Kuzniak-Glanowska Emilia, Glanowski Michał, Kurczab Rafał, Bojarski Andrzej J, Podgajny Robert
Faculty of Chemistry, Jagiellonian University Gronostajowa 2 30-387 Kraków Poland
Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences Niezapominajek 8 30-239 Kraków Poland.
Chem Sci. 2022 Mar 1;13(14):3984-3998. doi: 10.1039/d2sc00763k. eCollection 2022 Apr 6.
Mutual positioning and non-covalent interactions in anion-aromatic motifs are crucial for functional performance of biological systems. In this context, regular, comprehensive Protein Data Bank (PDB) screening that involves various scientific points of view and individual critical analysis is of utmost importance. Analysis of anions in spheres with radii of 5 Å around all 5- and 6-membered aromatic rings allowed us to distinguish 555 259 unique anion-aromatic motifs, including 92 660 structures out of the 171 588 structural files in the PDB. The use of a scarcely exploited (, ) coordinate system led to (i) identification of three separate areas of motif accumulation: A - over the ring, B - over the ring-substituent bonds, and C - roughly in the plane of the aromatic ring, and (ii) unprecedented simultaneous comparative description of various anion-aromatic motifs located in these areas. Of the various residues considered, aminoacids, nucleotides, and ligands, the latter two exhibited a considerable tendency to locate in region A archetypal anion-π contacts. The applied model not only enabled statistical quantitative analysis of space around the ring, but also enabled discussion of local intermolecular arrangements, as well as detailed sequence and secondary structure analysis, anion-π interactions in the GNRA tetraloop in RNA and protein helical structures. As a purely practical issue of this work, the new code source for the PDB research was produced, tested and made freely available at https://github.com/chemiczny/PDB_supramolecular_search.
阴离子 - 芳香基序中的相互定位和非共价相互作用对于生物系统的功能表现至关重要。在此背景下，涉及各种科学观点和个体批判性分析的常规、全面的蛋白质数据库（PDB）筛选极为重要。对所有 5 元和 6 元芳香环周围半径为 5 Å 的球体中的阴离子进行分析，使我们能够区分出 555259 个独特的阴离子 - 芳香基序，其中包括 PDB 中 171588 个结构文件中的 92660 个结构。使用一种很少被利用的（，）坐标系导致：（i）确定了基序积累的三个独立区域：A - 在环上方，B - 在环 - 取代基键上方，以及 C - 大致在芳香环平面内；（ii）对位于这些区域的各种阴离子 - 芳香基序进行了前所未有的同时比较描述。在考虑的各种残基中，氨基酸、核苷酸和配体，后两者表现出相当大的倾向定位于区域 A（典型的阴离子 - π 接触）。所应用的模型不仅能够对环周围的空间进行统计定量分析，还能够讨论局部分子间排列，以及详细的序列和二级结构分析，包括 RNA 中 GNRA 四环和蛋白质螺旋结构中的阴离子 - π 相互作用。作为这项工作的一个纯粹实际问题，PDB 研究的新代码源已制作完成、经过测试并可在 https://github.com/chemiczny/PDB_supramolecular_search 上免费获取。
