Literature DB >> 29196935

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

Eiichi Mizohata1,2, Takanori Nakane3,4, Yohta Fukuda5, Eriko Nango6,7, So Iwata6,7.   

Abstract

X-ray crystallography visualizes the world at the atomic level. It has been used as the most powerful technique for observing the three-dimensional structures of biological macromolecules and has pioneered structural biology. To determine a crystal structure with high resolution, it was traditionally required to prepare large crystals (> 200 μm). Later, synchrotron radiation facilities, such as SPring-8, that produce powerful X-rays were built. They enabled users to obtain good quality X-ray diffraction images even with smaller crystals (ca. 200-50 μm). In recent years, one of the most important technological innovations in structural biology has been the development of X-ray free electron lasers (XFELs). The SPring-8 Angstrom Compact free electron LAser (SACLA) in Japan generates the XFEL beam by accelerating electrons to relativistic speeds and directing them through in-vacuum, short-period undulators. Since user operation started in 2012, we have been involved in the development of serial femtosecond crystallography (SFX) measurement systems using XFEL at the SACLA. The SACLA generates X-rays a billion times brighter than SPring-8. The extremely bright XFEL pulses enable data collection with microcrystals (ca. 50-1 μm). Although many molecular analysis techniques exist, SFX is the only technique that can visualize radiation-damage-free structures of biological macromolecules at room temperature in atomic resolution and fast time resolution. Here, we review the achievements of the SACLA-SFX Project in the past 5 years. In particular, we focus on: (1) the measurement system for SFX; (2) experimental phasing by SFX; (3) enzyme chemistry based on damage-free room-temperature structures; and (4) molecular movie taken by time-resolved SFX.

Entities:  

Keywords:  Bioinorganic chemistry; De novo phasing; Detergent; Membrane protein; Structure–function relationship; Time-resolved analysis

Year:  2017        PMID: 29196935      PMCID: PMC5899704          DOI: 10.1007/s12551-017-0344-9

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  74 in total

Review 1.  Time-resolved biochemical crystallography: a mechanistic perspective.

Authors:  K Moffat
Journal:  Chem Rev       Date:  2001-06       Impact factor: 60.622

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.  Side-on copper-nitrosyl coordination by nitrite reductase.

Authors:  Elitza I Tocheva; Federico I Rosell; A Grant Mauk; Michael E P Murphy
Journal:  Science       Date:  2004-05-07       Impact factor: 47.728

Review 4.  Bacteriorhodopsin: a high-resolution structural view of vectorial proton transport.

Authors:  Richard Neutze; Eva Pebay-Peyroula; Karl Edman; Antoine Royant; Javier Navarro; Ehud M Landau
Journal:  Biochim Biophys Acta       Date:  2002-10-11

5.  Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein.

Authors:  Kanupriya Pande; Christopher D M Hutchison; Gerrit Groenhof; Andy Aquila; Josef S Robinson; Jason Tenboer; Shibom Basu; Sébastien Boutet; Daniel P DePonte; Mengning Liang; Thomas A White; Nadia A Zatsepin; Oleksandr Yefanov; Dmitry Morozov; Dominik Oberthuer; Cornelius Gati; Ganesh Subramanian; Daniel James; Yun Zhao; Jake Koralek; Jennifer Brayshaw; Christopher Kupitz; Chelsie Conrad; Shatabdi Roy-Chowdhury; Jesse D Coe; Markus Metz; Paulraj Lourdu Xavier; Thomas D Grant; Jason E Koglin; Gihan Ketawala; Raimund Fromme; Vukica Šrajer; Robert Henning; John C H Spence; Abbas Ourmazd; Peter Schwander; Uwe Weierstall; Matthias Frank; Petra Fromme; Anton Barty; Henry N Chapman; Keith Moffat; Jasper J van Thor; Marius Schmidt
Journal:  Science       Date:  2016-05-05       Impact factor: 47.728

Review 6.  Crystallographic phasing from weak anomalous signals.

Authors:  Qun Liu; Wayne A Hendrickson
Journal:  Curr Opin Struct Biol       Date:  2015-09-30       Impact factor: 6.809

7.  Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR.

Authors:  Daniel A Keedy; Henry van den Bedem; David A Sivak; Gregory A Petsko; Dagmar Ringe; Mark A Wilson; James S Fraser
Journal:  Structure       Date:  2014-05-29       Impact factor: 5.006

8.  Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal.

Authors:  Sam Horrell; Svetlana V Antonyuk; Robert R Eady; S Samar Hasnain; Michael A Hough; Richard W Strange
Journal:  IUCrJ       Date:  2016-06-15       Impact factor: 4.769

9.  Recent developments in CrystFEL.

Authors:  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 N Chapman
Journal:  J Appl Crystallogr       Date:  2016-03-29       Impact factor: 3.304

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

Authors:  Jacques-Philippe Colletier; Michael R Sawaya; Mari Gingery; Jose A Rodriguez; Duilio Cascio; Aaron S Brewster; Tara Michels-Clark; Robert H Hice; Nicolas Coquelle; Sébastien Boutet; Garth J Williams; Marc Messerschmidt; Daniel P DePonte; Raymond G Sierra; Hartawan Laksmono; Jason E Koglin; Mark S Hunter; Hyun-Woo Park; Monarin Uervirojnangkoorn; Dennis K Bideshi; Axel T Brunger; Brian A Federici; Nicholas K Sauter; David S Eisenberg
Journal:  Nature       Date:  2016-09-28       Impact factor: 49.962

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  5 in total

1.  In crystallo thermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase.

Authors:  Takeshi Murakawa; Seiki Baba; Yoshiaki Kawano; Hideyuki Hayashi; Takato Yano; Takashi Kumasaka; Masaki Yamamoto; Katsuyuki Tanizawa; Toshihide Okajima
Journal:  Proc Natl Acad Sci U S A       Date:  2018-12-18       Impact factor: 11.205

Review 2.  NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes.

Authors:  Kyle W East; Erin Skeens; Jennifer Y Cui; Helen B Belato; Brandon Mitchell; Rohaine Hsu; Victor S Batista; Giulia Palermo; George P Lisi
Journal:  Biophys Rev       Date:  2019-12-14

3.  Foreword to 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', a special issue in Honour of Fumio Arisaka's 70th birthday.

Authors:  Damien Hall; Junichi Takagi; Haruki Nakamura
Journal:  Biophys Rev       Date:  2018-03-02

4.  High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source.

Authors:  Jose M Martin-Garcia; Lan Zhu; Derek Mendez; Ming-Yue Lee; Eugene Chun; Chufeng Li; Hao Hu; Ganesh Subramanian; David Kissick; Craig Ogata; Robert Henning; Andrii Ishchenko; Zachary Dobson; Shangji Zhang; Uwe Weierstall; John C H Spence; Petra Fromme; Nadia A Zatsepin; Robert F Fischetti; Vadim Cherezov; Wei Liu
Journal:  IUCrJ       Date:  2019-04-05       Impact factor: 4.769

5.  Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX.

Authors:  Dongqing Pan; Ryo Oyama; Tomomi Sato; Takanori Nakane; Ryo Mizunuma; Keita Matsuoka; Yasumasa Joti; Kensuke Tono; Eriko Nango; So Iwata; Toru Nakatsu; Hiroaki Kato
Journal:  IUCrJ       Date:  2021-12-23       Impact factor: 4.769

  5 in total

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