Literature DB >> 26342144

Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers.

Jan Kern1, Vittal K Yachandra2, Junko Yano3.   

Abstract

Although the structure of enzymes and the chemistry at the catalytic sites have been studied intensively, an understanding of the atomic-scale chemistry requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the sample is destroyed. This review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism.
Copyright © 2015 Elsevier Ltd. All rights reserved.

Entities:  

Mesh:

Substances:

Year:  2015        PMID: 26342144      PMCID: PMC4821593          DOI: 10.1016/j.sbi.2015.07.014

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


  54 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.  Nanoflow electrospinning serial femtosecond crystallography.

Authors:  Raymond G Sierra; Hartawan Laksmono; Jan Kern; Rosalie Tran; Johan Hattne; Roberto Alonso-Mori; Benedikt Lassalle-Kaiser; Carina Glöckner; Julia Hellmich; Donald W Schafer; Nathaniel Echols; Richard J Gildea; Ralf W Grosse-Kunstleve; Jonas Sellberg; Trevor A McQueen; Alan R Fry; Marc M Messerschmidt; Alan Miahnahri; M Marvin Seibert; Christina Y Hampton; Dmitri Starodub; N Duane Loh; Dimosthenis Sokaras; Tsu-Chien Weng; Petrus H Zwart; Pieter Glatzel; Despina Milathianaki; William E White; Paul D Adams; Garth J Williams; Sébastien Boutet; Athina Zouni; Johannes Messinger; Nicholas K Sauter; Uwe Bergmann; Junko Yano; Vittal K Yachandra; Michael J Bogan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-10-18

Review 3.  X-ray free electron lasers motivate bioanalytical characterization of protein nanocrystals: serial femtosecond crystallography.

Authors:  Michael J Bogan
Journal:  Anal Chem       Date:  2013-03-21       Impact factor: 6.986

4.  Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.

Authors:  Kunio Hirata; Kyoko Shinzawa-Itoh; Naomine Yano; Shuhei Takemura; Koji Kato; Miki Hatanaka; Kazumasa Muramoto; Takako Kawahara; Tomitake Tsukihara; Eiki Yamashita; Kensuke Tono; Go Ueno; Takaaki Hikima; Hironori Murakami; Yuichi Inubushi; Makina Yabashi; Tetsuya Ishikawa; Masaki Yamamoto; Takashi Ogura; Hiroshi Sugimoto; Jian-Ren Shen; Shinya Yoshikawa; Hideo Ago
Journal:  Nat Methods       Date:  2014-05-11       Impact factor: 28.547

5.  Simultaneous detection of electronic structure changes from two elements of a bifunctional catalyst using wavelength-dispersive X-ray emission spectroscopy and in situ electrochemistry.

Authors:  Sheraz Gul; Jia Wei Desmond Ng; Roberto Alonso-Mori; Jan Kern; Dimosthenis Sokaras; Eitan Anzenberg; Benedikt Lassalle-Kaiser; Yelena Gorlin; Tsu-Chien Weng; Petrus H Zwart; Jin Z Zhang; Uwe Bergmann; Vittal K Yachandra; Thomas F Jaramillo; Junko Yano
Journal:  Phys Chem Chem Phys       Date:  2015-03-06       Impact factor: 3.676

6.  Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses.

Authors:  Michihiro Suga; Fusamichi Akita; Kunio Hirata; Go Ueno; Hironori Murakami; Yoshiki Nakajima; Tetsuya Shimizu; Keitaro Yamashita; Masaki Yamamoto; Hideo Ago; Jian-Ren Shen
Journal:  Nature       Date:  2014-11-26       Impact factor: 49.962

7.  Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser.

Authors:  David Arnlund; Linda C Johansson; Cecilia Wickstrand; Anton Barty; Garth J Williams; Erik Malmerberg; Jan Davidsson; Despina Milathianaki; Daniel P DePonte; Robert L Shoeman; Dingjie Wang; Daniel James; Gergely Katona; Sebastian Westenhoff; Thomas A White; Andrew Aquila; Sadia Bari; Peter Berntsen; Mike Bogan; Tim Brandt van Driel; R Bruce Doak; Kasper Skov Kjær; Matthias Frank; Raimund Fromme; Ingo Grotjohann; Robert Henning; Mark S Hunter; Richard A Kirian; Irina Kosheleva; Christopher Kupitz; Mengning Liang; Andrew V Martin; Martin Meedom Nielsen; Marc Messerschmidt; M Marvin Seibert; Jennie Sjöhamn; Francesco Stellato; Uwe Weierstall; Nadia A Zatsepin; John C H Spence; Petra Fromme; Ilme Schlichting; Sébastien Boutet; Gerrit Groenhof; Henry N Chapman; Richard Neutze
Journal:  Nat Methods       Date:  2014-08-10       Impact factor: 28.547

8.  Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography.

Authors:  Linda C Johansson; David Arnlund; Gergely Katona; Thomas A White; Anton Barty; Daniel P DePonte; Robert L Shoeman; Cecilia Wickstrand; Amit Sharma; Garth J Williams; Andrew Aquila; Michael J Bogan; Carl Caleman; Jan Davidsson; R Bruce Doak; Matthias Frank; Raimund Fromme; Lorenzo Galli; Ingo Grotjohann; Mark S Hunter; Stephan Kassemeyer; Richard A Kirian; Christopher Kupitz; Mengning Liang; Lukas Lomb; Erik Malmerberg; Andrew V Martin; Marc Messerschmidt; Karol Nass; Lars Redecke; M Marvin Seibert; Jennie Sjöhamn; Jan Steinbrener; Francesco Stellato; Dingjie Wang; Weixaio Y Wahlgren; Uwe Weierstall; Sebastian Westenhoff; Nadia A Zatsepin; Sébastien Boutet; John C H Spence; Ilme Schlichting; Henry N Chapman; Petra Fromme; Richard Neutze
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919

Review 9.  Mn4Ca cluster in photosynthesis: where and how water is oxidized to dioxygen.

Authors:  Junko Yano; Vittal Yachandra
Journal:  Chem Rev       Date:  2014-03-31       Impact factor: 60.622

10.  Diffraction before destruction.

Authors:  Henry N Chapman; Carl Caleman; Nicusor Timneanu
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2014-07-17       Impact factor: 6.237

View more
  10 in total

1.  Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources.

Authors:  Pierre Aller; Allen M Orville
Journal:  Methods Mol Biol       Date:  2021

Review 2.  Biophysics in drug discovery: impact, challenges and opportunities.

Authors:  Jean-Paul Renaud; Chun-Wa Chung; U Helena Danielson; Ursula Egner; Michael Hennig; Roderick E Hubbard; Herbert Nar
Journal:  Nat Rev Drug Discov       Date:  2016-08-12       Impact factor: 84.694

3.  Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases.

Authors:  Kelsey R Miller; Jonathan D Paretsky; Alec H Follmer; Tillmann Heinisch; Kaustuv Mittra; Sheraz Gul; In-Sik Kim; Franklin D Fuller; Alexander Batyuk; Kyle D Sutherlin; Aaron S Brewster; Asmit Bhowmick; Nicholas K Sauter; Jan Kern; Junko Yano; Michael T Green; Thomas R Ward; A S Borovik
Journal:  Inorg Chem       Date:  2020-04-20       Impact factor: 5.165

Review 4.  XFELs for structure and dynamics in biology.

Authors:  J C H Spence
Journal:  IUCrJ       Date:  2017-05-10       Impact factor: 4.769

5.  Perspective: A toolbox for protein structure determination in physiological environment through oriented, 2D ordered, site specific immobilization.

Authors:  M Altissimo; M Kiskinova; R Mincigrucci; L Vaccari; C Guarnaccia; C Masciovecchio
Journal:  Struct Dyn       Date:  2017-04-14       Impact factor: 2.920

6.  Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction.

Authors:  Nicholas K Sauter; Jan Kern; Junko Yano; James M Holton
Journal:  Acta Crystallogr D Struct Biol       Date:  2020-02-04       Impact factor: 7.652

7.  Stochastic stimulated electronic x-ray Raman spectroscopy.

Authors:  Victor Kimberg; Nina Rohringer
Journal:  Struct Dyn       Date:  2016-02-09       Impact factor: 2.920

Review 8.  Advances in methods for atomic resolution macromolecular structure determination.

Authors:  Michael C Thompson; Todd O Yeates; Jose A Rodriguez
Journal:  F1000Res       Date:  2020-07-02

9.  Scientific instrument Femtosecond X-ray Experiments (FXE): instrumentation and baseline experimental capabilities.

Authors:  Andreas Galler; Wojciech Gawelda; Mykola Biednov; Christina Bomer; Alexander Britz; Sandor Brockhauser; Tae Kyu Choi; Michael Diez; Paul Frankenberger; Marcus French; Dennis Görries; Matthiew Hart; Steffen Hauf; Dmitry Khakhulin; Martin Knoll; Timo Korsch; Katharina Kubicek; Markus Kuster; Philipp Lang; Frederico Alves Lima; Florian Otte; Sebastian Schulz; Peter Zalden; Christian Bressler
Journal:  J Synchrotron Radiat       Date:  2019-08-09       Impact factor: 2.616

10.  X-ray fluorescence detection for serial macromolecular crystallography using a JUNGFRAU pixel detector.

Authors:  Isabelle Martiel; Aldo Mozzanica; Nadia L Opara; Ezequiel Panepucci; Filip Leonarski; Sophie Redford; Istvan Mohacsi; Vitaliy Guzenko; Dmitry Ozerov; Celestino Padeste; Bernd Schmitt; Bill Pedrini; Meitian Wang
Journal:  J Synchrotron Radiat       Date:  2020-02-07       Impact factor: 2.616

  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.