Dabrowski-Tumanski Pawel, Stasiak Andrzej, Sulkowska Joanna I
Centre of New Technologies, Banacha 2c, 02-097, Warsaw, Poland.
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
PLoS One. 2016 Nov 2;11(11):e0165986. doi: 10.1371/journal.pone.0165986. eCollection 2016.
We analysed the structure of deeply knotted proteins representing three unrelated families of knotted proteins. We looked at the correlation between positions of knotted cores in these proteins and such local structural characteristics as the number of intra-chain contacts, structural stability and solvent accessibility. We observed that the knotted cores and especially their borders showed strong enrichment in the number of contacts. These regions showed also increased thermal stability, whereas their solvent accessibility was decreased. Interestingly, the active sites within these knotted proteins preferentially located in the regions with increased number of contacts that also have increased thermal stability and decreased solvent accessibility. Our results suggest that knotting of polypeptide chains provides a favourable environment for the active sites observed in knotted proteins. Some knotted proteins have homologues without a knot. Interestingly, these unknotted homologues form local entanglements that retain structural characteristics of the knotted cores.
我们分析了代表三个不相关的打结蛋白家族的深度打结蛋白的结构。我们研究了这些蛋白中打结核心位置与链内接触数量、结构稳定性和溶剂可及性等局部结构特征之间的相关性。我们观察到，打结核心尤其是其边界处的接触数量有显著富集。这些区域的热稳定性也有所增加，而其溶剂可及性则降低。有趣的是，这些打结蛋白中的活性位点优先位于接触数量增加、热稳定性增加且溶剂可及性降低的区域。我们的结果表明，多肽链的打结为在打结蛋白中观察到的活性位点提供了有利环境。一些打结蛋白有未打结的同源物。有趣的是，这些未打结的同源物形成局部缠结，保留了打结核心的结构特征。
