Literature DB >> 33603257

Synchrotron Radiation as a Tool for Macromolecular X-Ray Crystallography: a XXI Century Perspective.

Marek Grabowski1, David R Cooper1, Dariusz Brzezinski1,2,3, Joanna M Macnar4,5, Ivan G Shabalin1, Marcin Cymborowski1, Zbyszek Otwinowski6, Wladek Minor1.   

Abstract

Intense X-rays available at powerful synchrotron beamlines provide macromolecular crystallographers with an incomparable tool for investigating biological phenomena on an atomic scale. The resulting insights into the mechanism's underlying biological processes have played an essential role and shaped biomedical sciences during the last 30 years, considered the "golden age" of structural biology. In this review, we analyze selected aspects of the impact of synchrotron radiation on structural biology. Synchrotron beamlines have been used to determine over 70% of all macromolecular structures deposited into the Protein Data Bank (PDB). These structures were deposited by over 13,000 different research groups. Interestingly, despite the impressive advances in synchrotron technologies, the median resolution of macromolecular structures determined using synchrotrons has remained constant throughout the last 30 years, at about 2 Å. Similarly, the median times from the data collection to the deposition and release have not changed significantly. We describe challenges to reproducibility related to recording all relevant data and metadata during the synchrotron experiments, including diffraction images. Finally, we discuss some of the recent opinions suggesting a diminishing importance of X-ray crystallography due to impressive advances in Cryo-EM and theoretical modeling. We believe that synchrotrons of the future will increasingly evolve towards a life science center model, where X-ray crystallography, Cryo-EM, and other experimental and computational resources and knowledge are encompassed within a versatile research facility. The recent response of crystallographers to the COVID-19 pandemic suggests that X-ray crystallography conducted at synchrotron beamlines will continue to play an essential role in structural biology and drug discovery for years to come.

Entities:  

Year:  2021        PMID: 33603257      PMCID: PMC7886262          DOI: 10.1016/j.nimb.2020.12.016

Source DB:  PubMed          Journal:  Nucl Instrum Methods Phys Res B        ISSN: 0168-583X            Impact factor:   1.377


  49 in total

1.  The Protein Data Bank.

Authors:  Helen M Berman; Tammy Battistuz; T N Bhat; Wolfgang F Bluhm; Philip E Bourne; Kyle Burkhardt; Zukang Feng; Gary L Gilliland; Lisa Iype; Shri Jain; Phoebe Fagan; Jessica Marvin; David Padilla; Veerasamy Ravichandran; Bohdan Schneider; Narmada Thanki; Helge Weissig; John D Westbrook; Christine Zardecki
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-05-29

2.  Synchrotron radiation sources - present capabilities and future directions.

Authors:  H Winick
Journal:  J Synchrotron Radiat       Date:  1998-05-01       Impact factor: 2.616

3.  Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.

Authors:  Ivan Shabalin; Zbigniew Dauter; Mariusz Jaskolski; Wladek Minor; Alexander Wlodawer
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-08-28

Review 4.  How cryo-electron microscopy and X-ray crystallography complement each other.

Authors:  Hong-Wei Wang; Jia-Wei Wang
Journal:  Protein Sci       Date:  2016-09-07       Impact factor: 6.725

Review 5.  The Seattle Structural Genomics Center for Infectious Disease (SSGCID).

Authors:  P J Myler; R Stacy; L Stewart; B L Staker; W C Van Voorhis; G Varani; G W Buchko
Journal:  Infect Disord Drug Targets       Date:  2009-11

Review 6.  Structural genomics and drug discovery for infectious diseases.

Authors:  W F Anderson
Journal:  Infect Disord Drug Targets       Date:  2009-11

7.  Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors.

Authors:  Zhenming Jin; Xiaoyu Du; Yechun Xu; Yongqiang Deng; Meiqin Liu; Yao Zhao; Bing Zhang; Xiaofeng Li; Leike Zhang; Chao Peng; Yinkai Duan; Jing Yu; Lin Wang; Kailin Yang; Fengjiang Liu; Rendi Jiang; Xinglou Yang; Tian You; Xiaoce Liu; Xiuna Yang; Fang Bai; Hong Liu; Xiang Liu; Luke W Guddat; Wenqing Xu; Gengfu Xiao; Chengfeng Qin; Zhengli Shi; Hualiang Jiang; Zihe Rao; Haitao Yang
Journal:  Nature       Date:  2020-04-09       Impact factor: 49.962

8.  Structural genomics of infectious disease drug targets: the SSGCID.

Authors:  Robin Stacy; Darren W Begley; Isabelle Phan; Bart L Staker; Wesley C Van Voorhis; Gabriele Varani; Garry W Buchko; Lance J Stewart; Peter J Myler
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2011-08-13

Review 9.  Synchrotron radiation macromolecular crystallography: science and spin-offs.

Authors:  John R Helliwell; Edward P Mitchell
Journal:  IUCrJ       Date:  2015-02-03       Impact factor: 4.769

10.  Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models.

Authors:  Dariusz Brzezinski; Marcin Kowiel; David R Cooper; Marcin Cymborowski; Marek Grabowski; Alexander Wlodawer; Zbigniew Dauter; Ivan G Shabalin; Miroslaw Gilski; Bernhard Rupp; Mariusz Jaskolski; Wladek Minor
Journal:  Protein Sci       Date:  2020-10-08       Impact factor: 6.993

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  1 in total

1.  Optimal structure determination from sub-optimal diffraction data.

Authors:  Wladek Minor; Marcin Cymborowski; Dominika Borek; David R Cooper; Maksymilian Chruszcz; Zbyszek Otwinowski
Journal:  Protein Sci       Date:  2021-11-24       Impact factor: 6.725

  1 in total

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