but also increasingly with other X-ray sources. TheCrystFELsoftware suite has been under development since 2009, just before the first …

  52. Recombinant expression, purification, and biophysical characterization of the transmembrane and membrane proximal domains of HIV-1 gp41

    0.0 out of 5 stars 

    23 Aug 2014 | BioXFEL Publications | Contributor(s): Zhen Gong, Sarah A. Kessans, Lusheng Song, Katerina Dörner, Ho-Hsien Lee, Lydia R Meador, Joshua LaBaer, Brenda Hogue, Tsafrir S. Mor, Petra Fromme

    http://dx.doi.org/10.1002/pro.2540 journal-article Gong, Z. et al., 2014. Recombinant expression, purification, and biophysical characterization of the transmembrane and membrane proximal domains of HIV-1 gp41. Protein Science, 23(11), pp.1607–1618. Available at: …

  53. Reconstructing three-dimensional helical structure with an X-ray free electron laser

    0.0 out of 5 stars 

    23 Feb 2016 | BioXFEL Publications | Contributor(s): M. Uddin

    Recovery of three-dimensional structure from single-particle X-ray scattering of completely randomly oriented diffraction patterns as predicted a few decades ago has been realized owing to the advent of the new emerging X-ray free electron laser (XFEL) technology. Since the world's first XFEL …

  54. Reconstruction of an object from diffraction intensities averaged over multiple object clusters

    0.0 out of 5 stars 

    29 Sep 2016 | BioXFEL Publications | Contributor(s): J P J Chen, R D Arnal, A J Morgan, R J Bean, K R Beyerlein, H N Chapman, P J Bones, R P Millane, R A Kirian

    http://dx.doi.org/10.1088/2040-8978/18/11/114003 J P J Chen and R D Arnal and A J Morgan and R J Bean and K R Beyerlein and H N Chapman and P J Bones and R P Millane and R A Kirian Chen, J.P.J. et al., 2016. Reconstruction of an object from diffraction intensities averaged over multiple object …

  55. Reconstruction of Objects from Their Averaged Finite Crystal Diffraction Intensity

    0.0 out of 5 stars 

    26 Aug 2019 | BioXFEL Publications | Contributor(s): J. P. J. Chen, K. E. Schmidt, R. A. Kirian, J. J. Donatelli

    http://dx.doi.org/10.1109/icip.2019.8804468 proceedings-article Chen, J.P.J. et al., 2019. Reconstruction of Objects from Their Averaged Finite Crystal Diffraction Intensity. 2019 IEEE International Conference on Image Processing (ICIP). Available at: http://dx.doi.org/10.1109/icip.2019.8804468. …

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

    0.0 out of 5 stars 

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

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

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

    0.0 out of 5 stars 

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

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

  58. Relative Stability of Human Centrins and Its Relationship to Calcium Binding

    0.0 out of 5 stars 

    24 Jan 2013 | BioXFEL Publications | Contributor(s): Belinda Pastrana-Ríos, Myrna Reyes, Jessica De Orbeta, Verónica Meza, Daniel Narváez, Ana María Gómez, Aslin Marie Rodriguez Nassif, Ruth Almodovar, Adalberto Díaz Casas, José Robles, Ana María Ortiz, Lizbeth Irizarry, Melissa Campbell, Mara Colón

    journal-article http://dx.doi.org/10.1021/bi301417z Pastrana-Ríos, B. et al., 2013. Relative Stability of Human Centrins and Its Relationship to Calcium Binding. Biochemistry, 52(7), pp.1236–1248. Available at: http://dx.doi.org/10.1021/bi301417z. Belinda Pastrana-Ríos and Myrna Reyes and …

  59. Reply to 'Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein'

    0.0 out of 5 stars 

    21 Mar 2014 | BioXFEL Publications | Contributor(s): Yang Ouk Jung, Jae Hyuk Lee, Joonghan Kim, Marius Schmidt, Keith Moffat, Vukica Šrajer, Hyotcherl Ihee

    http://dx.doi.org/10.1038/nchem.1897 Yang Ouk Jung and Jae Hyuk Lee and Joonghan Kim and Marius Schmidt and Keith Moffat and Vukica Šrajer and Hyotcherl Ihee Jung, Y.O. et al., 2014. Reply to “Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein.” …

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

    0.0 out of 5 stars 

    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: …

  61. Rescue of Conformational Dynamics in Enzyme Catalysis by Directed Evolution

    0.0 out of 5 stars 

    06 Sep 2017 | BioXFEL Publications | Contributor(s): Renee Otten, Lin Liu, Lillian R. Kenner, Michael W. Clarkson, David Mavor, Dan S. Tawfik, Dorothee Kern, James Fraser

    http://dx.doi.org/10.1101/185009 Rational design and directed evolution have proved to be successful approaches to increase catalytic efficiencies of both natural and artificial enzymes. However, a comprehensive understanding of how evolution shapes the energy landscape of catalysis remains a …

  62. Rescue of conformational dynamics in enzyme catalysis by directed evolution

    0.0 out of 5 stars 

    03 Apr 2018 | BioXFEL Publications | Contributor(s): Renee Otten, Lin Liu, Lillian R. Kenner, Michael W. Clarkson, David Mavor, Dan S. Tawfik, Dorothee Kern, James Fraser

    http://dx.doi.org/10.1038/s41467-018-03562-9 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Otten, R. et al., 2018. Rescue of conformational dynamics in enzyme catalysis by directed evolution. Nature Communications, 9(1). Available at: …

  63. Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals

    0.0 out of 5 stars 

    22 Dec 2017 | BioXFEL Publications | Contributor(s): Cecilia M. Casadei, Ching-Ju Tsai, Anton Barty, Mark S. Hunter, Nadia Zatsepin, Celestino Padeste, Guido Capitani, W. Henry Benner, Sébastien Boutet, Stefan Hau-Riege, Christopher Kupitz, Marc Messerschmidt, John I. Ogren, Tom Pardini, Kenneth J. Rothschild, Leonardo Sala, Brent W. Segelke, Garth J. Williams, James E. Evans, Xiao-Dan Li, Matthew Coleman, Bill Pedrini, Matthias Frank

    http://dx.doi.org/10.1107/s2052252517017043 Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons …

  64. Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals

    0.0 out of 5 stars 

    22 Dec 2017 | BioXFEL Publications | Contributor(s): Cecilia M. Casadei, Ching-Ju Tsai, Anton Barty, Mark S. Hunter, Nadia Zatsepin, Celestino Padeste, Guido Capitani, W. Henry Benner, Sébastien Boutet, Stefan Hau-Riege, Christopher Kupitz, Marc Messerschmidt, John I. Ogren, Tom Pardini, Kenneth J. Rothschild, Leonardo Sala, Brent W. Segelke, Garth J. Williams, James E. Evans, Xiao-Dan Li, Matthew Coleman, Bill Pedrini, Matthias Frank

    http://dx.doi.org/10.1107/s2052252517017043/ec5006sup1.pdf component Casadei, C.M. et al., 2018. Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals. Available at: http://dx.doi.org/10.1107/s2052252517017043/ec5006sup1.pdf. …

  65. Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser

    0.0 out of 5 stars 

    14 Jun 2018 | BioXFEL Publications | Contributor(s): Przemyslaw Nogly, Tobias Weinert, Daniel James, Sergio Carbajo, Dmitry Ozerov, Antonia Furrer, Dardan Gashi, Veniamin Borin, Petr Skopintsev, Kathrin Jaeger, Karol Nass, Petra Båth, Robert William Bosman, Jason Koglin, Matthew Seaberg, Thomas Lane, Demet Kekilli, Steffen Brünle, Tomoyuki Tanaka, Wenting Wu, Christopher Milne, Thomas White, Anton Barty, Uwe Weierstall, Valerie Panneels, Eriko Nango, So Iwata, Mark S. Hunter, Igor Schapiro, Gebhard F.X. Schertler, Richard Neutze, Jörg Standfuss

    http://dx.doi.org/10.1126/science.aat0094 journal-article Nogly, P. et al., 2018. Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Science, p.eaat0094. Available at: http://dx.doi.org/10.1126/science.aat0094. Przemyslaw Nogly and Tobias Weinert and Daniel James …

  66. Retinal oxidative stress at the onset of diabetes determined by synchrotron FTIR widefield imaging: towards diabetes pathogenesis

    0.0 out of 5 stars 

    06 Feb 2017 | BioXFEL Publications | Contributor(s): Ebrahim Aboualizadeh, Mahsa Ranji, Christine M. Sorenson, Reyhaneh Sepehr, Nader Sheibani, Carol J. Hirschmugl

    A mechanistic understanding of oxidative damage in the retina and the significance of photoreceptors at the onset of diabetic retinopathy are reported. journal-article http://dx.doi.org/10.1039/c6an02603f Aboualizadeh, E. et al., 2017. Retinal oxidative stress at the onset of diabetes determined …

  67. Retrieving functional pathways of biomolecules from single-particle snapshots

    0.0 out of 5 stars 

    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 …

  68. Revealing Accessibility of Cryptic Protein Binding Sites within the Functional Collagen Fibril

    0.0 out of 5 stars 

    01 Nov 2017 | BioXFEL Publications | Contributor(s): Cody Hoop, Jie Zhu, Ana Nunes, David Case, Jean Baum

    http://dx.doi.org/10.3390/biom7040076 journal-article Hoop, C. et al., 2017. Revealing Accessibility of Cryptic Protein Binding Sites within the Functional Collagen Fibril. Biomolecules, 7(4), p.76. Available at: http://dx.doi.org/10.3390/biom7040076. Cody Hoop and Jie Zhu and Ana Nunes and …

  69. Revealing the distinct folding phases of an RNA three-helix junction

    0.0 out of 5 stars 

    24 Apr 2018 | BioXFEL Publications | Contributor(s): Alex Plumridge, Andrea Katz, George Douglas Calvey, Ron Elber, Serdal Kirmizialtin, Lois Pollack

    http://dx.doi.org/10.1093/nar/gky363 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Plumridge, A. et al., 2018. Revealing the distinct folding phases of an RNA three-helix junction. Nucleic Acids Research. Available at: http://dx.doi.org/10.1093/nar/gky363. Alex Plumridge and …

  70. Revealing transient structures of nucleosomes as DNA unwinds

    0.0 out of 5 stars 

    03 Jul 2014 | BioXFEL Publications | Contributor(s): Yujie Chen, Joshua M. Tokuda, Traci Topping, Julie L. Sutton, Steve P. Meisburger, Suzette A. Pabit, Lisa M. Gloss, Lois Pollack

    http://dx.doi.org/10.1093/nar/gku562 journal-article Chen, Y. et al., 2014. Revealing transient structures of nucleosomes as DNA unwinds. Nucleic Acids Research, 42(13), pp.8767–8776. Available at: http://dx.doi.org/10.1093/nar/gku562. Yujie Chen and Joshua M. Tokuda and Traci Topping and …

  71. Review: Serial femtosecond crystallography: A revolution in structural biology

    0.0 out of 5 stars 

    01 May 2016 | BioXFEL Publications | Contributor(s): Jose M. Martin-Garcia, Chelsie E Conrad, Jesse David Coe, Shatabdi Roy-Chowdhury, Petra Fromme

    http://dx.doi.org/10.1016/j.abb.2016.03.036 Jose M. Martin-Garcia and Chelsie E. Conrad and Jesse Coe and Shatabdi Roy-Chowdhury and Petra Fromme Martin-Garcia, J.M. et al., 2016. Serial femtosecond crystallography: A revolution in structural biology. Archives of Biochemistry and Biophysics, 602, …

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

    0.0 out of 5 stars 

    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 …

  73. Ribosomal protein L11 selectively stabilizes a tertiary structure of the GTPase Center rRNA domain

    0.0 out of 5 stars 

    23 Dec 2019 | BioXFEL Publications | Contributor(s): Robb Welty, Michael Rau, Suzette Pabit, Mark S. Dunstan, Graeme L. Conn, Lois Pollack, Kathleen B. Hall

    http://dx.doi.org/10.1016/j.jmb.2019.12.010 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Welty, R. et al., 2019. Ribosomal protein L11 selectively stabilizes a tertiary structure of the GTPase Center rRNA domain. Journal of Molecular Biology. Available at: …

  74. RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers

    0.0 out of 5 stars 

    27 Sep 2023 | BioXFEL Publications | Contributor(s): Kara Zielinski, Shuo Sui, Suzette A. Pabit, Daniel A. Rivera, Tong Wang, Qingyue Hu, Maithri M. Kashipathy, Stella Lisova, Chris B. Schaffer, Valerio Mariani, Mark S. Hunter, Christopher Kupitz, Frank R. Moss, Frédéric P. Poitevin, Thomas D. Grant, Lois Pollack

    http://dx.doi.org/10.1126/sciadv.adj3509 RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We …

  75. RNA Triplex Structures Revealed by WAXS-Driven MD Simulations

    0.0 out of 5 stars 

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

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

  76. Robust total X-ray scattering workflow to study correlated motion of proteins in crystals

    0.0 out of 5 stars 

    03 Mar 2023 | BioXFEL Publications | Contributor(s): Steve P. Meisburger, David Case, Nozomi Ando

    http://dx.doi.org/10.1038/s41467-023-36734-3 AbstractThe breathing motions of proteins are thought to play a critical role in function. However, current techniques to study key collective motions are limited to spectroscopy and computation. We present a high-resolution experimental approach based …

  77. Role of conformational dynamics in the catalytic mechanism of viral macrodomains

    0.0 out of 5 stars 

    08 Feb 2024 | BioXFEL Publications | Contributor(s): Rishav Mitra, James Fraser

    https://doi.org/10.1016/j.bpj.2023.11.2156 journal-article Mitra, R., & Fraser, J. (2024). Role of conformational dynamics in the catalytic mechanism of viral macrodomains. Biophysical Journal, 123(3), 356a–357a. https://doi.org/10.1016/j.bpj.2023.11.2156 Rishav Mitra and James Fraser

  78. Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions

    0.0 out of 5 stars 

    17 Nov 2014 | BioXFEL Publications | Contributor(s): Yahli Lorch, Barbara Maier-Davis, Roger Kornberg

    journal-article http://dx.doi.org/10.1101/gad.250704.114 Lorch, Y., Maier-Davis, B. & Kornberg, R.D., 2014. Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions. Genes & Development, 28(22), pp.2492–2497. Available at: …

  79. Role of Ion Valence in the Submillisecond Collapse and Folding of a Small RNA Domain

    0.0 out of 5 stars 

    12 Feb 2013 | BioXFEL Publications | Contributor(s): Suzette A. Pabit, Julie L. Sutton, Huimin Chen, Lois Pollack

    http://dx.doi.org/10.1021/bi3016636 journal-article Pabit, S.A. et al., 2013. Role of Ion Valence in the Submillisecond Collapse and Folding of a Small RNA Domain. Biochemistry, 52(9), pp.1539–1546. Available at: http://dx.doi.org/10.1021/bi3016636. Suzette A. Pabit and Julie L. Sutton and …

  80. Role of the MT1 and MT2 melatonin receptors in mediating depressive- and anxiety-like behaviors in C3H/HeN mice

    0.0 out of 5 stars 

    03 Feb 2017 | BioXFEL Publications | Contributor(s): J. Liu, S. J. Clough, M. L. Dubocovich

    http://dx.doi.org/10.1111/gbb.12369 journal-article Liu, J., Clough, S.J. & Dubocovich, M.L., 2017. Role of the MT1 and MT2 melatonin receptors in mediating depressive- and anxiety-like behaviors in C3H/HeN mice. Genes, Brain and Behavior, 16(5), pp.546–553. Available at: …

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

    0.0 out of 5 stars 

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

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

  82. Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage

    0.0 out of 5 stars 

    24 May 2024 | BioXFEL Publications | Contributor(s): Jingyou Rao, Ruiqi Xin, Christian Macdonald, Matthew K. Howard, Gabriella O. Estevam, Sook Wah Yee, Mingsen Wang, James Fraser, Willow Coyote-Maestas, Harold Pimentel

    http://dx.doi.org/10.1186/s13059-024-03279-7 AbstractDeep mutational scanning (DMS) measures the effects of thousands of genetic variants in a protein simultaneously. The small sample size renders classical statistical methods ineffective. For example, p-values cannot be correctly calibrated when …

  83. Salt Dependence of A-Form RNA Duplexes: Structures and Implications

    0.0 out of 5 stars 

    23 Oct 2019 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Lois Pollack

    http://dx.doi.org/10.1021/acs.jpcb.9b07502 journal-article Chen, Y.-L. & Pollack, L., 2019. Salt Dependence of A-Form RNA Duplexes: Structures and Implications. The Journal of Physical Chemistry B. Available at: http://dx.doi.org/10.1021/acs.jpcb.9b07502. Yen-Lin Chen and Lois Pollack

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

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    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 …

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

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

    http://dx.doi.org/10.1002/bip.23427 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Marchany‐Rivera, D. et al., 2021. SAXS structure of homodimeric oxyHemoglobin III from bivalve Lucina pectinata. Biopolymers. …

  86. SAXS studies of RNA: structures, dynamics, and interactions with partners

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    12 Apr 2016 | BioXFEL Publications | Contributor(s): Yujie Chen, Lois Pollack

    http://dx.doi.org/10.1002/wrna.1349 Yujie Chen and Lois Pollack Chen, Y. & Pollack, L., 2016. SAXS studies of RNA: structures, dynamics, and interactions with partners. WIREs RNA. Available at: http://dx.doi.org/10.1002/wrna.1349. NSF-STC Biology with X-ray Lasers (NSF-1231306) journal-article

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

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    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 …

  88. Scaling and merging time-resolved pink-beam diffraction with variational inference

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    08 Nov 2024 | BioXFEL Publications | Contributor(s): Kara Zielinski, Cole Dolamore, Harrison K. Wang, Robert W. Henning, Mark A. Wilson, Lois Pollack, Vukica Srajer, Doeke R. Hekstra, Kevin M. Dalton

    https://doi.org/10.1063/4.0000269 Time-resolved x-ray crystallography (TR-X) at synchrotrons and free electron lasers is a promising technique for recording dynamics of molecules at atomic resolution. While experimental methods for TR-X have proliferated and matured, data analysis is often …

  89. Scanning Compton X-ray Microscopy

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    10 Aug 2018 | BioXFEL Publications | Contributor(s): Pablo Villanueva-Perez, Sasa Bajt, Henry Chapman

    http://dx.doi.org/10.1017/s1431927618013259 journal-article Villanueva-Perez, P., Bajt, S. & Chapman, H.N., 2018. Scanning Compton X-ray Microscopy. Microscopy and Microanalysis, 24(S2), pp.182–183. Available at: http://dx.doi.org/10.1017/s1431927618013259. Pablo Villanueva-Perez and Sasa Bajt …

  90. Science in the age of machine learning

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    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

  91. Second harmonic generation correlation spectroscopy for characterizing translationally diffusing protein nanocrystals

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    24 Jun 2016 | BioXFEL Publications | Contributor(s): Ximeng Y. Dow, Christopher M. Dettmar, Emma L. DeWalt, Justin A. Newman, Alexander R. Dow, Shatabdi Roy-Chowdhury, Jesse David Coe, Christopher Kupitz, Petra Fromme, Garth J. Simpson

    Second harmonic generation correlation spectroscopy (SHG-CS) is demonstrated as a new approach to protein nanocrystal characterization. A novel line-scanning approach was performed to enable autocorrelation analysis without sample damage from the intense incident beam. An analytical model for …

  92. Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

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    29 Jan 2013 | BioXFEL Publications | Contributor(s): James D Zook, Trivikram R. Moulgu, Neil Jacobsen, Guangxin Lin, Brian Cherry, Michael F. Brown, Petra Fromme

    http://dx.doi.org/10.1016/j.bpj.2012.11.1248 journal-article Zook, J.D. et al., 2013. Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane. Biophysical Journal, 104(2), p.221a. Available at: http://dx.doi.org/10.1016/j.bpj.2012.11.1248. James D. Zook and …

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

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    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 …

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

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    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 …

  95. Selective trapping of single mammalian breast cancer cells by insulator-based dielectrophoresis

    0.0 out of 5 stars 

    09 Jan 2014 | BioXFEL Publications | Contributor(s): Sanchari Bhattacharya, Tzu-Chiao Chao, Nethmi Ariyasinghe, Yvette Ruiz, Douglas Lake, Robert Ros, Alexandra Ros

    http://dx.doi.org/10.1007/s00216-013-7598-2 journal-article Bhattacharya, S. et al., 2014. Selective trapping of single mammalian breast cancer cells by insulator-based dielectrophoresis. Analytical and Bioanalytical Chemistry, 406(7), pp.1855–1865. Available at: …

  96. Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser

    0.0 out of 5 stars 

    04 Nov 2016 | BioXFEL Publications | Contributor(s): Mark S. Hunter, Chun Hong Yoon, Hasan Demirci, Raymond G. Sierra, E. Han Dao, Radman Ahmadi, Fulya Aksit, Andrew L. Aquila, Halilibrahim Ciftci, Serge Guillet, Matt J. Hayes, Thomas J. Lane, Meng Liang, Ulf Lundström, Jason E. Koglin, Paul Mgbam, Yashas Rao, Lindsey Zhang, Soichi Wakatsuki, James Holton, Sébastien Boutet

    http://dx.doi.org/10.1038/ncomms13388 Mark S. Hunter and Chun Hong Yoon and Hasan DeMirci and Raymond G. Sierra and E. Han Dao and Radman Ahmadi and Fulya Aksit and Andrew L. Aquila and Halilibrahim Ciftci and Serge Guillet and Matt J. Hayes and Thomas J. Lane and Meng Liang and Ulf Lundström and …

  97. SENP1-mediated deSUMOylation of USP28 regulated HIF-1α accumulation and activation during hypoxia response

    0.0 out of 5 stars 

    02 Jan 2019 | BioXFEL Publications | Contributor(s): Shi-chun Du, Lan Zhu, Yu-xing Wang, Jie Liu, Die Zhang, Yu-lu Chen, Qing Peng, Wei Liu, Bin Liu

    http://dx.doi.org/10.1186/s12935-018-0722-9 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Du, S. et al., 2019. SENP1-mediated deSUMOylation of USP28 regulated HIF-1α accumulation and activation during hypoxia response. Cancer Cell International, 19(1). Available at: …

  98. Sensing the wavefront of x-ray free-electron lasers using aerosol spheres

    0.0 out of 5 stars 

    13 May 2013 | BioXFEL Publications | Contributor(s): N. Duane Loh, Dmitri Starodub, Lukas Lomb, Christina Y. Hampton, Andrew V. Martin, Raymond G. Sierra, Anton Barty, Andrew Aquila, Joachim Schulz, Jan Steinbrener, Robert L. Shoeman, Stephan Kassemeyer, Christoph Bostedt, John Bozek, Sascha W. Epp, Benjamin Erk, Robert Hartmann, Daniel Rolles, Artem Rudenko, Benedikt Rudek, Lutz Foucar, Nils Kimmel, Georg Weidenspointner, Guenter Hauser, Peter Holl, Emanuele Pedersoli, Mengning Liang, Mark S. Hunter, Lars Gumprecht, Nicola Coppola, Cornelia Wunderer, Heinz Graafsma, Filipe R.N.C. Maia, Tomas Ekeberg, Max Hantke, Holger Fleckenstein, Helmut Hirsemann, Karol Nass, Thomas A. White, Herbert J. Tobias, George R. Farquar, W. Henry Benner, Stefan Hau-Riege, Christian Reich, Andreas Hartmann, Heike Soltau, Stefano Marchesini, Sasa Bajt, Miriam Barthelmess, Lothar Strueder, Joachim Ullrich, Philip Bucksbaum, Matthias Frank, Ilme Schlichting, Henry Chapman, Michael J. Bogan

    journal-article http://dx.doi.org/10.1364/oe.21.012385 Loh, N.D. et al., 2013. Sensing the wavefront of x-ray free-electron lasers using aerosol spheres. Optics Express, 21(10), p.12385. Available at: http://dx.doi.org/10.1364/oe.21.012385. N. Duane Loh and Dmitri Starodub and Lukas Lomb and …

  99. Separation Phenomena in Tailored Micro- and Nanofluidic Environments

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    30 Jan 2019 | BioXFEL Publications | Contributor(s): Mukul Sonker, Daihyun Kim, Ana Egatz-Gomez, Alexandra Ros

    http://dx.doi.org/10.1146/annurev-anchem-061417-125758 journal-article Sonker, M. et al., 2019. Separation Phenomena in Tailored Micro- and Nanofluidic Environments. Annual Review of Analytical Chemistry, 12(1). Available at: http://dx.doi.org/10.1146/annurev-anchem-061417-125758. Mukul Sonker …

  100. Sequence Analysis and Biophysical Characterization Reveals the Presence of a Long Disordered Region in the CapA Membrane Protein from F. Tularensis

    0.0 out of 5 stars 

    18 Apr 2015 | BioXFEL Publications | Contributor(s): Jose M. Martin, Debra T. Hansen, Andrrey Loskutov, Mark D. Robida, Felicia M. Craciunescu, Kathryn Sykes, Rebekka M. Wachter, Petra Fromme, James P. Allen

    http://dx.doi.org/10.1016/j.bpj.2013.11.3806 journal-article Martin, J.M. et al., 2014. Sequence Analysis and Biophysical Characterization Reveals the Presence of a Long Disordered Region in the CapA Membrane Protein from F. Tularensis. Biophysical Journal, 106(2), p.688a. Available at: …