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

摘要

In a recently published paper [Yao, S., Flight, R.M., Rouchka, E.C. & Moseley, H.N. (2015). Proteins >83, 1470–1487] the authors propose 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 advocate 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.