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

Shabalin I, Dauter Z, Jaskolski M, Minor W, Wlodawer A
Acta Crystallogr D Biol Crystallogr 71 1965-79 (2015)
Related entries: 4lt0, 4lt3, 4nsg, 4nsh, 4nsi, 4nsj, 4ydx, 4yea, 4yen, 4yeo

Cited: 28 times
EuropePMC logo PMID: 26327386

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.

Articles - 4yem mentioned but not cited (2)

  1. Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin. Shabalin I, Dauter Z, Jaskolski M, Minor W, Wlodawer A. Acta Crystallogr D Biol Crystallogr 71 1965-1979 (2015)
  2. Research Support, Non-U.S. Gov't Re-refinement of 4xan: hen egg-white lysozyme with carboplatin in sodium bromide solution. Tanley SW, Schreurs AM, Kroon-Batenburg LM, Helliwell JR. Acta Crystallogr F Struct Biol Commun 72 251-252 (2016)


Reviews citing this publication (4)

  1. A close look onto structural models and primary ligands of metallo-β-lactamases. Raczynska JE, Shabalin IG, Minor W, Wlodawer A, Jaskolski M. Drug Resist Updat 40 1-12 (2018)
  2. X-ray crystallography over the past decade for novel drug discovery - where are we heading next? Zheng H, Handing KB, Zimmerman MD, Shabalin IG, Almo SC, Minor W. Expert Opin Drug Discov 10 975-989 (2015)
  3. Databases, Repositories, and Other Data Resources in Structural Biology. Zheng H, Porebski PJ, Grabowski M, Cooper DR, Minor W. Methods Mol Biol 1607 643-665 (2017)
  4. Will the Interactions of Some Platinum (II)-Based Drugs with B-Vitamins Reduce Their Therapeutic Effect in Cancer Patients? Comparison of Chemotherapeutic Agents such as Cisplatin, Carboplatin and Oxaliplatin-A Review. Szefler B, Czeleń P. Int J Mol Sci 24 1548 (2023)

Articles citing this publication (22)

  1. A public database of macromolecular diffraction experiments. Grabowski M, Langner KM, Cymborowski M, Porebski PJ, Sroka P, Zheng H, Cooper DR, Zimmerman MD, Elsliger MA, Burley SK, Minor W. Acta Crystallogr D Struct Biol 72 1181-1193 (2016)
  2. Characterizing metal-binding sites in proteins with X-ray crystallography. Handing KB, Niedzialkowska E, Shabalin IG, Kuhn ML, Zheng H, Minor W. Nat Protoc 13 1062-1090 (2018)
  3. Ligand-centered assessment of SARS-CoV-2 drug target models in the Protein Data Bank. Wlodawer A, Dauter Z, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Minor W, Rupp B, Jaskolski M. FEBS J 287 3703-3718 (2020)
  4. Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps. Porebski PJ, Sroka P, Zheng H, Cooper DR, Minor W. Protein Sci 27 86-94 (2018)
  5. Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment. Shabalin IG, Porebski PJ, Minor W. Crystallogr Rev 24 236-262 (2018)
  6. Protein metalation by metal-based drugs: X-ray crystallography and mass spectrometry studies. Messori L, Merlino A. Chem Commun (Camb) 53 11622-11633 (2017)
  7. The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years. Grabowski M, Cymborowski M, Porebski PJ, Osinski T, Shabalin IG, Cooper DR, Minor W. Struct Dyn 6 064301 (2019)
  8. Prediction of the interaction of metallic moieties with proteins: An update for protein-ligand docking techniques. Sciortino G, Rodríguez-Guerra Pedregal J, Lledós A, Garribba E, Maréchal JD. J Comput Chem 39 42-51 (2018)
  9. Effect of temperature on the interaction of cisplatin with the model protein hen egg white lysozyme. Ferraro G, Pica A, Russo Krauss I, Pane F, Amoresano A, Merlino A. J Biol Inorg Chem 21 433-442 (2016)
  10. Crystallographic models of SARS-CoV-2 3CLpro: in-depth assessment of structure quality and validation. Jaskolski M, Dauter Z, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Rupp B, Wlodawer A. IUCrJ 8 238-256 (2021)
  11. Machine learning differentiates enzymatic and non-enzymatic metals in proteins. Feehan R, Franklin MW, Slusky JSG. Nat Commun 12 3712 (2021)
  12. Principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign metal ligands. Russo Krauss I, Ferraro G, Pica A, Márquez JA, Helliwell JR, Merlino A. Metallomics 9 1534-1547 (2017)
  13. On the evolution of the quality of macromolecular models in the PDB. Brzezinski D, Dauter Z, Minor W, Jaskolski M. FEBS J 287 2685-2698 (2020)
  14. The Affinity of Carboplatin to B-Vitamins and Nucleobases. Szefler B, Czeleń P, Krawczyk P. Int J Mol Sci 22 3634 (2021)
  15. Interactions of cisplatin analogues with lysozyme: a comparative analysis. Ferraro G, De Benedictis I, Malfitano A, Morelli G, Novellino E, Marasco D. Biometals 30 733-746 (2017)
  16. Comment on "Structural dynamics of cisplatin binding to histidine in a protein" [Struct. Dyn. 1, 034701 (2014)]. Tanley SW, Helliwell JR. Struct Dyn 3 037101 (2016)
  17. research-article Perspectives and expectations in structural bioinformatics of metalloproteins. Yao S, Flight RM, Rouchka EC, Moseley HN. Proteins 85 938-944 (2017)
  18. Rapid response to emerging biomedical challenges and threats. Grabowski M, Macnar JM, Cymborowski M, Cooper DR, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Dauter Z, Rupp B, Wlodawer A, Jaskolski M, Minor W. IUCrJ 8 395-407 (2021)
  19. Structural insights into protein folding, stability and activity using in vivo perdeuteration of hen egg-white lysozyme. Ramos J, Laux V, Haertlein M, Boeri Erba E, McAuley KE, Forsyth VT, Mossou E, Larsen S, Langkilde AE. IUCrJ 8 372-386 (2021)
  20. Synchrotron Radiation as a Tool for Macromolecular X-Ray Crystallography: a XXI Century Perspective. Grabowski M, Cooper DR, Brzezinski D, Macnar JM, Shabalin IG, Cymborowski M, Otwinowski Z, Minor W. Nucl Instrum Methods Phys Res B 489 30-40 (2021)
  21. Crystal Structure of the Human Copper Chaperone ATOX1 Bound to Zinc Ion. Mangini V, Belviso BD, Nardella MI, Natile G, Arnesano F, Caliandro R. Biomolecules 12 1494 (2022)
  22. research-article Online tools for enhancing presentation, understanding, and retention of 3D structural data. Wlodawer A. FEBS J 284 3974-3976 (2017)


Related citations provided by authors (1)

  1. Carboplatin binding to histidine.. Tanley SW, Diederichs K, Kroon-Batenburg LM, Levy C, Schreurs AM, Helliwell JR Acta Crystallogr F Struct Biol Commun 70 1135-42 (2014)

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