Analysis and Design of Coiled Coil Partnering

描述(由申请人提供)：拟议工作的广泛、长期目标是了解蛋白质如何在单个结构域的水平上建立相互作用的特异性，并在可用于计算预测和设计的模型中捕捉这一点。这个问题是人类健康问题的核心。突变或错误调节的蛋白质之间的不正确相互作用可能导致疾病，深入了解这种情况是如何发生的是重要的。此外，设计新的蛋白质或多肽来特异性地抑制天然蛋白质复合体将为未来的治疗提供一条途径。通过关注一个普遍存在但结构简单的蛋白质-蛋白质相互作用基序：α-螺旋螺旋线圈，可以简化相互作用的专一性问题。盘状卷曲存在于所有物种的蛋白质组中，并与多种功能相关。它们的序列和结构特性使它们易于进行计算分析，盘绕的线圈也便于使用生物物理方法进行实验研究。拟议的研究涉及收集系统的实验相互作用数据，并使用它来开发和测试预测相互作用的各种计算技术。还将开发设计盘绕状多肽的计算方法，并提出实验来表征设计。这项建议的具体目标是：(1)测试和改进预测螺旋线圈结构、能量和相互作用的方法，(2)扩展现有的螺旋线圈设计能力，以处理更广泛的靶点，(3)在动物物种中广泛测量bZIP螺旋线圈相互作用，并开发一个蛋白质-蛋白质相互作用专一性如何演变的模型，以及(4)识别2-组分受体组氨酸激酶的相互作用特异性决定因素，并操纵这些决定因素来产生异种蛋白激酶。目标1和目标2的预测和设计方法将主要使用基于结构的技术。将使用物理激励的能量函数进行评估，并结合更多的经验方法进行测试。目标3涉及开发一种新的蛋白质-蛋白质相互作用分析方法，并将其用于测量&gt；10,000种可能的关联。这些数据将被用于分析bZIP转录因子相互作用的进化，也将对测试AIM 1的计算方法有价值。AIM 4检验了原核生物组氨酸激酶主要同源相关的假设，并提出了识别其相互作用特异性决定因素的计算和实验技术。这四个目标共同组成了一个结构建模、生物物理和生物信息学分析以及实验测试的综合计划，旨在了解盘绕线圈相互作用的特异性。 公共卫生相关性：蛋白质之间的相互作用对细胞的正常功能至关重要。重要的是，正确的复合体形成，而不正确的复合体不形成，即使存在许多密切相关的可能性。这个项目解决了螺旋螺旋蛋白质的序列和结构如何决定它们的相互作用性质，并提出了使用计算技术预测和修改螺旋螺旋相互作用的方法。

DESCRIPTION (provided by applicant): The broad, long-term objectives of the proposed work are to understand how proteins establish interaction specificity at the level of individual domains and to capture this in models that can be used for computational prediction and design. The problem is central to issues of human health. Improper interactions among mutated or mis-regulated proteins can lead to disease, and achieving a deeper understanding of how this occurs is important. Further, the design of novel proteins or peptides to specifically inhibit native protein complexes would provide a route to future therapies. The interaction specificity problem can be simplified by focusing on a ubiquitous yet structurally simple protein-protein interaction motif: the alpha-helical coiled coil. Coiled coils occur throughout the proteomes of all species and are associated with a wide variety of functions. Their sequence and structural properties make them tractable for computational analysis, and coiled coils are also convenient for experimental study using biophysical methods. The proposed research involves collecting systematic experimental interaction data and using it to develop and test diverse computational techniques for predicting interactions. Computational methods will also be developed for designing coiled-coil-like peptides, and experiments are proposed to characterize the designs. The specific aims of this proposal are: (1) To test and improve methods for predicting coiled-coil structures, energies and interactions, (2) To extend existing coiled-coil design capabilities to treat a broader range of targets, (3) To measure bZIP coiled-coil interactions broadly across animal species and to develop a model of how protein- protein interaction specificity can evolve, and (4) To identify interaction specificity determinants of 2- component receptor histidine kinases and manipulate these to generate heterospecific kinases. The prediction and design methods of Aims 1 and 2 will use primarily structure-based techniques. Physically motivated energy functions will be used for evaluation, and also tested in conjunction with more empirical approaches. Aim 3 involves the development of a new protein-protein interaction assay and its use to measure >10,000 possible associations. These data will be applied to analyze the evolution of bZIP transcription factor interactions and will also be valuable for testing the computational methods of Aim 1. Aim 4 tests the hypothesis that prokaryotic histidine kinases primarily homoassociate, and proposes computational and experimental techniques for identifying determinants of their interaction specificity. Together, the four aims comprise an integrated program of structural modeling, biophysical and bioinformatic analysis and experimental testing aimed at understanding coiled-coil interaction specificity. PUBLIC HEALTH RELEVANCE: Interactions between proteins are essential to the proper functioning of cells. It is important that the correct complexes form and the incorrect ones do not, even when many closely related possibilities exist. This project addresses how the sequences and structures of coiled-coil proteins determine their interaction properties, and proposes methods for predicting and modifying coiled-coil interactions using computational techniques.