晶体学和化学应该总是结合在一起:顺铂和卡铂的蛋白质复合物的警示故事。

Ivan Shabalin, Zbigniew Dauter, Mariusz Jaskolski, Wladek Minor, Alexander Wlodawer
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引用次数: 48

摘要

含铂类药物如顺铂和卡铂的抗癌活性被认为主要来自于它们与核酸的相互作用;然而,这些药物或其水解产物也会与蛋白质结合,从而可能导致已知的治疗副作用。在这里,超过40晶体结构沉积在蛋白质数据库(PDB)的顺铂和卡铂配合物的几种蛋白质进行了分析。在大多数提出的原子模型中发现了晶体学或化学性质的重大问题,这些问题可以追溯到数据收集和改进过程中或多或少的严重缺陷。对这些数据和模型的重新评估是可能的,这要归功于它们被强制或自愿地储存在公开可用的数据库中,这强调了这类数据的可用性对于结构科学的可重复性至关重要。基于对一组大分子结构的分析,强调了原始衍射数据沉积的重要性,并提出了沉积、跟踪和使用重新细化的晶体学模型的方法。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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

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.

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