Prior knowledge or freedom of interpretation? A critical look at a recently published classification of "novel" Zn binding sites
Prior knowledge or freedom of interpretation? A critical look at a recently published classification of "novel" Zn binding sites
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DOI：
10.1002/prot.25024
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发表时间：
2016-06-01
影响因子：
2.9
通讯作者：
Jaskolski, Mariusz
中科院分区：
文献类型：
--
作者：
Raczynska, Joanna E.;Wlodawer, Alexander;Jaskolski, Mariusz
在最近发表的一篇文章中（Yao，Flight，Rouchka，and莫斯利，Proteins 2015;83：1470-1487），作者提出了蛋白质结构中新的Zn配位模式，显然是使用对蛋白质数据库（PDB）中收集的信息的无偏见方法发现的，他们主张这比先验知识知情的范式优越上级。在我们对这些命题的评估中，我们在这里证明了大多数（如果不是全部的话）“新”配位几何是虚构的，因为它们是基于错误解释的蛋白质晶体结构，而这些结构本身往往不是没有错误的。解释的缺陷包括部分或错误的锌网站，错过或错误的配位体，忽略晶体对称性和配位体等。总之，我们警告不要使用这种和类似的荟萃分析，忽视化学和晶体学知识，并强调保护结构数据库对坏苹果的重要性。(C)2016 Wiley Periodicals，Inc.
In a recently published article (Yao, Flight, Rouchka, and Moseley, Proteins 2015;83:1470-1487) the authors proposed novel Zn coordination patterns in protein structures, apparently discovered using an unprejudiced approach to the information collected in the Protein data Bank (PDB), which they advocated as superior to the prior-knowledge-informed paradigm. In our assessment of those propositions we demonstrate here that most, if not all, of the "new" coordination geometries are fictitious, as they are based on incorrectly interpreted protein crystal structures, which in themselves are often not error-free. The flaws of interpretation include partial or wrong Zn sites, missed or wrong ligands, ignored crystal symmetry and ligands, etc. In conclusion, we warn against using this and similar meta-analyses that ignore chemical and crystallographic knowledge, and emphasize the importance of safeguarding structural databases against bad apples. (C) 2016 Wiley Periodicals, Inc.