Literature DB >> 24914164

In vivo crystallography at X-ray free-electron lasers: the next generation of structural biology?

François-Xavier Gallat1, Naohiro Matsugaki1, Nathan P Coussens2, Koichiro J Yagi3, Marion Boudes4, Tetsuya Higashi5, Daisuke Tsuji5, Yutaka Tatano6, Mamoru Suzuki7, Eiichi Mizohata8, Kensuke Tono9, Yasumasa Joti9, Takashi Kameshima9, Jaehyun Park10, Changyong Song10, Takaki Hatsui10, Makina Yabashi10, Eriko Nango10, Kohji Itoh5, Fasséli Coulibaly4, Stephen Tobe3, S Ramaswamy11, Barbara Stay12, So Iwata13, Leonard M G Chavas14.   

Abstract

The serendipitous discovery of the spontaneous growth of protein crystals inside cells has opened the field of crystallography to chemically unmodified samples directly available from their natural environment. On the one hand, through in vivo crystallography, protocols for protein crystal preparation can be highly simplified, although the technique suffers from difficulties in sampling, particularly in the extraction of the crystals from the cells partly due to their small sizes. On the other hand, the extremely intense X-ray pulses emerging from X-ray free-electron laser (XFEL) sources, along with the appearance of serial femtosecond crystallography (SFX) is a milestone for radiation damage-free protein structural studies but requires micrometre-size crystals. The combination of SFX with in vivo crystallography has the potential to boost the applicability of these techniques, eventually bringing the field to the point where in vitro sample manipulations will no longer be required, and direct imaging of the crystals from within the cells will be achievable. To fully appreciate the diverse aspects of sample characterization, handling and analysis, SFX experiments at the Japanese SPring-8 angstrom compact free-electron laser were scheduled on various types of in vivo grown crystals. The first experiments have demonstrated the feasibility of the approach and suggest that future in vivo crystallography applications at XFELs will be another alternative to nano-crystallography.
© 2014 The Author(s) Published by the Royal Society. All rights reserved.

Keywords:  X-ray free-electron laser; in vivo crystallography; serial femtosecond crystallography

Mesh:

Substances:

Year:  2014        PMID: 24914164      PMCID: PMC4052873          DOI: 10.1098/rstb.2013.0497

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  11 in total

1.  Room temperature femtosecond X-ray diffraction of photosystem II microcrystals.

Authors:  Jan Kern; Roberto Alonso-Mori; Julia Hellmich; Rosalie Tran; Johan Hattne; Hartawan Laksmono; Carina Glöckner; Nathaniel Echols; Raymond G Sierra; Jonas Sellberg; Benedikt Lassalle-Kaiser; Richard J Gildea; Pieter Glatzel; Ralf W Grosse-Kunstleve; Matthew J Latimer; Trevor A McQueen; Dörte DiFiore; Alan R Fry; Marc Messerschmidt; Alan Miahnahri; Donald W Schafer; M Marvin Seibert; Dimosthenis Sokaras; Tsu-Chien Weng; Petrus H Zwart; William E White; Paul D Adams; Michael J Bogan; Sébastien Boutet; Garth J Williams; Johannes Messinger; Nicholas K Sauter; Athina Zouni; Uwe Bergmann; Junko Yano; Vittal K Yachandra
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-04       Impact factor: 11.205

Review 2.  The process of structure-based drug design.

Authors:  Amy C Anderson
Journal:  Chem Biol       Date:  2003-09

3.  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

4.  The molecular organization of cypovirus polyhedra.

Authors:  Fasséli Coulibaly; Elaine Chiu; Keiko Ikeda; Sascha Gutmann; Peter W Haebel; Clemens Schulze-Briese; Hajime Mori; Peter Metcalf
Journal:  Nature       Date:  2007-03-01       Impact factor: 49.962

5.  In vivo calcineurin crystals formed using the baculovirus expression system.

Authors:  G Y Fan; F Maldonado; Y Zhang; R Kincaid; M H Ellisman; L N Gastinel
Journal:  Microsc Res Tech       Date:  1996-05-01       Impact factor: 2.769

6.  In vivo crystallization of human IgG in the endoplasmic reticulum of engineered Chinese hamster ovary (CHO) cells.

Authors:  Haruki Hasegawa; John Wendling; Feng He; Egor Trilisky; Riki Stevenson; Heather Franey; Francis Kinderman; Gary Li; Deirdre Murphy Piedmonte; Timothy Osslund; Min Shen; Randal R Ketchem
Journal:  J Biol Chem       Date:  2011-04-04       Impact factor: 5.157

7.  Femtosecond X-ray protein nanocrystallography.

Authors:  Henry N Chapman; Petra Fromme; Anton Barty; Thomas A White; Richard A Kirian; Andrew Aquila; Mark S Hunter; Joachim Schulz; Daniel P DePonte; Uwe Weierstall; R Bruce Doak; Filipe R N C Maia; Andrew V Martin; Ilme Schlichting; Lukas Lomb; Nicola Coppola; Robert L Shoeman; Sascha W Epp; Robert Hartmann; Daniel Rolles; Artem Rudenko; Lutz Foucar; Nils Kimmel; Georg Weidenspointner; Peter Holl; Mengning Liang; Miriam Barthelmess; Carl Caleman; Sébastien Boutet; Michael J Bogan; Jacek Krzywinski; Christoph Bostedt; Saša Bajt; Lars Gumprecht; Benedikt Rudek; Benjamin Erk; Carlo Schmidt; André Hömke; Christian Reich; Daniel Pietschner; Lothar Strüder; Günter Hauser; Hubert Gorke; Joachim Ullrich; Sven Herrmann; Gerhard Schaller; Florian Schopper; Heike Soltau; Kai-Uwe Kühnel; Marc Messerschmidt; John D Bozek; Stefan P Hau-Riege; Matthias Frank; Christina Y Hampton; Raymond G Sierra; Dmitri Starodub; Garth J Williams; Janos Hajdu; Nicusor Timneanu; M Marvin Seibert; Jakob Andreasson; Andrea Rocker; Olof Jönsson; Martin Svenda; Stephan Stern; Karol Nass; Robert Andritschke; Claus-Dieter Schröter; Faton Krasniqi; Mario Bott; Kevin E Schmidt; Xiaoyu Wang; Ingo Grotjohann; James M Holton; Thomas R M Barends; Richard Neutze; Stefano Marchesini; Raimund Fromme; Sebastian Schorb; Daniela Rupp; Marcus Adolph; Tais Gorkhover; Inger Andersson; Helmut Hirsemann; Guillaume Potdevin; Heinz Graafsma; Björn Nilsson; John C H Spence
Journal:  Nature       Date:  2011-02-03       Impact factor: 49.962

Review 8.  Molecular pathology of NEU1 gene in sialidosis.

Authors:  Volkan Seyrantepe; Helena Poupetova; Roseline Froissart; Marie-Thérèse Zabot; Irène Maire; Alexey V Pshezhetsky
Journal:  Hum Mutat       Date:  2003-11       Impact factor: 4.878

9.  Evolution of a novel function: nutritive milk in the viviparous cockroach, Diploptera punctata.

Authors:  Anna Williford; Barbara Stay; Debashish Bhattacharya
Journal:  Evol Dev       Date:  2004 Mar-Apr       Impact factor: 1.930

10.  Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser.

Authors:  Lars Redecke; Karol Nass; Daniel P DePonte; Thomas A White; Dirk Rehders; Anton Barty; Francesco Stellato; Mengning Liang; Thomas R M Barends; Sébastien Boutet; Garth J Williams; Marc Messerschmidt; M Marvin Seibert; Andrew Aquila; David Arnlund; Sasa Bajt; Torsten Barth; Michael J Bogan; Carl Caleman; Tzu-Chiao Chao; R Bruce Doak; Holger Fleckenstein; Matthias Frank; Raimund Fromme; Lorenzo Galli; Ingo Grotjohann; Mark S Hunter; Linda C Johansson; Stephan Kassemeyer; Gergely Katona; Richard A Kirian; Rudolf Koopmann; Chris Kupitz; Lukas Lomb; Andrew V Martin; Stefan Mogk; Richard Neutze; Robert L Shoeman; Jan Steinbrener; Nicusor Timneanu; Dingjie Wang; Uwe Weierstall; Nadia A Zatsepin; John C H Spence; Petra Fromme; Ilme Schlichting; Michael Duszenko; Christian Betzel; Henry N Chapman
Journal:  Science       Date:  2012-11-29       Impact factor: 47.728

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  16 in total

Review 1.  In vivo protein crystallization in combination with highly brilliant radiation sources offers novel opportunities for the structural analysis of post-translationally modified eukaryotic proteins.

Authors:  Michael Duszenko; Lars Redecke; Celestin Nzanzu Mudogo; Benjamin Philip Sommer; Stefan Mogk; Dominik Oberthuer; Christian Betzel
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2015-07-29       Impact factor: 1.056

Review 2.  Understanding pre-mRNA splicing through crystallography.

Authors:  Sara Espinosa; Lingdi Zhang; Xueni Li; Rui Zhao
Journal:  Methods       Date:  2017-05-12       Impact factor: 3.608

Review 3.  Diffraction Techniques in Structural Biology.

Authors:  Martin Egli
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2016-06-01

4.  The birth of a new field.

Authors:  John C H Spence; Henry N Chapman
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2014-07-17       Impact factor: 6.237

5.  ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants.

Authors:  Arnaud Hungler; Afaque Momin; Kay Diederichs; Stefan T Arold
Journal:  J Appl Crystallogr       Date:  2016-11-02       Impact factor: 3.304

6.  Microcrystallography of Protein Crystals and In Cellulo Diffraction.

Authors:  Marion Boudes; Damià Garriga; Fasséli Coulibaly
Journal:  J Vis Exp       Date:  2017-07-21       Impact factor: 1.355

7.  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 8.  Serial femtosecond crystallography: A revolution in structural biology.

Authors:  Jose M Martin-Garcia; Chelsie E Conrad; Jesse Coe; Shatabdi Roy-Chowdhury; Petra Fromme
Journal:  Arch Biochem Biophys       Date:  2016-04-30       Impact factor: 4.013

9.  Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals.

Authors:  J Mia Lahey-Rudolph; Robert Schönherr; Miriam Barthelmess; Pontus Fischer; Carolin Seuring; Armin Wagner; Alke Meents; Lars Redecke
Journal:  IUCrJ       Date:  2021-06-18       Impact factor: 4.769

Review 10.  Can (We Make) Bacillus thuringiensis Crystallize More Than Its Toxins?

Authors:  Guillaume Tetreau; Elena A Andreeva; Anne-Sophie Banneville; Elke De Zitter; Jacques-Philippe Colletier
Journal:  Toxins (Basel)       Date:  2021-06-26       Impact factor: 4.546

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