DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar.
DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar.
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DOI：
10.1093/nar/gku269
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发表时间：
2014-06
影响因子：
14.9
通讯作者：
Wetmore SD
中科院分区：
文献类型：
--
作者：
Wilson KA;Kellie JL;Wetmore SD
选择428个高分辨率dna -蛋白质复合物进行生物信息学研究。虽然164个晶体结构（38%）不包含相互作用，但使用严格的标准，包括目测，鉴定出芳香氨基酸与DNA核碱基或脱氧核糖之间的574个离散π接触。通过明确地将接触分为π -π堆叠、π -π t形或糖-π接触，确定了相互作用的丰度和结构。在175个晶体结构中发现了344个核碱基-氨基酸π -π接触（占所有相互作用的60%）。在137个涉及C-H··π和/或孤对··π相互作用的晶体结构中，发现了230个dna -蛋白糖-π接触（占所有已确定相互作用的40%），这些晶体结构包含任何氨基酸，可以根据所涉及的糖原子进行分类。π -π和糖-π相互作用都显示出相对单体取向的范围，因此相互作用能（使用量子化学计算确定的中性（带电）相互作用可达-50 (-70)kJ mol - 1）。总的来说，dna -蛋白质π相互作用比目前公认的更为普遍，这种相互作用在许多生物过程中的作用可能尚未被揭示。
Four hundred twenty-eight high-resolution DNA–protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π–contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteria, including visual inspection. The abundance and structure of the interactions were determined by unequivocally classifying the contacts as either π–π stacking, π–π T-shaped or sugar–π contacts. Three hundred forty-four nucleobase–amino acid π–π contacts (60% of all interactions identified) were identified in 175 of the crystal structures searched. Unprecedented in the literature, 230 DNA–protein sugar–π contacts (40% of all interactions identified) were identified in 137 crystal structures, which involve C–H···π and/or lone–pair···π interactions, contain any amino acid and can be classified according to sugar atoms involved. Both π–π and sugar–π interactions display a range of relative monomer orientations and therefore interaction energies (up to –50 (–70) kJ mol−1 for neutral (charged) interactions as determined using quantum chemical calculations). In general, DNA–protein π-interactions are more prevalent than perhaps currently accepted and the role of such interactions in many biological processes may yet to be uncovered.
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