Literature DB >> 29353938

Watching Proteins Function with Time-resolved X-ray Crystallography.

Vukica Šrajer1, Marius Schmidt2.   

Abstract

Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron X-ray sources. An expansive database of more than 100,000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al., 2005a; Schmidt 2008; Neutze and Moffat, 2012; Šrajer 2014). In this approach, short and intense X-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron X-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard X-rays (XFELs; 5-20 keV), which provide exceptionally intense, femtosecond X-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al., 2014; Barends et al., 2015; Pande et al., 2016). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline challenges and further developments necessary to broaden the application of these methods to many important proteins and enzymes of biomedical relevance.

Entities:  

Year:  2017        PMID: 29353938      PMCID: PMC5771432          DOI: 10.1088/1361-6463/aa7d32

Source DB:  PubMed          Journal:  J Phys D Appl Phys        ISSN: 0022-3727            Impact factor:   3.207


  111 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.  Ligand-linked structural transitions in crystals of a cooperative dimeric hemoglobin.

Authors:  James E Knapp; William E Royer
Journal:  Biochemistry       Date:  2003-04-29       Impact factor: 3.162

3.  X-ray diffraction from membrane protein nanocrystals.

Authors:  M S Hunter; D P DePonte; D A Shapiro; R A Kirian; X Wang; D Starodub; S Marchesini; U Weierstall; R B Doak; J C H Spence; P Fromme
Journal:  Biophys J       Date:  2011-01-05       Impact factor: 4.033

4.  Bond shortening (1.4 Å) in the singlet and triplet excited states of [Ir2(dimen)4]2+ in solution determined by time-resolved X-ray scattering.

Authors:  Kristoffer Haldrup; Tobias Harlang; Morten Christensen; Asmus Dohn; Tim Brandt van Driel; Kasper Skov Kjær; Niels Harrit; Johan Vibenholt; Laurent Guerin; Michael Wulff; Martin Meedom Nielsen
Journal:  Inorg Chem       Date:  2011-08-08       Impact factor: 5.165

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

6.  Mutation of residue Phe97 to Leu disrupts the central allosteric pathway in Scapharca dimeric hemoglobin.

Authors:  A Pardanani; Q H Gibson; G Colotti; W E Royer
Journal:  J Biol Chem       Date:  1997-05-16       Impact factor: 5.157

7.  Diffraction methods for biological macromolecules. Flow cell construction and use.

Authors:  G A Petsko
Journal:  Methods Enzymol       Date:  1985       Impact factor: 1.600

8.  Structure of the covalent adduct formed between Mycobacterium tuberculosis beta-lactamase and clavulanate.

Authors:  Lee W Tremblay; Jean-Emmanuel Hugonnet; John S Blanchard
Journal:  Biochemistry       Date:  2008-04-19       Impact factor: 3.162

9.  New Python-based methods for data processing.

Authors:  Nicholas K Sauter; Johan Hattne; Ralf W Grosse-Kunstleve; Nathaniel Echols
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-06-18

10.  Fixed-target protein serial microcrystallography with an x-ray free electron laser.

Authors:  Mark S Hunter; Brent Segelke; Marc Messerschmidt; Garth J Williams; Nadia A Zatsepin; Anton Barty; W Henry Benner; David B Carlson; Matthew Coleman; Alexander Graf; Stefan P Hau-Riege; Tommaso Pardini; M Marvin Seibert; James Evans; Sébastien Boutet; Matthias Frank
Journal:  Sci Rep       Date:  2014-08-12       Impact factor: 4.379

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  14 in total

1.  Single-molecule FRET methods to study the dynamics of proteins at work.

Authors:  Hisham Mazal; Gilad Haran
Journal:  Curr Opin Biomed Eng       Date:  2019-08-23

Review 2.  The future of quantum biology.

Authors:  Adriana Marais; Betony Adams; Andrew K Ringsmuth; Marco Ferretti; J Michael Gruber; Ruud Hendrikx; Maria Schuld; Samuel L Smith; Ilya Sinayskiy; Tjaart P J Krüger; Francesco Petruccione; Rienk van Grondelle
Journal:  J R Soc Interface       Date:  2018-11-14       Impact factor: 4.118

3.  Seed-skewness algorithm for X-ray diffraction signal detection in time-resolved synchrotron Laue photocrystallography.

Authors:  Dariusz Szarejko; Radosław Kamiński; Piotr Łaski; Katarzyna N Jarzembska
Journal:  J Synchrotron Radiat       Date:  2020-02-11       Impact factor: 2.616

Review 4.  Serial Crystallography for Structure-Based Drug Discovery.

Authors:  Lan Zhu; Xiaoyu Chen; Enrique E Abola; Liang Jing; Wei Liu
Journal:  Trends Pharmacol Sci       Date:  2020-09-16       Impact factor: 14.819

5.  Segmented flow generator for serial crystallography at the European X-ray free electron laser.

Authors:  Austin Echelmeier; Jorvani Cruz Villarreal; Marc Messerschmidt; Daihyun Kim; Jesse D Coe; Darren Thifault; Sabine Botha; Ana Egatz-Gomez; Sahir Gandhi; Gerrit Brehm; Chelsie E Conrad; Debra T Hansen; Caleb Madsen; Saša Bajt; J Domingo Meza-Aguilar; Dominik Oberthür; Max O Wiedorn; Holger Fleckenstein; Derek Mendez; Juraj Knoška; Jose M Martin-Garcia; Hao Hu; Stella Lisova; Aschkan Allahgholi; Yaroslav Gevorkov; Kartik Ayyer; Steve Aplin; Helen Mary Ginn; Heinz Graafsma; Andrew J Morgan; Dominic Greiffenberg; Alexander Klujev; Torsten Laurus; Jennifer Poehlsen; Ulrich Trunk; Davide Mezza; Bernd Schmidt; Manuela Kuhn; Raimund Fromme; Jolanta Sztuk-Dambietz; Natascha Raab; Steffen Hauf; Alessandro Silenzi; Thomas Michelat; Chen Xu; Cyril Danilevski; Andrea Parenti; Leonce Mekinda; Britta Weinhausen; Grant Mills; Patrik Vagovic; Yoonhee Kim; Henry Kirkwood; Richard Bean; Johan Bielecki; Stephan Stern; Klaus Giewekemeyer; Adam R Round; Joachim Schulz; Katerina Dörner; Thomas D Grant; Valerio Mariani; Anton Barty; Adrian P Mancuso; Uwe Weierstall; John C H Spence; Henry N Chapman; Nadia Zatsepin; Petra Fromme; Richard A Kirian; Alexandra Ros
Journal:  Nat Commun       Date:  2020-09-09       Impact factor: 14.919

6.  Molecular Dynamics Simulations of Macromolecular Crystals.

Authors:  David S Cerutti; David A Case
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2018-11-16

7.  Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques-Searching for Mechanism and Kinetics of Biomolecular Functions.

Authors:  Hiroshi Fujisaki; Kei Moritsugu; Yasuhiro Matsunaga
Journal:  Int J Mol Sci       Date:  2018-10-15       Impact factor: 5.923

8.  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

9.  Modular microfluidics enables kinetic insight from time-resolved cryo-EM.

Authors:  Märt-Erik Mäeots; Byungjin Lee; Andrea Nans; Seung-Geun Jeong; Mohammad M N Esfahani; Shan Ding; Daniel J Smith; Chang-Soo Lee; Sung Sik Lee; Matthias Peter; Radoslav I Enchev
Journal:  Nat Commun       Date:  2020-07-10       Impact factor: 14.919

Review 10.  Four-dimensional metal-organic frameworks.

Authors:  Jack D Evans; Volodymyr Bon; Irena Senkovska; Hui-Chun Lee; Stefan Kaskel
Journal:  Nat Commun       Date:  2020-06-01       Impact factor: 14.919

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