Abstract

Histone-like HU proteins are global regulators of the topology of the bacterial genome and are involved in transcriptional regulation. These proteins are essential for the survival of the simplest free-living microorganisms of the Mollicutes class and a number of pathogenic bacteria, including Mycobacterium tuberculosis and Streptococcus pneumonia, and are promising targets for the design of new antibiotics. However, the competitive inhibition of the DNA-binding ability of HU proteins is inefficient because of high flexibility and the large size of the DNA-binding site. Hence, an alternative approach was employed based on searching for molecules targeting the interface between two monomers. The three-dimensional structure of the HU protein from Spiroplasma melliferum (HUSpm) was used as a target for the virtual screening of the compound library and for the modeling of HUSpm in complex with the inhibitor. An analysis of the molecular dynamics trajectory calculated for the HUSpm–inhibitor complex confirmed the fact that the binding of the inhibitor at the interface between monomers leads to the disruption of conformational dynamics in the region of the DNA-binding domain. The gel retardation assay showed that the inhibitor actually disturbs DNA-binding activity of the protein, thereby indicating that this is a promising approach.

中文翻译：

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靶向螺旋藻HU蛋白单体之间界面的抑制剂破坏了蛋白的构象动力学和DNA结合特性

摘要

组蛋白样HU蛋白是细菌基因组拓扑结构的整体调节剂，并参与转录调节。这些蛋白质对于Mollicutes类最简单的自由生存微生物和包括结核分枝杆菌和肺炎链球菌在内的许多致病细菌的生存至关重要，并且是设计新抗生素的有希望的目标。但是，由于高柔韧性和较大的DNA结合位点，竞争性抑制HU蛋白的DNA结合能力是无效的。因此，基于寻找靶向两种单体之间的界面的分子，采用了替代方法。HU蛋白的三维结构螺螺旋体（HUSpm）用作虚拟筛选化合物库和与抑制剂复合的HUSpm建模的靶标。对HUSpm-抑制剂复合物计算的分子动力学轨迹的分析证实了以下事实：抑制剂在单体之间的界面处的结合会导致DNA结合结构域区域中构象动力学的破坏。凝胶阻滞分析表明该抑制剂实际上干扰了蛋白质的DNA结合活性，从而表明这是一种很有前途的方法。