Analysis and Design of Coiled Coil Partnering

描述（由申请人提供）：本提案的目标是通过结合计算和实验方法来预测和设计特定的蛋白质相互作用。为了降低问题的复杂性，我们以盘绕线圈介导的相互作用为目标。盘绕的线圈是一个简单而重要的相互作用基序，估计大约在所有蛋白质的3-5%中出现，包括许多对人类疾病重要的蛋白质。在过去的15年里，人们对它进行了广泛的研究。因此，现有的知识提供了一个框架，在其中尝试交互预测和设计的挑战性问题。该提案的具体目的是：(1)测量在人类和酵母bZIP转录因子中发现的卷曲线圈之间发生的配对。这将通过大规模的蛋白质微阵列检测来完成。所得数据将用于开发计算方法，以预测线圈-线圈相互作用的序列。bZIP相互作用筛选也将为研究涉及人类致癌基因的转录调控网络提供丰富的数据，包括Fos和Jun。

DESCRIPTION (provided by applicant): The goal of this proposal is to predict and design specific protein interactions by using a combination of computational and experimental methods. To reduce the complexity of the problem, we target interactions mediated by the coiled coil. The coiled coil is a simple and important interaction motif estimated to occur in roughly 3-5% of all proteins, including many important for human disease. It has been studied extensively over the past 15 years. Consequently, existing knowledge provides a framework in which to attempt the challenging problems of interaction prediction and design. The specific aims of the proposal are: (1) To measure the pairings that occur among coiled coils found in human and yeast bZIP transcription factors. This will be accomplished using a large-scale protein microarray assay. The resulting data will be used to develop computational methods for predicting coiled-coil interactions from sequence. The bZIP interaction screen will also provide a wealth of data for the study of transcriptional regulatory networks that involve human oncogenes, including Fos and Jun. (2) To improve computational methods that have been developed for protein design so that these are more suitable for the problem of designing interaction specificity. 3) To use computationally-guided methods from Aim 2 to design peptides that bind specifically to targeted human bZIP coiled-coil domains, and to test these designs experimentally. This will provide a comparison of designed peptides with naturally occurring ones (Aim 1) that share similar interaction properties. It will also constitute a rigorous test of our basic understanding of coiled-coil recognition, and it will provide useful reagents for perturbing transcriptional regulatory networks. (4) To design a peptide that acts as an inhibitor of the oligomerization of BcrAbl, a human oncoprotein. The coiled coil-mediated dimerization of Bcr is implicated in more than 95% of chronic myelogenous leukemias. Together, these studies will improve our understanding of the molecular basis of protein interaction specificity and provide tools that can be used to rationally alter protein structure and function. The methods proposed can be applied to a wide range of different domain-domain interactions, so the insights that we achieve will have broad significance for the study of protein-protein associations generally.