Computational Methods for Requirement-Driven Protein Design

需求驱动的蛋白质设计的计算方法

• 批准号: 9056243
• 负责人: BRIAN A KUHLMAN
• 金额: $ 29.31万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-25 至 2019-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9056243
• 关键词: Base Sequence; Binding; Binding Sites; Biological Models; Calcium Binding; Catalysis; Cells; Cleaved cell; Computers; Computing Methodologies; DNA Binding; EF Hand Motifs; Elements; Engineering; Genetic Recombination; Goals; Helix-Loop-Helix Motifs; Ligand Binding; Medicine; Membrane Proteins; Methods; Modeling; Molecular; Mutation; Nature; Pattern; Peptides; Procedures; Process; Protein Binding; Proteins; Protocols documentation; Research; Set protein; Side; Site; Structure; Testing; X-Ray Crystallography; base; design; improved; interest; meetings; novel; novel therapeutics; programs; protein folding; protein function; protein structure; protein structure function; public health relevance; research study; scaffold; tool

 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.

 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理解的严格测试，并且已使用多种设计方法来创建在研究和医学中具有有价值应用的蛋白质。几乎所有从头蛋白质设计的努力都集中在创建由规范结构元素组成的理想化蛋白质。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。这些研究非常适合探索蛋白质结构的最小决定因素，但理想化的结构可能不是工程新蛋白质功能的最有效起点。蛋白质中的功能位点通常位于口袋、凹槽或环中，这些口袋、凹槽或环是由未形成规范或对称模式的二级结构组装而成的。在这里，我们建议创建并测试一种基于计算机的蛋白质设计策略，称为 SEWING，该策略并不专注于创建特定的理想化结构，而是可以产生多种结构，这些结构都满足一组预定义的要求。例如，在我们的一个具体目标中，我们将要求所有设计都包含功能性 EF 手钙结合位点，但超出这一要求，将不会为蛋白质的最终三级结构预先确定目标。通过 SEWING，三级结构由天然蛋白质中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素。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本质上可设计的构建模块以及整合天然存在的蛋白质（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（例如裂缝和结合袋）的螺旋束，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。