Literature DB >> 25384243

Grease matrix as a versatile carrier of proteins for serial crystallography.

Michihiro Sugahara1, Eiichi Mizohata2, Eriko Nango1, Mamoru Suzuki3, Tomoyuki Tanaka1, Tetsuya Masuda4, Rie Tanaka1, Tatsuro Shimamura5, Yoshiki Tanaka5, Chiyo Suno5, Kentaro Ihara5, Dongqing Pan6, Keisuke Kakinouchi7, Shigeru Sugiyama7, Michio Murata7, Tsuyoshi Inoue2, Kensuke Tono8, Changyong Song1, Jaehyun Park1, Takashi Kameshima8, Takaki Hatsui1, Yasumasa Joti8, Makina Yabashi1, So Iwata9.   

Abstract

Serial femtosecond X-ray crystallography (SFX) has revolutionized atomic-resolution structural investigation by expanding applicability to micrometer-sized protein crystals, even at room temperature, and by enabling dynamics studies. However, reliable crystal-carrying media for SFX are lacking. Here we introduce a grease-matrix carrier for protein microcrystals and obtain the structures of lysozyme, glucose isomerase, thaumatin and fatty acid-binding protein type 3 under ambient conditions at a resolution of or finer than 2 Å.

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Year:  2014        PMID： 25384243     DOI： 10.1038/nmeth.3172

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


  23 in total

1.  The Rossmann Fourier autoindexing algorithm in MOSFLM.

Authors:  H R Powell
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-10

2.  Potential for biomolecular imaging with femtosecond X-ray pulses.

Authors:  R Neutze; R Wouts; D van der Spoel; E Weckert; J Hajdu
Journal:  Nature       Date:  2000-08-17       Impact factor: 49.962

3.  High-resolution structure of the recombinant sweet-tasting protein thaumatin I.

Authors:  Tetsuya Masuda; Keisuke Ohta; Bunzo Mikami; Naofumi Kitabatake
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2011-05-24

4.  Lipidic phase membrane protein serial femtosecond crystallography.

Authors:  Linda C Johansson; David Arnlund; Thomas A White; Gergely Katona; Daniel P Deponte; Uwe Weierstall; R Bruce Doak; Robert L Shoeman; Lukas Lomb; Erik Malmerberg; Jan Davidsson; Karol Nass; Mengning Liang; Jakob Andreasson; Andrew Aquila; Saša Bajt; Miriam Barthelmess; Anton Barty; Michael J Bogan; Christoph Bostedt; John D Bozek; Carl Caleman; Ryan Coffee; Nicola Coppola; Tomas Ekeberg; Sascha W Epp; Benjamin Erk; Holger Fleckenstein; Lutz Foucar; Heinz Graafsma; Lars Gumprecht; Janos Hajdu; Christina Y Hampton; Robert Hartmann; Andreas Hartmann; Günter Hauser; Helmut Hirsemann; Peter Holl; Mark S Hunter; Stephan Kassemeyer; Nils Kimmel; Richard A Kirian; Filipe R N C Maia; Stefano Marchesini; Andrew V Martin; Christian Reich; Daniel Rolles; Benedikt Rudek; Artem Rudenko; Ilme Schlichting; Joachim Schulz; M Marvin Seibert; Raymond G Sierra; Heike Soltau; Dmitri Starodub; Francesco Stellato; Stephan Stern; Lothar Strüder; Nicusor Timneanu; Joachim Ullrich; Weixiao Y Wahlgren; Xiaoyu Wang; Georg Weidenspointner; Cornelia Wunderer; Petra Fromme; Henry N Chapman; John C H Spence; Richard Neutze
Journal:  Nat Methods       Date:  2012-01-29       Impact factor: 28.547

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

Authors:  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
Journal:  Nature       Date:  2013-11-24       Impact factor: 49.962

6.  Development of an X-ray pixel detector with multi-port charge-coupled device for X-ray free-electron laser experiments.

Authors:  Takashi Kameshima; Shun Ono; Togo Kudo; Kyosuke Ozaki; Yoichi Kirihara; Kazuo Kobayashi; Yuichi Inubushi; Makina Yabashi; Toshio Horigome; Andrew Holland; Karen Holland; David Burt; Hajime Murao; Takaki Hatsui
Journal:  Rev Sci Instrum       Date:  2014-03       Impact factor: 1.523

7.  Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature.

Authors:  Jan Kern; Roberto Alonso-Mori; Rosalie Tran; Johan Hattne; Richard J Gildea; Nathaniel Echols; Carina Glöckner; Julia Hellmich; Hartawan Laksmono; Raymond G Sierra; Benedikt Lassalle-Kaiser; Sergey Koroidov; Alyssa Lampe; Guangye Han; Sheraz Gul; Dörte Difiore; Despina Milathianaki; Alan R Fry; Alan Miahnahri; Donald W Schafer; Marc Messerschmidt; M Marvin Seibert; Jason E Koglin; Dimosthenis Sokaras; Tsu-Chien Weng; Jonas Sellberg; Matthew J Latimer; Ralf W Grosse-Kunstleve; Petrus H Zwart; William E White; Pieter Glatzel; Paul D Adams; Michael J Bogan; Garth J Williams; Sébastien Boutet; Johannes Messinger; Athina Zouni; Nicholas K Sauter; Vittal K Yachandra; Uwe Bergmann; Junko Yano
Journal:  Science       Date:  2013-02-14       Impact factor: 47.728

8.  Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements.

Authors:  Anton Barty; Carl Caleman; Andrew Aquila; Nicusor Timneanu; Lukas Lomb; Thomas A White; Jakob Andreasson; David Arnlund; Saša Bajt; Thomas R M Barends; Miriam Barthelmess; Michael J Bogan; Christoph Bostedt; John D Bozek; Ryan Coffee; Nicola Coppola; Jan Davidsson; Daniel P Deponte; R Bruce Doak; Tomas Ekeberg; Veit Elser; Sascha W Epp; Benjamin Erk; Holger Fleckenstein; Lutz Foucar; Petra Fromme; Heinz Graafsma; Lars Gumprecht; Janos Hajdu; Christina Y Hampton; Robert Hartmann; Andreas Hartmann; Günter Hauser; Helmut Hirsemann; Peter Holl; Mark S Hunter; Linda Johansson; Stephan Kassemeyer; Nils Kimmel; Richard A Kirian; Mengning Liang; Filipe R N C Maia; Erik Malmerberg; Stefano Marchesini; Andrew V Martin; Karol Nass; Richard Neutze; Christian Reich; Daniel Rolles; Benedikt Rudek; Artem Rudenko; Howard Scott; Ilme Schlichting; Joachim Schulz; M Marvin Seibert; Robert L Shoeman; Raymond G Sierra; Heike Soltau; John C H Spence; Francesco Stellato; Stephan Stern; Lothar Strüder; Joachim Ullrich; X Wang; Georg Weidenspointner; Uwe Weierstall; Cornelia B Wunderer; Henry N Chapman
Journal:  Nat Photonics       Date:  2012       Impact factor: 38.771

Review 9.  The integration of macromolecular diffraction data.

Authors:  Andrew G W Leslie
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-12-14

10.  Phaser crystallographic software.

Authors:  Airlie J McCoy; Ralf W Grosse-Kunstleve; Paul D Adams; Martyn D Winn; Laurent C Storoni; Randy J Read
Journal:  J Appl Crystallogr       Date:  2007-07-13       Impact factor: 3.304
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  87 in total

Review 1.  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

2.  Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent.

Authors:  Takanori Nakane; Shinya Hanashima; Mamoru Suzuki; Haruka Saiki; Taichi Hayashi; Keisuke Kakinouchi; Shigeru Sugiyama; Satoshi Kawatake; Shigeru Matsuoka; Nobuaki Matsumori; Eriko Nango; Jun Kobayashi; Tatsuro Shimamura; Kanako Kimura; Chihiro Mori; Naoki Kunishima; Michihiro Sugahara; Yoko Takakyu; Shigeyuki Inoue; Tetsuya Masuda; Toshiaki Hosaka; Kensuke Tono; Yasumasa Joti; Takashi Kameshima; Takaki Hatsui; Makina Yabashi; Tsuyoshi Inoue; Osamu Nureki; So Iwata; Michio Murata; Eiichi Mizohata
Journal:  Proc Natl Acad Sci U S A       Date:  2016-10-31       Impact factor: 11.205

3.  Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.

Authors:  Yohta Fukuda; Ka Man Tse; Takanori Nakane; Toru Nakatsu; Mamoru Suzuki; Michihiro Sugahara; Shigeyuki Inoue; Tetsuya Masuda; Fumiaki Yumoto; Naohiro Matsugaki; Eriko Nango; Kensuke Tono; Yasumasa Joti; Takashi Kameshima; Changyong Song; Takaki Hatsui; Makina Yabashi; Osamu Nureki; Michael E P Murphy; Tsuyoshi Inoue; So Iwata; Eiichi Mizohata
Journal:  Proc Natl Acad Sci U S A       Date:  2016-02-29       Impact factor: 11.205

Review 4.  Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology.

Authors:  Eiichi Mizohata; Takanori Nakane; Yohta Fukuda; Eriko Nango; So Iwata
Journal:  Biophys Rev       Date:  2017-12-01

5.  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

6.  High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States.

Authors:  Vivek Srinivas; Rahul Banerjee; Hugo Lebrette; Jason C Jones; Oskar Aurelius; In-Sik Kim; Cindy C Pham; Sheraz Gul; Kyle D Sutherlin; Asmit Bhowmick; Juliane John; Esra Bozkurt; Thomas Fransson; Pierre Aller; Agata Butryn; Isabel Bogacz; Philipp Simon; Stephen Keable; Alexander Britz; Kensuke Tono; Kyung Sook Kim; Sang-Youn Park; Sang Jae Lee; Jaehyun Park; Roberto Alonso-Mori; Franklin D Fuller; Alexander Batyuk; Aaron S Brewster; Uwe Bergmann; Nicholas K Sauter; Allen M Orville; Vittal K Yachandra; Junko Yano; John D Lipscomb; Jan Kern; Martin Högbom
Journal:  J Am Chem Soc       Date:  2020-08-05       Impact factor: 15.419

7.  The Conformational Flexibility of the Acyltransferase from the Disorazole Polyketide Synthase Is Revealed by an X-ray Free-Electron Laser Using a Room-Temperature Sample Delivery Method for Serial Crystallography.

Authors:  Irimpan I Mathews; Kim Allison; Thomas Robbins; Artem Y Lyubimov; Monarin Uervirojnangkoorn; Axel T Brunger; Chaitan Khosla; Hasan DeMirci; Scott E McPhillips; Michael Hollenbeck; Michael Soltis; Aina E Cohen
Journal:  Biochemistry       Date:  2017-08-31       Impact factor: 3.162

8.  Serial femtosecond crystallography opens new avenues for Structural Biology.

Authors:  Jesse Coe; Petra Fromme
Journal:  Protein Pept Lett       Date:  2016       Impact factor: 1.890

Review 9.  Structural biology of G protein-coupled receptors: new opportunities from XFELs and cryoEM.

Authors:  Andrii Ishchenko; Cornelius Gati; Vadim Cherezov
Journal:  Curr Opin Struct Biol       Date:  2018-03-16       Impact factor: 6.809

10.  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
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