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: 9315841
• 负责人: BRIAN A KUHLMAN
• 金额: $ 29.92万
• 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/9315841
• 关键词: Base Sequence; Binding; Binding Proteins; Binding Sites; Biological Models; Calcium Binding; Catalysis; Cells; 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 Engineering; Proteins; Protocols documentation; Research; Set protein; Side; Site; Structure; TYRP1 gene; Testing; X-Ray Crystallography; base; beta pleated sheet; design; experimental study; improved; novel; novel therapeutics; programs; protein B; protein folding; protein function; protein structure; public health relevance; 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（通过应用程序提供）：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，并且已经使用了多种设计方法来创建在研究和医学中具有宝贵应用的蛋白质。从头蛋白质设计的几乎所有努力都集中在创建由规范结构元素组成的理想蛋白质上。例子包括设计盘绕螺旋，上向下的螺旋束和α/β蛋白的设计，次级结构元件之间的连接非常短。这些研究非常适合探索蛋白质结构的最小决定剂，但理想化的结构可能不是工程新型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从未形成规范或对称模式的二级结构组件中产生的口袋，凹槽或环中。在这里，我们建议创建和测试一种基于计算机的设计蛋白质的策略，即缝制，而不是专注于创建特定的理想结构，而是可以生产一系列符合一组预定义要求的潜水结构。例如，在我们的特定目标之一中，我们将要求所有设计都包含功能性的EF手钙结合位点，但是除了此要求之外，蛋白质的最终Tertiar结构将不存在预定的目标。随着缝制，三级结构是由在天然存在的蛋白质中发现的结构基序组装的。基序在主要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次级结构的要素。在两个基序中的结构相似性区域的叠加区域将图案缝合在一起。这种方法的优点包括使用固有设计的构件以及从天然存在的蛋白质（例如蛋白质和配体）合并功能基序的能力 绑定位点。为了探索缝纫的实用性，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，例如裂缝和结合口袋，将功能基序嵌入蛋白质中以创建蛋白质粘合剂，并创建包含多个结合位点的蛋白质。