Literature DB >> 22922042

Emerging opportunities in structural biology with X-ray free-electron lasers.

Ilme Schlichting1, Jianwei Miao.   

Abstract

X-ray free-electron lasers (X-FELs) produce X-ray pulses with extremely brilliant peak intensity and ultrashort pulse duration. It has been proposed that radiation damage can be 'outrun' by using an ultra intense and short X-FEL pulse that passes a biological sample before the onset of significant radiation damage. The concept of 'diffraction-before-destruction' has been demonstrated recently at the Linac Coherent Light Source, the first operational hard X-ray FEL, for protein nanocrystals and giant virus particles. The continuous diffraction patterns from single particles allow solving the classical 'phase problem' by the oversampling method with iterative algorithms. If enough data are collected from many identical copies of a (biological) particle, its three-dimensional structure can be reconstructed. We review the current status and future prospects of serial femtosecond crystallography (SFX) and single-particle coherent diffraction imaging (CDI) with X-FELs.
Copyright © 2012 Elsevier Ltd. All rights reserved.

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Year:  2012        PMID: 22922042      PMCID: PMC3495068          DOI: 10.1016/j.sbi.2012.07.015

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  56 in total

1.  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

2.  Diffraction imaging of single particles and biomolecules.

Authors:  G Huldt; A Szoke; J Hajdu
Journal:  J Struct Biol       Date:  2003 Oct-Nov       Impact factor: 2.867

3.  Automated screening of 2D crystallization trials using transmission electron microscopy: a high-throughput tool-chain for sample preparation and microscopic analysis.

Authors:  Nicolas Coudray; Gilles Hermann; Daniel Caujolle-Bert; Argyro Karathanou; Françoise Erne-Brand; Jean-Luc Buessler; Pamela Daum; Juergen M Plitzko; Mohamed Chami; Urs Mueller; Hubert Kihl; Jean-Philippe Urban; Andreas Engel; Hervé-W Rémigy
Journal:  J Struct Biol       Date:  2010-09-22       Impact factor: 2.867

Review 4.  Methods for separating nucleation and growth in protein crystallisation.

Authors:  Naomi E Chayen
Journal:  Prog Biophys Mol Biol       Date:  2005-07       Impact factor: 3.667

5.  Quantitative image reconstruction of GaN quantum dots from oversampled diffraction intensities alone.

Authors:  Jianwei Miao; Yoshinori Nishino; Yoshiki Kohmura; Bart Johnson; Changyong Song; Subhash H Risbud; Tetsuya Ishikawa
Journal:  Phys Rev Lett       Date:  2005-08-17       Impact factor: 9.161

6.  Three-dimensional structure determination from a single view.

Authors:  Kevin S Raines; Sara Salha; Richard L Sandberg; Huaidong Jiang; Jose A Rodríguez; Benjamin P Fahimian; Henry C Kapteyn; Jincheng Du; Jianwei Miao
Journal:  Nature       Date:  2009-12-16       Impact factor: 49.962

7.  Reconstruction algorithm for single-particle diffraction imaging experiments.

Authors:  Ne-Te Duane Loh; Veit Elser
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-08-24

8.  Ultrafast transitions from solid to liquid and plasma states of graphite induced by x-ray free-electron laser pulses.

Authors:  S P Hau-Riege; A Graf; T Döppner; R A London; J Krzywinski; C Fortmann; S H Glenzer; M Frank; K Sokolowski-Tinten; M Messerschmidt; C Bostedt; S Schorb; J A Bradley; A Lutman; D Rolles; A Rudenko; B Rudek
Journal:  Phys Rev Lett       Date:  2012-05-23       Impact factor: 9.161

9.  Femtosecond protein nanocrystallography-data analysis methods.

Authors:  Richard A Kirian; Xiaoyu Wang; Uwe Weierstall; Kevin E Schmidt; John C H Spence; Mark Hunter; Petra Fromme; Thomas White; Henry N Chapman; James Holton
Journal:  Opt Express       Date:  2010-03-15       Impact factor: 3.894

10.  Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser.

Authors:  Lukas Lomb; Thomas R M Barends; Stephan Kassemeyer; Andrew Aquila; Sascha W Epp; Benjamin Erk; Lutz Foucar; Robert Hartmann; Benedikt Rudek; Daniel Rolles; Artem Rudenko; Robert L Shoeman; Jakob Andreasson; Sasa Bajt; Miriam Barthelmess; Anton Barty; Michael J Bogan; Christoph Bostedt; John D Bozek; Carl Caleman; Ryan Coffee; Nicola Coppola; Daniel P Deponte; R Bruce Doak; Tomas Ekeberg; Holger Fleckenstein; Petra Fromme; Maike Gebhardt; Heinz Graafsma; Lars Gumprecht; Christina Y Hampton; Andreas Hartmann; Günter Hauser; Helmut Hirsemann; Peter Holl; James M Holton; Mark S Hunter; Wolfgang Kabsch; Nils Kimmel; Richard A Kirian; Mengning Liang; Filipe R N C Maia; Anton Meinhart; Stefano Marchesini; Andrew V Martin; Karol Nass; Christian Reich; Joachim Schulz; M Marvin Seibert; Raymond Sierra; Heike Soltau; John C H Spence; Jan Steinbrener; Francesco Stellato; Stephan Stern; Nicusor Timneanu; Xiaoyu Wang; Georg Weidenspointner; Uwe Weierstall; Thomas A White; Cornelia Wunderer; Henry N Chapman; Joachim Ullrich; Lothar Strüder; Ilme Schlichting
Journal:  Phys Rev B Condens Matter Mater Phys       Date:  2011-12-01
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  35 in total

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

Authors:  Michihiro Sugahara; Eiichi Mizohata; Eriko Nango; Mamoru Suzuki; Tomoyuki Tanaka; Tetsuya Masuda; Rie Tanaka; Tatsuro Shimamura; Yoshiki Tanaka; Chiyo Suno; Kentaro Ihara; Dongqing Pan; Keisuke Kakinouchi; Shigeru Sugiyama; Michio Murata; Tsuyoshi Inoue; Kensuke Tono; Changyong Song; Jaehyun Park; Takashi Kameshima; Takaki Hatsui; Yasumasa Joti; Makina Yabashi; So Iwata
Journal:  Nat Methods       Date:  2014-11-10       Impact factor: 28.547

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.  Analytic 3D imaging of mammalian nucleus at nanoscale using coherent x-rays and optical fluorescence microscopy.

Authors:  Changyong Song; Masatoshi Takagi; Jaehyun Park; Rui Xu; Marcus Gallagher-Jones; Naoko Imamoto; Tetsuya Ishikawa
Journal:  Biophys J       Date:  2014-09-02       Impact factor: 4.033

4.  Time-, frequency-, and wavevector-resolved x-ray diffraction from single molecules.

Authors:  Kochise Bennett; Jason D Biggs; Yu Zhang; Konstantin E Dorfman; Shaul Mukamel
Journal:  J Chem Phys       Date:  2014-05-28       Impact factor: 3.488

Review 5.  Introduction to protein crystallization.

Authors:  Alexander McPherson; Jose A Gavira
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2013-12-24       Impact factor: 1.056

Review 6.  Opportunities in multidimensional trace metal imaging: taking copper-associated disease research to the next level.

Authors:  Stefan Vogt; Martina Ralle
Journal:  Anal Bioanal Chem       Date:  2012-10-19       Impact factor: 4.142

7.  Oversampling smoothness: an effective algorithm for phase retrieval of noisy diffraction intensities.

Authors:  Jose A Rodriguez; Rui Xu; Chien-Chun Chen; Yunfei Zou; Jianwei Miao
Journal:  J Appl Crystallogr       Date:  2013-02-23       Impact factor: 3.304

8.  Rapid X-ray photoreduction of dimetal-oxygen cofactors in ribonucleotide reductase.

Authors:  Kajsa G V Sigfridsson; Petko Chernev; Nils Leidel; Ana Popovic-Bijelic; Astrid Gräslund; Michael Haumann
Journal:  J Biol Chem       Date:  2013-02-11       Impact factor: 5.157

Review 9.  Assessment of microcrystal quality by transmission electron microscopy for efficient serial femtosecond crystallography.

Authors:  Christopher O Barnes; Elena G Kovaleva; Xiaofeng Fu; Hilary P Stevenson; Aaron S Brewster; Daniel P DePonte; Elizabeth L Baxter; Aina E Cohen; Guillermo Calero
Journal:  Arch Biochem Biophys       Date:  2016-03-02       Impact factor: 4.013

Review 10.  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

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