Bartas М, Bažantová P, Brázda V, Liao J С, Červeň J, Pečinka P
Department of Biology and Ecology / Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, 71000 Czech Republic.
Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Brno, 61265 Czech Republic.
Mol Biol (Mosk). 2019 Jan-Feb;53(1):120-131. doi: 10.1134/S0026898419010026.
Cruciform structures are preferential targets for many architectural and regulatory proteins, as well as a number of DNA binding proteins with weak sequence specificity. Some of these proteins are also capable of inducing the formation of cruciform structures upon DNA binding. In this paper we analyzed the amino acid composition of eighteen cruciform binding proteins of Homo sapiens. Comparison with general amino acid frequencies in all human proteins revealed unique differences, with notable enrichment for lysine and serine and/or depletion for alanine, glycine, glutamine, arginine, tyrosine and tryptophan residues. Based on bootstrap resampling and fuzzy cluster analysis, multiple molecular mechanisms of interaction with cruciform DNA structures could be suggested, including those involved in DNA repair, transcription and chromatin regulation. The proteins DEK, HMGB1 and TOP1 in particular formed a very distinctive group. Nonetheless, a strong interaction network connecting nearly all the cruciform binding proteins studied was demonstrated. Data reported here will be very useful for future prediction of new cruciform binding proteins or even construction of predictive tool/web-based application.
十字形结构是许多结构和调节蛋白以及一些序列特异性较弱的DNA结合蛋白的优先作用靶点。其中一些蛋白在与DNA结合时也能够诱导十字形结构的形成。在本文中，我们分析了18种人类十字形结合蛋白的氨基酸组成。与所有人类蛋白质的一般氨基酸频率进行比较，发现了独特的差异，赖氨酸和丝氨酸显著富集，而丙氨酸、甘氨酸、谷氨酰胺、精氨酸、酪氨酸和色氨酸残基则有所减少。基于自展重采样和模糊聚类分析，可以提出与十字形DNA结构相互作用的多种分子机制，包括那些参与DNA修复、转录和染色质调节的机制。特别是DEK、HMGB1和TOP1蛋白形成了一个非常独特的组。尽管如此，我们还是证明了一个连接几乎所有所研究的十字形结合蛋白的强大相互作用网络。本文报道的数据对于未来预测新的十字形结合蛋白甚至构建预测工具/基于网络的应用程序将非常有用。
