Literature DB >> 34294694

An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography.

Agata Butryn1,2, Philipp S Simon3, Pierre Aller1,2, Philip Hinchliffe4, Ramzi N Massad3, Gabriel Leen5,6, Catherine L Tooke4, Isabel Bogacz3, In-Sik Kim3, Asmit Bhowmick3, Aaron S Brewster3, Nicholas E Devenish1, Jürgen Brem7, Jos J A G Kamps7,1, Pauline A Lang7, Patrick Rabe7, Danny Axford1, John H Beale1,8, Bradley Davy1,9, Ali Ebrahim1, Julien Orlans1,10, Selina L S Storm1,11, Tiankun Zhou1,2, Shigeki Owada12,13, Rie Tanaka12,14, Kensuke Tono12,13, Gwyndaf Evans1, Robin L Owen1, Frances A Houle15, Nicholas K Sauter3, Christopher J Schofield7, James Spencer4, Vittal K Yachandra3, Junko Yano3, Jan F Kern16, Allen M Orville17,18.   

Abstract

Serial femtosecond crystallography has opened up many new opportunities in structural biology. In recent years, several approaches employing light-inducible systems have emerged to enable time-resolved experiments that reveal protein dynamics at high atomic and temporal resolutions. However, very few enzymes are light-dependent, whereas macromolecules requiring ligand diffusion into an active site are ubiquitous. In this work we present a drop-on-drop sample delivery system that enables the study of enzyme-catalyzed reactions in microcrystal slurries. The system delivers ligand solutions in bursts of multiple picoliter-sized drops on top of a larger crystal-containing drop inducing turbulent mixing and transports the mixture to the X-ray interaction region with temporal resolution. We demonstrate mixing using fluorescent dyes, numerical simulations and time-resolved serial femtosecond crystallography, which show rapid ligand diffusion through microdroplets. The drop-on-drop method has the potential to be widely applicable to serial crystallography studies, particularly of enzyme reactions with small molecule substrates.
© 2021. Crown.

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Year:  2021        PMID: 34294694     DOI: 10.1038/s41467-021-24757-7

Source DB:  PubMed          Journal:  Nat Commun        ISSN: 2041-1723            Impact factor:   14.919


  38 in total

1.  Time-resolved protein activation by proximal decaging in living systems.

Authors:  Jie Wang; Yuan Liu; Yanjun Liu; Siqi Zheng; Xin Wang; Jingyi Zhao; Fan Yang; Gong Zhang; Chu Wang; Peng R Chen
Journal:  Nature       Date:  2019-05-08       Impact factor: 49.962

Review 2.  X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules.

Authors:  Henry N Chapman
Journal:  Annu Rev Biochem       Date:  2019-01-02       Impact factor: 23.643

Review 3.  Real-time crystallographic studies of the adenine riboswitch using an X-ray free-electron laser.

Authors:  Jason R Stagno; Yuba R Bhandari; Chelsie E Conrad; Yu Liu; Yun-Xing Wang
Journal:  FEBS J       Date:  2017-08-01       Impact factor: 5.542

Review 4.  Recent results in time resolved serial femtosecond crystallography at XFELs.

Authors:  Allen M Orville
Journal:  Curr Opin Struct Biol       Date:  2020-10-10       Impact factor: 6.809

5.  Liquid application method for time-resolved analyses by serial synchrotron crystallography.

Authors:  Pedram Mehrabi; Eike C Schulz; Michael Agthe; Sam Horrell; Gleb Bourenkov; David von Stetten; Jan-Philipp Leimkohl; Hendrik Schikora; Thomas R Schneider; Arwen R Pearson; Friedjof Tellkamp; R J Dwayne Miller
Journal:  Nat Methods       Date:  2019-09-16       Impact factor: 28.547

6.  Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers.

Authors:  Franklin D Fuller; Sheraz Gul; Ruchira Chatterjee; E Sethe Burgie; Iris D Young; Hugo Lebrette; Vivek Srinivas; Aaron S Brewster; Tara Michels-Clark; Jonathan A Clinger; Babak Andi; Mohamed Ibrahim; Ernest Pastor; Casper de Lichtenberg; Rana Hussein; Christopher J Pollock; Miao Zhang; Claudiu A Stan; Thomas Kroll; Thomas Fransson; Clemens Weninger; Markus Kubin; Pierre Aller; Louise Lassalle; Philipp Bräuer; Mitchell D Miller; Muhamed Amin; Sergey Koroidov; Christian G Roessler; Marc Allaire; Raymond G Sierra; Peter T Docker; James M Glownia; Silke Nelson; Jason E Koglin; Diling Zhu; Matthieu Chollet; Sanghoon Song; Henrik Lemke; Mengning Liang; Dimosthenis Sokaras; Roberto Alonso-Mori; Athina Zouni; Johannes Messinger; Uwe Bergmann; Amie K Boal; J Martin Bollinger; Carsten Krebs; Martin Högbom; George N Phillips; Richard D Vierstra; Nicholas K Sauter; Allen M Orville; Jan Kern; Vittal K Yachandra; Junko Yano
Journal:  Nat Methods       Date:  2017-02-27       Impact factor: 28.547

7.  Structural enzymology using X-ray free electron lasers.

Authors:  Christopher Kupitz; Jose L Olmos; Mark Holl; Lee Tremblay; Kanupriya Pande; Suraj Pandey; Dominik Oberthür; Mark Hunter; Mengning Liang; Andrew Aquila; Jason Tenboer; George Calvey; Andrea Katz; Yujie Chen; Max O Wiedorn; Juraj Knoska; Alke Meents; Valerio Majriani; Tyler Norwood; Ishwor Poudyal; Thomas Grant; Mitchell D Miller; Weijun Xu; Aleksandra Tolstikova; Andrew Morgan; Markus Metz; Jose M Martin-Garcia; James D Zook; Shatabdi Roy-Chowdhury; Jesse Coe; Nirupa Nagaratnam; Domingo Meza; Raimund Fromme; Shibom Basu; Matthias Frank; Thomas White; Anton Barty; Sasa Bajt; Oleksandr Yefanov; Henry N Chapman; Nadia Zatsepin; Garrett Nelson; Uwe Weierstall; John Spence; Peter Schwander; Lois Pollack; Petra Fromme; Abbas Ourmazd; George N Phillips; Marius Schmidt
Journal:  Struct Dyn       Date:  2016-12-15       Impact factor: 2.920

8.  Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.

Authors:  Takehiko Tosha; Takashi Nomura; Takuma Nishida; Naoya Saeki; Kouta Okubayashi; Raika Yamagiwa; Michihiro Sugahara; Takanori Nakane; Keitaro Yamashita; Kunio Hirata; Go Ueno; Tetsunari Kimura; Tamao Hisano; Kazumasa Muramoto; Hitomi Sawai; Hanae Takeda; Eiichi Mizohata; Ayumi Yamashita; Yusuke Kanematsu; Yu Takano; Eriko Nango; Rie Tanaka; Osamu Nureki; Osami Shoji; Yuka Ikemoto; Hironori Murakami; Shigeki Owada; Kensuke Tono; Makina Yabashi; Masaki Yamamoto; Hideo Ago; So Iwata; Hiroshi Sugimoto; Yoshitsugu Shiro; Minoru Kubo
Journal:  Nat Commun       Date:  2017-11-17       Impact factor: 14.919

9.  Entering an era of dynamic structural biology….

Authors:  Allen M Orville
Journal:  BMC Biol       Date:  2018-05-31       Impact factor: 7.431

10.  Mix-and-diffuse serial synchrotron crystallography.

Authors:  Kenneth R Beyerlein; Dennis Dierksmeyer; Valerio Mariani; Manuela Kuhn; Iosifina Sarrou; Angelica Ottaviano; Salah Awel; Juraj Knoska; Silje Fuglerud; Olof Jönsson; Stephan Stern; Max O Wiedorn; Oleksandr Yefanov; Luigi Adriano; Richard Bean; Anja Burkhardt; Pontus Fischer; Michael Heymann; Daniel A Horke; Katharina E J Jungnickel; Elena Kovaleva; Olga Lorbeer; Markus Metz; Jan Meyer; Andrew Morgan; Kanupriya Pande; Saravanan Panneerselvam; Carolin Seuring; Aleksandra Tolstikova; Julia Lieske; Steve Aplin; Manfred Roessle; Thomas A White; Henry N Chapman; Alke Meents; Dominik Oberthuer
Journal:  IUCrJ       Date:  2017-10-09       Impact factor: 4.769

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  5 in total

1.  Combination of an inject-and-transfer system for serial femtosecond crystallography.

Authors:  Keondo Lee; Jihan Kim; Sangwon Baek; Jaehyun Park; Sehan Park; Jong-Lam Lee; Wan Kyun Chung; Yunje Cho; Ki Hyun Nam
Journal:  J Appl Crystallogr       Date:  2022-07-05       Impact factor: 4.868

2.  XFEL serial crystallography reveals the room temperature structure of methyl-coenzyme M reductase.

Authors:  Christopher J Ohmer; Medhanjali Dasgupta; Anjali Patwardhan; Isabel Bogacz; Corey Kaminsky; Margaret D Doyle; Percival Yang-Ting Chen; Stephen M Keable; Hiroki Makita; Philipp S Simon; Ramzi Massad; Thomas Fransson; Ruchira Chatterjee; Asmit Bhowmick; Daniel W Paley; Nigel W Moriarty; Aaron S Brewster; Leland B Gee; Roberto Alonso-Mori; Frank Moss; Franklin D Fuller; Alexander Batyuk; Nicholas K Sauter; Uwe Bergmann; Catherine L Drennan; Vittal K Yachandra; Junko Yano; Jan F Kern; Stephen W Ragsdale
Journal:  J Inorg Biochem       Date:  2022-02-17       Impact factor: 4.155

3.  Penicillanic Acid Sulfones Inactivate the Extended-Spectrum β-Lactamase CTX-M-15 through Formation of a Serine-Lysine Cross-Link: an Alternative Mechanism of β-Lactamase Inhibition.

Authors:  Philip Hinchliffe; Catherine L Tooke; Christopher R Bethel; Benlian Wang; Christopher Arthur; Kate J Heesom; Stuart Shapiro; Daniela M Schlatzer; Krisztina M Papp-Wallace; Robert A Bonomo; James Spencer
Journal:  mBio       Date:  2022-05-25       Impact factor: 7.786

Review 4.  Best practices for time-resolved serial synchrotron crystallography.

Authors:  Eike C Schulz; Briony A Yorke; Arwen R Pearson; Pedram Mehrabi
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-01-01       Impact factor: 7.652

5.  Hit and Indexing Rate in Serial Crystallography: Incomparable Statistics.

Authors:  Ki Hyun Nam
Journal:  Front Mol Biosci       Date:  2022-03-25
  5 in total

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