Molecular Mimics of Protein Tertiary Folding from Primary Sequence Information

描述(由申请人提供)：抑制蛋白质-蛋白质与设计分子的结合作用是生物医学科学的前沿挑战。蛋白质的功能是三维折叠构象的直接结果。因此，创造一种模仿特定蛋白质功能的分子需要该分子表现出原型折叠状态的关键结构特征。在简单二级结构的模拟方面已经取得了重大进展；然而，对于能够产生与天然蛋白质相同的复杂的三级折叠的非自然物种的设计策略的需求还没有得到满足。PI实验室的长期研究目标是发明一套工具来设计天然蛋白质类似物，在具有增强的折叠和/或生理稳定性的支架上显示原型的关键结构和功能特征。本提案的总体目标是 开发一种基于序列的非自然骨架模拟蛋白质三级折叠的方法，并将该方法应用于两个具有生物医学意义的靶点，其中三级折叠是功能所必需的。指导这项工作的中心假设是，任何天然蛋白质序列都可以作为设计其自身非自然类似物的起点，前提是存在系统的骨架修饰规则。这项工作的基本原理是，一种真正基于序列的非自然骨架模仿蛋白质三级折叠的通用方法将打开解决任意复杂性折叠的可能性。中心假说将通过追求三个具体目标得到验证：(1)建立非天然主干低聚物基于序列的模仿蛋白质三级折叠的设计原则；(2)开发一种将噬菌体衍生的亲和配体转换为抗蛋白酶类似物的通用方法，并应用该方法创建肿瘤显像剂；(3)设计一种能抑制疟疾和弓形虫病疾病进展中常见的保守的蛋白质-蛋白质相互作用的抑制剂。拟议工作的预期结果包括设计一种显示天然蛋白质三级折叠模式的抗蛋白酶物种的一般战略， 将基于噬菌体的序列选择与非自然骨架、识别癌症相关细胞表面蛋白的肿瘤显像剂以及针对疟疾和其他寄生虫感染的共同途径的寡聚体连接起来的范例。这项研究的意义源于丰富的新功能，当复杂的第三级折叠模式对非自然的脊椎可用时，这些功能将成为可能。提出的想法的创新来自于通过一种基于序列的设计方法来解决三级结构模拟的重要挑战，这种设计方法可推广到本提案中讨论的那些蛋白质。

DESCRIPTION (provided by applicant): Inhibiting protein-protein binding interactions with designed molecules is a frontier challenge in biomedical science. Protein function is a direct result of 3-dimensional folded conformation. Thus, creating a molecule that mimics the function of a particular protein requires that the molecule manifest key structural features of the folded state of the prototype. Significant advances have been made in the mimicry of simple secondary structures; however, there is an unmet need for a design strategy capable of generating unnatural species that show the same complex tertiary folds as natural proteins. A long-term goal of research in the PI's lab is to invent a suite of tools for the design of natural protein analogues that manifest key structural and functional features of the prototype on scaffolds with enhanced folded and/or physiological stability. The overall objective of the present proposal is to develop a sequence-based method for the mimicry of protein tertiary folding by unnatural backbones and to apply this method to two biomedically significant targets where a tertiary fold is essential for function. The central hypothesis guiding the work is that any natural protein sequence can serve as the starting point for the design of its own unnatural analogue, provided systematic rules for backbone modification exist. The rationale motivating this work is that a general method for mimicry of protein tertiary folding by unnatural backbones that is truly sequence-based will open the possibility to address folds of arbitrary complexity. The central hypothesis will be tested through pursuit of three specific aims: (1) Establish design principles for sequence-based mimicry of protein tertiary folding by unnatural-backbone oligomers; (2) Develop a general method for the conversion of phage-derived affinity ligands to protease-resistant analogues and apply this method to create tumor imaging agents; (3) Design inhibitors of a conserved protein-protein interaction common to disease progression in malaria and toxoplasmosis. Expected outcomes of the proposed work include a general strategy for the design of protease-resistant species that manifest tertiary folding patterns of natural proteins, a paradigm to connect phage-based sequence selection to unnatural backbones, tumor imaging agents that recognize cancer-associated cell-surface proteins, and oligomers that target a common pathway in infection by malaria and other parasites. The significance of the research stems from the wealth of new functions that will become possible when complex tertiary folding patterns are accessible to unnatural backbones. The innovation of the proposed idea arises from addressing the important challenge of tertiary structure mimicry by a design approach that is sequence-based and generalizable to proteins beyond those discussed in the present proposal.