Literature DB >> 32939282

Anaerobic fixed-target serial crystallography.

Patrick Rabe1, John H Beale2, Agata Butryn2, Pierre Aller2, Anna Dirr1, Pauline A Lang1, Danny N Axford2, Stephen B Carr3, Thomas M Leissing1, Michael A McDonough1, Bradley Davy2, Ali Ebrahim2,4, Julien Orlans2,5, Selina L S Storm2, Allen M Orville2, Christopher J Schofield1, Robin L Owen2.   

Abstract

Cryogenic X-ray diffraction is a powerful tool for crystallographic studies on enzymes including oxygenases and oxidases. Amongst the benefits that cryo-conditions (usually employing a nitro-gen cryo-stream at 100 K) enable, is data collection of di-oxy-gen-sensitive samples. Although not strictly anaerobic, at low temperatures the vitreous ice conditions severely restrict O2 diffusion into and/or through the protein crystal. Cryo-conditions limit chemical reactivity, including reactions that require significant conformational changes. By contrast, data collection at room temperature imposes fewer restrictions on diffusion and reactivity; room-temperature serial methods are thus becoming common at synchrotrons and XFELs. However, maintaining an anaerobic environment for di-oxy-gen-dependent enzymes has not been explored for serial room-temperature data collection at synchrotron light sources. This work describes a methodology that employs an adaptation of the 'sheet-on-sheet' sample mount, which is suitable for the low-dose room-temperature data collection of anaerobic samples at synchrotron light sources. The method is characterized by easy sample preparation in an anaerobic glovebox, gentle handling of crystals, low sample consumption and preservation of a localized anaerobic environment over the timescale of the experiment (<5 min). The utility of the method is highlighted by studies with three X-ray-radiation-sensitive Fe(II)-containing model enzymes: the 2-oxoglutarate-dependent l-arginine hy-droxy-lase VioC and the DNA repair enzyme AlkB, as well as the oxidase isopenicillin N synthase (IPNS), which is involved in the biosynthesis of all penicillin and cephalosporin antibiotics. © Patrick Rabe et al. 2020.

Entities:  

Keywords:  2-oxoglutarate/α-ketoglutarate oxygenases; anaerobic crystallization; oxygen-employing enzymes; penicillin biosynthesis; serial crystallography

Year:  2020        PMID: 32939282      PMCID: PMC7467159          DOI: 10.1107/S2052252520010374

Source DB:  PubMed          Journal:  IUCrJ        ISSN: 2052-2525            Impact factor:   4.769


  53 in total

1.  Dynamic combinatorial mass spectrometry leads to inhibitors of a 2-oxoglutarate-dependent nucleic acid demethylase.

Authors:  Esther C Y Woon; Marina Demetriades; Eleanor A L Bagg; WeiShen Aik; Svetlana M Krylova; Jerome H Y Ma; MunChiang Chan; Louise J Walport; David W Wegman; Kevin N Dack; Michael A McDonough; Sergey N Krylov; Christopher J Schofield
Journal:  J Med Chem       Date:  2012-02-22       Impact factor: 7.446

Review 2.  Flavin dependent monooxygenases.

Authors:  Mieke M E Huijbers; Stefania Montersino; Adrie H Westphal; Dirk Tischler; Willem J H van Berkel
Journal:  Arch Biochem Biophys       Date:  2013-12-17       Impact factor: 4.013

Review 3.  Chromatin proteins and modifications as drug targets.

Authors:  Kristian Helin; Dashyant Dhanak
Journal:  Nature       Date:  2013-10-24       Impact factor: 49.962

4.  Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation.

Authors:  P L Roach; I J Clifton; C M Hensgens; N Shibata; C J Schofield; J Hajdu; J E Baldwin
Journal:  Nature       Date:  1997-06-19       Impact factor: 49.962

5.  Structure of photosystem II and substrate binding at room temperature.

Authors:  Iris D Young; Mohamed Ibrahim; Ruchira Chatterjee; Sheraz Gul; Franklin Fuller; Sergey Koroidov; Aaron S Brewster; Rosalie Tran; Roberto Alonso-Mori; Thomas Kroll; Tara Michels-Clark; Hartawan Laksmono; Raymond G Sierra; Claudiu A Stan; Rana Hussein; Miao Zhang; Lacey Douthit; Markus Kubin; Casper de Lichtenberg; Pham Long Vo; Håkan Nilsson; Mun Hon Cheah; Dmitriy Shevela; Claudio Saracini; Mackenzie A Bean; Ina Seuffert; Dimosthenis Sokaras; Tsu-Chien Weng; Ernest Pastor; Clemens Weninger; Thomas Fransson; Louise Lassalle; Philipp Bräuer; Pierre Aller; Peter T Docker; Babak Andi; Allen M Orville; James M Glownia; Silke Nelson; Marcin Sikorski; Diling Zhu; Mark S Hunter; Thomas J Lane; Andy Aquila; Jason E Koglin; Joseph Robinson; Mengning Liang; Sébastien Boutet; Artem Y Lyubimov; Monarin Uervirojnangkoorn; Nigel W Moriarty; Dorothee Liebschner; Pavel V Afonine; David G Waterman; Gwyndaf Evans; Philippe Wernet; Holger Dobbek; William I Weis; Axel T Brunger; Petrus H Zwart; Paul D Adams; Athina Zouni; Johannes Messinger; Uwe Bergmann; Nicholas K Sauter; Jan Kern; Vittal K Yachandra; Junko Yano
Journal:  Nature       Date:  2016-11-21       Impact factor: 49.962

6.  Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography.

Authors:  Christian G Roessler; Rakhi Agarwal; Marc Allaire; Roberto Alonso-Mori; Babak Andi; José F R Bachega; Martin Bommer; Aaron S Brewster; Michael C Browne; Ruchira Chatterjee; Eunsun Cho; Aina E Cohen; Matthew Cowan; Sammy Datwani; Victor L Davidson; Jim Defever; Brent Eaton; Richard Ellson; Yiping Feng; Lucien P Ghislain; James M Glownia; Guangye Han; Johan Hattne; Julia Hellmich; Annie Héroux; Mohamed Ibrahim; Jan Kern; Anthony Kuczewski; Henrik T Lemke; Pinghua Liu; Lars Majlof; William M McClintock; Stuart Myers; Silke Nelsen; Joe Olechno; Allen M Orville; Nicholas K Sauter; Alexei S Soares; S Michael Soltis; Heng Song; Richard G Stearns; Rosalie Tran; Yingssu Tsai; Monarin Uervirojnangkoorn; Carrie M Wilmot; Vittal Yachandra; Junko Yano; Erik T Yukl; Diling Zhu; Athina Zouni
Journal:  Structure       Date:  2016-03-17       Impact factor: 5.006

7.  Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase.

Authors:  Chengqi Yi; Guifang Jia; Guanhua Hou; Qing Dai; Wen Zhang; Guanqun Zheng; Xing Jian; Cai-Guang Yang; Qiang Cui; Chuan He
Journal:  Nature       Date:  2010-11-11       Impact factor: 49.962

8.  Improved crystal orientation and physical properties from single-shot XFEL stills.

Authors:  Nicholas K Sauter; Johan Hattne; Aaron S Brewster; Nathaniel Echols; Petrus H Zwart; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-11-28

9.  The mechanism of error induction by the antibiotic viomycin provides insight into the fidelity mechanism of translation.

Authors:  Mikael Holm; Chandra Sekhar Mandava; Måns Ehrenberg; Suparna Sanyal
Journal:  Elife       Date:  2019-06-07       Impact factor: 8.140

10.  Crystallography on a chip - without the chip: sheet-on-sheet sandwich.

Authors:  R Bruce Doak; Gabriela Nass Kovacs; Alexander Gorel; Lutz Foucar; Thomas R M Barends; Marie Luise Grünbein; Mario Hilpert; Marco Kloos; Christopher M Roome; Robert L Shoeman; Miriam Stricker; Kensuke Tono; Daehyun You; Kiyoshi Ueda; Darren A Sherrell; Robin L Owen; Ilme Schlichting
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-10-02       Impact factor: 7.652

View more
  4 in total

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

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

2.  X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis.

Authors:  Patrick Rabe; Jos J A G Kamps; Kyle D Sutherlin; James D S Linyard; Pierre Aller; Cindy C Pham; Hiroki Makita; Ian Clifton; Michael A McDonough; Thomas M Leissing; Denis Shutin; Pauline A Lang; Agata Butryn; Jürgen Brem; Sheraz Gul; Franklin D Fuller; In-Sik Kim; Mun Hon Cheah; Thomas Fransson; Asmit Bhowmick; Iris D Young; Lee O'Riordan; Aaron S Brewster; Ilaria Pettinati; Margaret Doyle; Yasumasa Joti; Shigeki Owada; Kensuke Tono; Alexander Batyuk; Mark S Hunter; Roberto Alonso-Mori; Uwe Bergmann; Robin L Owen; Nicholas K Sauter; Timothy D W Claridge; Carol V Robinson; Vittal K Yachandra; Junko Yano; Jan F Kern; Allen M Orville; Christopher J Schofield
Journal:  Sci Adv       Date:  2021-08-20       Impact factor: 14.957

Review 3.  Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis.

Authors:  Michael A Hough; Robin L Owen
Journal:  Curr Opin Struct Biol       Date:  2021-08-26       Impact factor: 6.809

4.  Can Second Coordination Sphere and Long-Range Interactions Modulate Hydrogen Atom Transfer in a Non-Heme Fe(II)-Dependent Histone Demethylase?

Authors:  Shobhit S Chaturvedi; Simahudeen Bathir Jaber Sathik Rifayee; Sodiq O Waheed; Jon Wildey; Cait Warner; Christopher J Schofield; Tatyana G Karabencheva-Christova; Christo Z Christov
Journal:  JACS Au       Date:  2022-08-18
  4 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.