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首页> 外文期刊>European Biophysics Journal >Study of intermolecular contacts in the proline-rich homeodomain (PRH) - DNA complex using molecular dynamics simulations
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Study of intermolecular contacts in the proline-rich homeodomain (PRH) - DNA complex using molecular dynamics simulations

机译：使用分子动力学模拟研究富含脯氨酸的同源域（PRH）-DNA复合物中的分子间接触

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The proline-rich homeodomain (PRH)-DNA complex consists of a protein with 60 residues and a 13-base-pair DNA. The PRH protein is a transcription factor that plays a key role in the regulation of gene expression. PRH is a significant member of the Q50 class of homeodomain proteins. The homeodomain section of PRH is essential for binding to DNA and mediates sequence-specific DNA binding. Three 20-ns molecular dynamics (MD) simulations (free protein, free DNA and protein-DNA complex) in explicit solvent water were performed to elucidate the intermolecular contacts in the PRH-DNA complex and the role of dynamics of water molecules forming water-mediated contacts. The simulation provides a detailed explanation of the trajectory of hydration water molecules. The simulations show that some water molecules in the protein-DNA interface exchange with bulk waters. The simulation identifies that most of the contacts consisted of direct interactions between the protein and DNA including specific and non-specific contacts, but several water-mediated polar contacts were also observed. The specific interaction between Gln50 and C18 and water-mediated hydrogen bond between Gln50 and T7 were found to be present during almost the entire time of the simulation. These results show good consistency with experimental and previous computational studies. Structural properties such as root-mean-square deviations (RMSD), root-mean-square fluctuations (RMSF) and secondary structure were also analyzed as a function of time. Analyses of the trajectories showed that the dynamic fluctuations of both the protein and the DNA were lowered by the complex formation.
机译：富含脯氨酸的同源结构域（PRH）-DNA复合物由具有60个残基的蛋白质和13个碱基对的DNA组成。 PRH蛋白是一种转录因子，在调节基因表达中起关键作用。 PRH是同源域Q50类的重要成员。 PRH的同源域部分对于与DNA结合并介导序列特异性DNA结合至关重要。在显式溶剂水中进行了三个20 ns分子动力学（MD）模拟（游离蛋白质，游离DNA和蛋白质-DNA络合物），以阐明PRH-DNA络合物中的分子间接触以及形成水分子的水分子动力学的作用。中介的联系。模拟为水化水分子的轨迹提供了详细的解释。模拟显示蛋白质-DNA界面中的一些水分子与大量水交换。模拟结果表明，大多数接触是蛋白质与DNA之间的直接相互作用，包括特异性和非特异性接触，但也观察到了几种水介导的极性接触。发现在几乎整个模拟过程中都存在Gln50和C18之间的特定相互作用以及Gln50和T7之间的水介导的氢键。这些结果表明与实验和先前的计算研究具有良好的一致性。还分析了诸如均方根偏差（RMSD），均方根波动（RMSF）和二级结构等结构特性随时间的变化。轨迹分析表明，复合物的形成降低了蛋白质和DNA的动态波动。

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