Role of Helix Formation in Mediating Protein-Protein Interactions

蛋白质与靶点的相互作用是生物体内最重要的过程之一， 生物系统。这种相互作用的一个子组发生在一个戏剧性的 二级结构的变化：从未结合时的非结构化（卷曲）到非常 当它处于结合状态时，它具有独特的结构（螺旋）。详细的统计 热力学研究影响这种转变的因素（从线圈到螺旋），以及 这些因素如何影响蛋白质与其靶标之间的相互作用是非常重要的。 重要的是，放松管制会导致生物机器的严重故障， 最终可能致命 我们将利用泛素和泛素相互作用基序之间的相互作用 (UIM)作为一个模型系统来研究结构、动力学和热力学细节 泛素-UIM复合物的形成。泛素是一种非常小的蛋白质， 细胞中的多种调节功能包括蛋白质降解， 运输，细胞周期控制，DNA修复，转录调节和基因沉默， 应激反应和信号传导。所有这些功能都是以翻译后的形式出现的 通过单或多泛素化修饰蛋白质。的程度和 泛素化作为调节细胞机制的重要性是广泛存在的， 一些估计，只有蛋白质磷酸化超过。在众多目标中， 结合泛素的序列，UIM可能是最简单的。它是一个短的20-氨基 在与泛素结合时经历卷曲-螺旋转变的酸序列。规则 影响这种相互作用中特异性和亲和力的因素将是至关重要的， 计算生物学和生物信息学，以更好地预测靶序列， 与泛素相互作用。 为了实现这些目标，我们将使用实验和计算 研究泛素-UIM复合物形成的方法。实验方法将 包括定点诱变、量热法、荧光和圆二色性 光谱、结构和弛豫NMR分析。计算方法 将涉及分子动力学模拟模型的相互作用的能量。 这将使我们能够建立可用于调节蛋白质螺旋的一般规则 通过影响一些控制螺旋-卷曲转变的性质， 靶序列。这些规则将为合理设计治疗方案奠定基础 泛素的有效靶序列。

Th Protein-target interaction is one of the most important processes occurring in biological systems. One subgroup of such interactions takes place with a dramatic change in the secondary structure: from unstructured (coil) when it is unbound to a very characteristic structure (helix) when it is in the bound state. A detailed statistical thermodynamics study of the factors that affect this transition (from coil to helix), and how these factors affect the interaction between the protein and its target is very important as deregulation can result in a serious malfunction of the biological machinery and ultimately can be lethal. We will use the interactions between ubiquitin and ubiquitin interacting motif (UIM) as a model system to study in structural, dynamics and thermodynamics details the ubiquitin-UIM complex formation. Ubiquitin is a very small protein, yet it performs a wide variety of regulatory functions in the cell including protein degradation, trafficking, cell-cycle control, DNA repair, transcription regulation and gene silencing, stress response and signaling. All these functions are in the form of post-translational modifications of proteins via mono- or poly- ubiquitinylation. The extent and importance of ubiquitinylation as a regulatory cellular mechanism is widespread, and by some estimates, is surpassed only by protein phosphorylation. Among numerous target sequences that bind ubiquitin, the UIM is perhaps the simplest. It is a short 20-amino acid sequence that undergoes a coil-helix transition upon binding to ubiquitin. Rules that affect specificity and affinity in this type of interaction will be crucial in computational biology and bioinformatics to better predict target sequences that can interact with ubiquitin. To achieve these goals we will use both experimental and computational approaches to study ubiquitin-UIM complex formation. Experimental methods will include site-directed mutagenesis, calorimetry, fluorescence and circular dichroism spectroscopies, structural and relaxation NMR analysis. The computational approach will involve molecular dynamics simulations to model the energetics of interactions. This will allow us to establish general rules that can be used to modulate protein-helix interactions by affecting some of the properties that govern the helix-coil transition in target sequences. Such rules will lay the foundation for rational design of therapeutically effective target sequences for ubiquitin.