Literature DB >> 28250468

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

Franklin D Fuller1, Sheraz Gul1, Ruchira Chatterjee1, E Sethe Burgie2, Iris D Young1, Hugo Lebrette3, Vivek Srinivas3, Aaron S Brewster1, Tara Michels-Clark1, Jonathan A Clinger4, Babak Andi5, Mohamed Ibrahim6, Ernest Pastor1, Casper de Lichtenberg7, Rana Hussein6, Christopher J Pollock8, Miao Zhang6, Claudiu A Stan9, Thomas Kroll10, Thomas Fransson9, Clemens Weninger9,11, Markus Kubin12, Pierre Aller13, Louise Lassalle1, Philipp Bräuer13,14, Mitchell D Miller4, Muhamed Amin1, Sergey Koroidov7,9, Christian G Roessler5, Marc Allaire1, Raymond G Sierra11, Peter T Docker13, James M Glownia11, Silke Nelson11, Jason E Koglin11, Diling Zhu11, Matthieu Chollet11, Sanghoon Song11, Henrik Lemke11, Mengning Liang11, Dimosthenis Sokaras10, Roberto Alonso-Mori11, Athina Zouni6, Johannes Messinger7,15, Uwe Bergmann9, Amie K Boal8,16, J Martin Bollinger8,16, Carsten Krebs8,16, Martin Högbom3,17, George N Phillips4,18, Richard D Vierstra2, Nicholas K Sauter1, Allen M Orville13, Jan Kern1,11, Vittal K Yachandra1, Junko Yano1.   

Abstract

X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.

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Year:  2017        PMID: 28250468      PMCID: PMC5376230          DOI: 10.1038/nmeth.4195

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  49 in total

1.  Nanoflow electrospinning serial femtosecond crystallography.

Authors:  Raymond G Sierra; Hartawan Laksmono; Jan Kern; Rosalie Tran; Johan Hattne; Roberto Alonso-Mori; Benedikt Lassalle-Kaiser; Carina Glöckner; Julia Hellmich; Donald W Schafer; Nathaniel Echols; Richard J Gildea; Ralf W Grosse-Kunstleve; Jonas Sellberg; Trevor A McQueen; Alan R Fry; Marc M Messerschmidt; Alan Miahnahri; M Marvin Seibert; Christina Y Hampton; Dmitri Starodub; N Duane Loh; Dimosthenis Sokaras; Tsu-Chien Weng; Petrus H Zwart; Pieter Glatzel; Despina Milathianaki; William E White; Paul D Adams; Garth J Williams; Sébastien Boutet; Athina Zouni; Johannes Messinger; Nicholas K Sauter; Uwe Bergmann; Junko Yano; Vittal K Yachandra; Michael J Bogan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-10-18

2.  Probing the 3d spin momentum with X-ray emission spectroscopy: the case of molecular-spin transitions.

Authors:  György Vankó; Thomas Neisius; Gabor Molnar; Franz Renz; Szilvia Karpati; Abhay Shukla; Frank M F de Groot
Journal:  J Phys Chem B       Date:  2006-06-22       Impact factor: 2.991

3.  Absence of Mn-centered oxidation in the S(2) --> S(3) transition: implications for the mechanism of photosynthetic water oxidation.

Authors:  J Messinger; J H Robblee; U Bergmann; C Fernandez; P Glatzel; H Visser; R M Cinco; K L McFarlane; E Bellacchio; S A Pizarro; S P Cramer; K Sauer; M P Klein; V K Yachandra
Journal:  J Am Chem Soc       Date:  2001-08-15       Impact factor: 15.419

Review 4.  Assembly of nonheme Mn/Fe active sites in heterodinuclear metalloproteins.

Authors:  Julia J Griese; Vivek Srinivas; Martin Högbom
Journal:  J Biol Inorg Chem       Date:  2014-04-26       Impact factor: 3.358

5.  New Python-based methods for data processing.

Authors:  Nicholas K Sauter; Johan Hattne; Ralf W Grosse-Kunstleve; Nathaniel Echols
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-06-18

6.  The X-ray Pump-Probe instrument at the Linac Coherent Light Source.

Authors:  Matthieu Chollet; Roberto Alonso-Mori; Marco Cammarata; Daniel Damiani; Jim Defever; James T Delor; Yiping Feng; James M Glownia; J Brian Langton; Silke Nelson; Kelley Ramsey; Aymeric Robert; Marcin Sikorski; Sanghoon Song; Daniel Stefanescu; Venkat Srinivasan; Diling Zhu; Henrik T Lemke; David M Fritz
Journal:  J Synchrotron Radiat       Date:  2015-04-21       Impact factor: 2.616

Review 7.  Mn4Ca cluster in photosynthesis: where and how water is oxidized to dioxygen.

Authors:  Junko Yano; Vittal Yachandra
Journal:  Chem Rev       Date:  2014-03-31       Impact factor: 60.622

8.  Fixed-target protein serial microcrystallography with an x-ray free electron laser.

Authors:  Mark S Hunter; Brent Segelke; Marc Messerschmidt; Garth J Williams; Nadia A Zatsepin; Anton Barty; W Henry Benner; David B Carlson; Matthew Coleman; Alexander Graf; Stefan P Hau-Riege; Tommaso Pardini; M Marvin Seibert; James Evans; Sébastien Boutet; Matthias Frank
Journal:  Sci Rep       Date:  2014-08-12       Impact factor: 4.379

9.  High-density grids for efficient data collection from multiple crystals.

Authors:  Elizabeth L Baxter; Laura Aguila; Roberto Alonso-Mori; Christopher O Barnes; Christopher A Bonagura; Winnie Brehmer; Axel T Brunger; Guillermo Calero; Tom T Caradoc-Davies; Ruchira Chatterjee; William F Degrado; James S Fraser; Mohamed Ibrahim; Jan Kern; Brian K Kobilka; Andrew C Kruse; Karl M Larsson; Heinrik T Lemke; Artem Y Lyubimov; Aashish Manglik; Scott E McPhillips; Erik Norgren; Siew S Pang; S M Soltis; Jinhu Song; Jessica Thomaston; Yingssu Tsai; William I Weis; Rahel A Woldeyes; Vittal Yachandra; Junko Yano; Athina Zouni; Aina E Cohen
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-01-01       Impact factor: 7.652

10.  Improvements in serial femtosecond crystallography of photosystem II by optimizing crystal uniformity using microseeding procedures.

Authors:  Mohamed Ibrahim; Ruchira Chatterjee; Julia Hellmich; Rosalie Tran; Martin Bommer; Vittal K Yachandra; Junko Yano; Jan Kern; Athina Zouni
Journal:  Struct Dyn       Date:  2015       Impact factor: 2.920

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  52 in total

1.  Crystal-on-crystal chips for in situ serial diffraction at room temperature.

Authors:  Zhong Ren; Medine Ayhan; Sepalika Bandara; Kalinga Bowatte; Indika Kumarapperuma; Semini Gunawardana; Heewhan Shin; Cong Wang; Xiaoli Zeng; Xiaojing Yang
Journal:  Lab Chip       Date:  2018-07-24       Impact factor: 6.799

2.  DIY XES - development of an inexpensive, versatile, and easy to fabricate XES analyzer and sample delivery system.

Authors:  Scott C Jensen; Brendan Sullivan; Daniel A Hartzler; Yulia Pushkar
Journal:  Xray Spectrom       Date:  2019-02-13       Impact factor: 1.488

Review 3.  A Bright Future for Serial Femtosecond Crystallography with XFELs.

Authors:  Linda C Johansson; Benjamin Stauch; Andrii Ishchenko; Vadim Cherezov
Journal:  Trends Biochem Sci       Date:  2017-07-18       Impact factor: 13.807

4.  Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources.

Authors:  Pierre Aller; Allen M Orville
Journal:  Methods Mol Biol       Date:  2021

5.  Photoreversible interconversion of a phytochrome photosensory module in the crystalline state.

Authors:  E Sethe Burgie; Jonathan A Clinger; Mitchell D Miller; Aaron S Brewster; Pierre Aller; Agata Butryn; Franklin D Fuller; Sheraz Gul; Iris D Young; Cindy C Pham; In-Sik Kim; Asmit Bhowmick; Lee J O'Riordan; Kyle D Sutherlin; Joshua V Heinemann; Alexander Batyuk; Roberto Alonso-Mori; Mark S Hunter; Jason E Koglin; Junko Yano; Vittal K Yachandra; Nicholas K Sauter; Aina E Cohen; Jan Kern; Allen M Orville; George N Phillips; Richard D Vierstra
Journal:  Proc Natl Acad Sci U S A       Date:  2019-12-18       Impact factor: 11.205

Review 6.  An outlook on using serial femtosecond crystallography in drug discovery.

Authors:  Alexey Mishin; Anastasiia Gusach; Aleksandra Luginina; Egor Marin; Valentin Borshchevskiy; Vadim Cherezov
Journal:  Expert Opin Drug Discov       Date:  2019-06-11       Impact factor: 6.098

7.  3D printed droplet generation devices for serial femtosecond crystallography enabled by surface coating.

Authors:  Austin Echelmeier; Daihyun Kim; Jorvani Cruz Villarreal; Jesse Coe; Sebastian Quintana; Gerrit Brehm; Ana Egatz-Gomez; Reza Nazari; Raymond G Sierra; Jason E Koglin; Alexander Batyuk; Mark S Hunter; Sébastien Boutet; Nadia Zatsepin; Richard A Kirian; Thomas D Grant; Petra Fromme; Alexandra Ros
Journal:  J Appl Crystallogr       Date:  2019-08-29       Impact factor: 3.304

8.  An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography.

Authors:  Agata Butryn; Philipp S Simon; Pierre Aller; Philip Hinchliffe; Ramzi N Massad; Gabriel Leen; Catherine L Tooke; Isabel Bogacz; In-Sik Kim; Asmit Bhowmick; Aaron S Brewster; Nicholas E Devenish; Jürgen Brem; Jos J A G Kamps; Pauline A Lang; Patrick Rabe; Danny Axford; John H Beale; Bradley Davy; Ali Ebrahim; Julien Orlans; Selina L S Storm; Tiankun Zhou; Shigeki Owada; Rie Tanaka; Kensuke Tono; Gwyndaf Evans; Robin L Owen; Frances A Houle; Nicholas K Sauter; Christopher J Schofield; James Spencer; Vittal K Yachandra; Junko Yano; Jan F Kern; Allen M Orville
Journal:  Nat Commun       Date:  2021-07-22       Impact factor: 14.919

9.  Anaerobic fixed-target serial crystallography.

Authors:  Patrick Rabe; John H Beale; Agata Butryn; Pierre Aller; Anna Dirr; Pauline A Lang; Danny N Axford; Stephen B Carr; Thomas M Leissing; Michael A McDonough; Bradley Davy; Ali Ebrahim; Julien Orlans; Selina L S Storm; Allen M Orville; Christopher J Schofield; Robin L Owen
Journal:  IUCrJ       Date:  2020-08-21       Impact factor: 4.769

10.  X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser.

Authors:  Thomas Fransson; Ruchira Chatterjee; Franklin D Fuller; Sheraz Gul; Clemens Weninger; Dimosthenis Sokaras; Thomas Kroll; Roberto Alonso-Mori; Uwe Bergmann; Jan Kern; Vittal K Yachandra; Junko Yano
Journal:  Biochemistry       Date:  2018-06-28       Impact factor: 3.162

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