Literature DB >> 27074249

X-ray radiation-induced addition of oxygen atoms to protein residues.

Jimin Wang1.   

Abstract

The additions of oxygen and peroxide to residues that result when proteins are exposed to the free radicals produced using the Fenton reaction or X-rays have been studied for over a century. Nevertheless little is known about the impact these modifications have on protein crystal structures. Here evidence is presented that both kinds of modifications occur in protein crystals on a significant scale during the collection of X-ray diffraction data. For example, at least 538 of the 5,351 residues of protein molecules in the crystal used to obtain the structure for photosystem II described by the PDB accession number 3ARC became oxygenated during data collection.
© 2016 The Protein Society.

Entities:  

Keywords:  X-ray crystallography; direct methods; normalized electron density E-maps; phase problem; photosystem II; radiation chemistry

Mesh:

Substances:

Year:  2016        PMID: 27074249      PMCID: PMC4989999          DOI: 10.1002/pro.2934

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  26 in total

1.  Unit-cell volume change as a metric of radiation damage in crystals of macromolecules.

Authors:  Raimond B G Ravelli; Pascal Theveneau; Sean McSweeney; Martin Caffrey
Journal:  J Synchrotron Radiat       Date:  2002-11-01       Impact factor: 2.616

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Authors:  P Therese Lang; Ho-Leung Ng; James S Fraser; Jacob E Corn; Nathaniel Echols; Mark Sales; James M Holton; Tom Alber
Journal:  Protein Sci       Date:  2010-07       Impact factor: 6.725

4.  Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å.

Authors:  Yasufumi Umena; Keisuke Kawakami; Jian-Ren Shen; Nobuo Kamiya
Journal:  Nature       Date:  2011-04-17       Impact factor: 49.962

5.  Why are protein crystallographic R-values so high?

Authors:  E E Lattman
Journal:  Proteins       Date:  1996-05

6.  On the validation of crystallographic symmetry and the quality of structures.

Authors:  Jimin Wang
Journal:  Protein Sci       Date:  2014-12-09       Impact factor: 6.725

7.  Histidine and proline are important sites of free radical damage to proteins.

Authors:  R T Dean; S P Wolff; M A McElligott
Journal:  Free Radic Res Commun       Date:  1989

8.  Identification of oxidized amino acid residues in the vicinity of the Mn(4)CaO(5) cluster of Photosystem II: implications for the identification of oxygen channels within the Photosystem.

Authors:  Laurie K Frankel; Larry Sallans; Patrick A Limbach; Terry M Bricker
Journal:  Biochemistry       Date:  2012-08-02       Impact factor: 3.162

9.  Structural characterization of the products of hydroxyl-radical damage to leucine and their detection on proteins.

Authors:  S L Fu; R T Dean
Journal:  Biochem J       Date:  1997-05-15       Impact factor: 3.857

10.  Studies of the limited degradation of mucus glycoproteins. The effect of dilute hydrogen peroxide.

Authors:  J M Creeth; B Cooper; A S Donald; J R Clamp
Journal:  Biochem J       Date:  1983-05-01       Impact factor: 3.857

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  9 in total

1.  Oxygen additions in serial femtosecond crystallographic protein structures.

Authors:  Jimin Wang
Journal:  Protein Sci       Date:  2016-07-26       Impact factor: 6.725

2.  Systematic analysis of residual density suggests that a major limitation in well-refined X-ray structures of proteins is the omission of ordered solvent.

Authors:  Jimin Wang
Journal:  Protein Sci       Date:  2017-03-07       Impact factor: 6.725

3.  On the damage done to the structure of the Thermoplasma acidophilum proteasome by electron radiation.

Authors:  Jimin Wang; Zheng Liu; Robert H Crabtree; Joachim Frank; Peter B Moore
Journal:  Protein Sci       Date:  2018-11-05       Impact factor: 6.725

4.  Destruction-and-diffraction by X-ray free-electron laser.

Authors:  Jimin Wang
Journal:  Protein Sci       Date:  2016-06-13       Impact factor: 6.725

5.  Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation.

Authors:  Henry van den Bedem; Mark A Wilson
Journal:  J Synchrotron Radiat       Date:  2019-06-13       Impact factor: 2.616

Review 6.  Insights into Photosystem II from Isomorphous Difference Fourier Maps of Femtosecond X-ray Diffraction Data and Quantum Mechanics/Molecular Mechanics Structural Models.

Authors:  Jimin Wang; Mikhail Askerka; Gary W Brudvig; Victor S Batista
Journal:  ACS Energy Lett       Date:  2017-01-12       Impact factor: 23.101

7.  High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams.

Authors:  Koji Kato; Naoyuki Miyazaki; Tasuku Hamaguchi; Yoshiki Nakajima; Fusamichi Akita; Koji Yonekura; Jian-Ren Shen
Journal:  Commun Biol       Date:  2021-03-22

8.  Reactive oxygen species leave a damage trail that reveals water channels in Photosystem II.

Authors:  Daniel A Weisz; Michael L Gross; Himadri B Pakrasi
Journal:  Sci Adv       Date:  2017-11-17       Impact factor: 14.136

9.  Crystallographic Data Support the Carousel Mechanism of Water Supply to the Oxygen-Evolving Complex of Photosystem II.

Authors:  Jimin Wang; Mikhail Askerka; Gary W Brudvig; Victor S Batista
Journal:  ACS Energy Lett       Date:  2017-09-07       Impact factor: 23.101

  9 in total

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