Computational Methods for Requirement-Driven Protein Design

 描述（由申请人提供）：蛋白质设计是对我们对蛋白质折叠和稳定性的理解的严格测试，各种设计方法已用于创建在研究和医学中具有宝贵应用的蛋白质。几乎所有从头设计蛋白质的努力都集中在创造由典型结构元件组成的理想化蛋白质上。例子包括卷曲螺旋、上下螺旋束和二级结构元件之间连接非常短的α/β蛋白的设计。这些研究对于探索蛋白质结构的最小决定因素是非常好的，但是理想化的结构可能不是设计新蛋白质功能的最有效的起点。蛋白质中的功能位点通常位于口袋、凹槽或环中，这些口袋、凹槽或环是由二级结构组装而成的，这些二级结构没有形成规范或对称的模式。在这里，我们建议创建和测试一个基于计算机的策略，用于设计蛋白质，称为缝合，这不是专注于创建一个特定的理想化结构，而是可以产生一系列不同的结构，都符合一组预定义的要求。例如，在我们的一个特定目标中，我们将要求所有设计都包含功能性EF-手型钙结合位点，但超出此要求，蛋白质的最终三级结构将没有预定义的目标。通过SEWING，三级结构由天然存在的蛋白质中发现的结构基序组装而成。基序在一级序列中可以是连续的或不连续的，并且通常包含两个或三个二级结构元件。通过叠加两个图案中结构相似的区域，将图案缝合在一起。这种方法的优点包括使用固有可设计的结构单元和掺入来自天然存在的蛋白质（例如蛋白质和配体）的功能基序的能力 结合位点。为了探索SEWING的实用性，我们将追求几个设计目标，包括：创建具有不同结构特征的螺旋束，如裂缝和结合口袋，在蛋白质中嵌入功能基序以创建蛋白质结合剂，以及创建包含多个结合位点的蛋白质。

 DESCRIPTION (provided by applicant): Protein design is a rigorous test of our understanding of protein folding and stability, and a variety of design methods have been used to create proteins that have valuable applications in research and medicine. Almost all efforts in de novo protein design have been focused on creating idealized proteins composed of canonical structural elements. Examples include the design of coiled-coils, up-down helical bundles, and α/β proteins with very short connections between the secondary structural elements. These studies are excellent for exploring the minimal determinants of protein structure, but idealized structures may not be the most effective starting points for engineering novel protein functions. Functional sites in proteins are often located in pockets, grooves or loops that are created from assemblies of secondary structure that are not forming canonical or symmetric patterns. Here, we propose to create and test a computer-based strategy for designing proteins, called SEWING, that is not focused on creating a particular idealized structure, but rather can produce a diverse array of structures that all meet a set of predefined requirements. For instance, in one of our specific aims we will require that all the designs contain functional EF-hand calcium-binding sites, but beyond this requirement there will not be predefined goals for the final tertiar structures of the proteins. With SEWING, tertiary structures are assembled from structural motifs found in naturally occurring proteins. Motifs can be continuous or discontinuous in primary sequence, and generally contain two or three elements of secondary structure. Motifs are stitched together by superimposing regions of structural similarity in two motifs. Advantages of this approach include the use of building blocks that are inherently designable and the ability to incorporate functional motifs from naturally occurring proteins, for instance protein and ligand binding sites. To explore the utility of SEWING we will pursue several design goals including: the creation of helical bundles with diverse structural features such as clefts and binding pockets, embedding functional motifs in proteins to create protein binders, and creating proteins that contain multiple binding sites.