Analysis and Design of Coiled Coil Partnering

线圈配对分析与设计

• 批准号: 7176891
• 负责人: AMY E KEATING
• 金额: $ 26.51万
• 依托单位: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-02-01 至 2009-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7176891
• 关键词: Address; Affinity; Algorithms; Binding; Biological Assay; Biology; Characteristics; Chronic Myeloid Leukemia; Coiled-Coil Domain; Complex; Computer Simulation; Computing Methodologies; Custom; Data; Dimerization; Generations; Goals; Helix (Snails); Homodimerization; Human; Knowledge; Life; Ligands; Measures; Mediating; Methods; Microarray Analysis; Modeling; Molecular; Mouse-ear Cress; Numbers; Oncogene Proteins; Oncogenes; Pathology; Peptides; Process; Property; Protein Binding; Protein Biochemistry; Protein Microarray Assay; Protein Microchips; Proteins; Range; Reagent; Research; Research Personnel; Solutions; Specificity; Structure; Study models; Testing; X-Ray Crystallography; Yeasts; base; design; desire; ear helix; human disease; improved; inhibitor/antagonist; insight; leukemia; monomer; prevent; programs; protein folding; protein protein interaction; protein structure function; tool; transcription factor

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.

描述（由申请人提供）：本提案的目标是通过使用计算和实验方法的组合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，我们的目标是由卷曲螺旋介导的相互作用。 卷曲螺旋是一种简单而重要的相互作用基序，估计在所有蛋白质的大约3-5%中发生，包括许多对人类疾病重要的蛋白质。 在过去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，在其中尝试相互作用的预测和设计的挑战性问题。 该提案的具体目标是：（1）测量在人类和酵母bZIP转录因子中发现的卷曲螺旋之间发生的配对。 这将使用大规模蛋白质微阵列测定来完成。 由此产生的数据将用于开发预测卷曲螺旋相互作用的计算方法。 bZIP相互作用筛选也将为涉及人类癌基因（包括Fos和Jun）的转录调控网络的研究提供丰富的数据。 (2)为了改善已经开发的蛋白质设计的计算方法，使这些更适合于设计相互作用特异性的问题。 3)使用目标2中的计算指导方法设计与靶向人bZIP卷曲螺旋结构域特异性结合的肽，并通过实验测试这些设计。 这将提供设计的肽与天然存在的肽（目标1）的比较，其具有相似的相互作用性质。 它也将构成一个严格的测试，我们的基本理解卷曲螺旋识别，它将提供有用的试剂，扰乱转录调控网络。 (4)设计一种抑制人癌蛋白BcrAbl寡聚化的肽。 卷曲螺旋介导的Bcr二聚化与95%以上的慢性粒细胞白血病有关。 总之，这些研究将提高我们对蛋白质相互作用特异性的分子基础的理解，并提供可用于合理改变蛋白质结构和功能的工具。 所提出的方法可以应用于各种不同的结构域-结构域相互作用，因此我们所获得的见解将对蛋白质-蛋白质关联的研究具有广泛的意义。