Literature DB >> 26327386

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

Ivan Shabalin1, Zbigniew Dauter2, Mariusz Jaskolski3, Wladek Minor1, Alexander Wlodawer4.   

Abstract

The anticancer activity of platinum-containing drugs such as cisplatin and carboplatin is considered to primarily arise from their interactions with nucleic acids; nevertheless, these drugs, or the products of their hydrolysis, also bind to proteins, potentially leading to the known side effects of the treatments. Here, over 40 crystal structures deposited in the Protein Data Bank (PDB) of cisplatin and carboplatin complexes of several proteins were analysed. Significant problems of either a crystallographic or a chemical nature were found in most of the presented atomic models and they could be traced to less or more serious deficiencies in the data-collection and refinement procedures. The re-evaluation of these data and models was possible thanks to their mandatory or voluntary deposition in publicly available databases, emphasizing the point that the availability of such data is critical for making structural science reproducible. Based on this analysis of a selected group of macromolecular structures, the importance of deposition of raw diffraction data is stressed and a procedure for depositing, tracking and using re-refined crystallographic models is suggested.

Entities:  

Keywords:  carboplatin; cisplatin; crystal structure; data reprocessing; error corrections; reproducibility; structural databases; structure re-refinement; validation

Mesh:

Substances:

Year:  2015        PMID: 26327386      PMCID: PMC4556316          DOI: 10.1107/S139900471500629X

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  51 in total

1.  SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

Authors:  A A Vaguine; J Richelle; S J Wodak
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-01-01

2.  The Cambridge Structural Database: a quarter of a million crystal structures and rising.

Authors:  Frank H Allen
Journal:  Acta Crystallogr B       Date:  2002-05-29

3.  Structural biology. The ribosome is a ribozyme.

Authors:  T R Cech
Journal:  Science       Date:  2000-08-11       Impact factor: 47.728

4.  Coot: model-building tools for molecular graphics.

Authors:  Paul Emsley; Kevin Cowtan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-11-26

5.  The Uppsala Electron-Density Server.

Authors:  Gerard J Kleywegt; Mark R Harris; Jin Yu Zou; Thomas C Taylor; Anders Wählby; T Alwyn Jones
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-11-26

6.  HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes.

Authors:  Wladek Minor; Marcin Cymborowski; Zbyszek Otwinowski; Maksymilian Chruszcz
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2006-07-18

7.  ESI mass spectrometry and X-ray diffraction studies of adducts between anticancer platinum drugs and hen egg white lysozyme.

Authors:  Angela Casini; Guido Mastrobuoni; Claudia Temperini; Chiara Gabbiani; Simona Francese; Gloriano Moneti; Claudiu T Supuran; Andrea Scozzafava; Luigi Messori
Journal:  Chem Commun (Camb)       Date:  2006-10-26       Impact factor: 6.222

8.  Structural investigation of cisplatin-protein interactions: selective platination of His19 in a cuprozinc superoxide dismutase.

Authors:  Vito Calderone; Angela Casini; Stefano Mangani; Luigi Messori; Pier Luigi Orioli
Journal:  Angew Chem Int Ed Engl       Date:  2006-02-13       Impact factor: 15.336

9.  Ultrahigh-resolution structure of a BPTI mutant.

Authors:  A Addlagatta; S Krzywda; H Czapinska; J Otlewski; M Jaskolski
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2001-04-24

Review 10.  Cellular processing of platinum anticancer drugs.

Authors:  Dong Wang; Stephen J Lippard
Journal:  Nat Rev Drug Discov       Date:  2005-04       Impact factor: 84.694

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  29 in total

1.  Prior knowledge or freedom of interpretation? A critical look at a recently published classification of "novel" Zn binding sites.

Authors:  Joanna E Raczynska; Alexander Wlodawer; Mariusz Jaskolski
Journal:  Proteins       Date:  2016-03-10

Review 2.  X-ray crystallography over the past decade for novel drug discovery - where are we heading next?

Authors:  Heping Zheng; Katarzyna B Handing; Matthew D Zimmerman; Ivan G Shabalin; Steven C Almo; Wladek Minor
Journal:  Expert Opin Drug Discov       Date:  2015-07-15       Impact factor: 6.098

3.  A public database of macromolecular diffraction experiments.

Authors:  Marek Grabowski; Karol M Langner; Marcin Cymborowski; Przemyslaw J Porebski; Piotr Sroka; Heping Zheng; David R Cooper; Matthew D Zimmerman; Marc André Elsliger; Stephen K Burley; Wladek Minor
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-10-28       Impact factor: 7.652

Review 4.  A close look onto structural models and primary ligands of metallo-β-lactamases.

Authors:  Joanna E Raczynska; Ivan G Shabalin; Wladek Minor; Alexander Wlodawer; Mariusz Jaskolski
Journal:  Drug Resist Updat       Date:  2018-08-25       Impact factor: 18.500

5.  Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps.

Authors:  Przemyslaw J Porebski; Piotr Sroka; Heping Zheng; David R Cooper; Wladek Minor
Journal:  Protein Sci       Date:  2017-09-13       Impact factor: 6.725

6.  Online tools for enhancing presentation, understanding, and retention of 3D structural data.

Authors:  Alexander Wlodawer
Journal:  FEBS J       Date:  2017-12       Impact factor: 5.542

7.  Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment.

Authors:  Ivan G Shabalin; Przemyslaw J Porebski; Wladek Minor
Journal:  Crystallogr Rev       Date:  2018-09-21       Impact factor: 2.467

8.  Characterizing metal-binding sites in proteins with X-ray crystallography.

Authors:  Katarzyna B Handing; Ewa Niedzialkowska; Ivan G Shabalin; Misty L Kuhn; Heping Zheng; Wladek Minor
Journal:  Nat Protoc       Date:  2018-04-19       Impact factor: 13.491

9.  Perspectives and expectations in structural bioinformatics of metalloproteins.

Authors:  Sen Yao; Robert M Flight; Eric C Rouchka; Hunter N B Moseley
Journal:  Proteins       Date:  2017-03-15

Review 10.  Databases, Repositories, and Other Data Resources in Structural Biology.

Authors:  Heping Zheng; Przemyslaw J Porebski; Marek Grabowski; David R Cooper; Wladek Minor
Journal:  Methods Mol Biol       Date:  2017
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