Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 166 10 Prague 6, Czech Republic.
Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czech Republic.
Int J Mol Sci. 2020 Jun 2;21(11):3986. doi: 10.3390/ijms21113986.
Interaction with the DNA minor groove is a significant contributor to specific sequence recognition in selected families of DNA-binding proteins. Based on a statistical analysis of 3D structures of protein-DNA complexes, we propose that distortion of the DNA minor groove resulting from interactions with hydrophobic amino acid residues is a universal element of protein-DNA recognition. We provide evidence to support this by associating each DNA minor groove-binding amino acid residue with the local dimensions of the DNA double helix using a novel algorithm. The widened DNA minor grooves are associated with high GC content. However, some AT-rich sequences contacted by hydrophobic amino acids (e.g., phenylalanine) display extreme values of minor groove width as well. For a number of hydrophobic amino acids, distinct secondary structure preferences could be identified for residues interacting with the widened DNA minor groove. These results hold even after discarding the most populous families of minor groove-binding proteins.
与 DNA 小沟的相互作用是某些 DNA 结合蛋白家族中特异性序列识别的重要贡献因素。基于对蛋白质-DNA 复合物 3D 结构的统计分析，我们提出与疏水性氨基酸残基相互作用导致的 DNA 小沟扭曲是蛋白质-DNA 识别的普遍因素。我们通过使用一种新算法将每个与 DNA 小沟结合的氨基酸残基与 DNA 双螺旋的局部尺寸相关联，为这一观点提供了证据支持。变宽的 DNA 小沟与高 GC 含量相关。然而，一些与疏水性氨基酸（如苯丙氨酸）相互作用的富含 AT 的序列也显示出小沟宽度的极值。对于许多疏水性氨基酸，可以为与变宽的 DNA 小沟相互作用的残基识别出明显的二级结构偏好。即使在丢弃最常见的小沟结合蛋白家族后，这些结果仍然成立。
