Structure and stability of 3_alpha vs alpha_beta folds

3_alpha 与 alpha_beta 折叠的结构和稳定性

• 批准号: 8665434
• 负责人: PHILIP N BRYAN
• 金额: $ 30.78万
• 依托单位: UNIV OF MARYLAND, COLLEGE PARK
• 依托单位国家: 美国
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-03-01 至 2017-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8665434
• 关键词: Adopted; Algorithm Design; Algorithms; Amino Acid Sequence; Amino Acids; Binding; Characteristics; Code; Complex; Computing Methodologies; Data; Destinations; Development; Disease; Engineering; Environment; Equilibrium; Future; Goals; Knowledge; Lead; Letters; Methods; Mutation; NMR Spectroscopy; Outcome; Pathway interactions; Peptide Sequence Determination; Phage Display; Population; Positioning Attribute; Procedures; Proteins; SWI1; Series; Structure; Subtilisins; Surface; Thermodynamics; Transplantation; base; design; engineering design; grasp; improved; insight; maltose-binding protein; microcalorimetry; migration; mutant; polypeptide; protein structure; public health relevance; research study; simulation; three dimensional structure

DESCRIPTION (provided by applicant): Most proteins conform to the classical view that a polypeptide chain populates a single, stable native state. However, the phenomenon of fold switching, where protein sequences can exist at the interface between completely different folds, creates serious challenges to our understanding of how amino acid sequence encodes 3D structure. Additionally, it has many implications for understanding how proteins evolve, how mutation is related to disease, and how function is annotated to sequences of unknown structure. Here, the overall objective is to determine experimentally how amino acid sequences migrate through fold space. We will determine the generality of fold switching and define its common principles by designing, engineering and analyzing a number of strategic protein switches. Our proposed studies employ small proteins that are widely used in experimental and computational folding studies, connecting our future results to a large body of knowledge. We aim to show that: 1) many folds can switch into other completely different topologies; 2) such switches can be designed/evolved; 3) structures and energetics of switches can be understood; 4) understanding can lead to prediction of other switches. Previous examination of both natural and engineered fold switches has shown that three conditions are generally necessary for a fold switch: 1) low stability of both folds; 2) compatibility of hydrophobic cores between folds; and 3) long range interactions in one fold which can override local interactions in the other. Methodical studies of fold switching require design and selection methods robust enough to create multiple examples of switches. To create different switches, we have chosen a series of origin folds that represent a range of common topologies (orthogonal bundle, 3-helix bundle, ¿- grasp, SH3 barrel) that will be switched into different context-driven, destination folds (¿/¿ plait, ¿/¿ sandwich, Rossman-like). This approach allows us to satisfy the three general conditions of switching mentioned above. It also mimics evolutionary migration of sub-domains through fold space. Selection through the use of phage display methods will produce heteromorphic and bi-functional proteins that will be used for structural and energetic analysis. These proteins will be studied by a variety of physical methods including microcalorimetry, CD and NMR. Detailed structural and thermodynamic analysis will give important insights into the physicochemical basis for fold switching. The energetic and structural results will reveal how multiple folds are connected through short mutational pathways. These mutational connectivities in fold space will create networks of probable fold migrations. Our results will also enable computational biologists to use these data in folding simulations, fold network studies, and for further development and refinement of stability and structure prediction algorithms.

描述（由申请人提供）：大多数蛋白质符合多肽链形成单一、稳定的天然状态的经典观点。然而，蛋白质序列可能存在于完全不同折叠之间的界面处的折叠转换现象带来了严峻的挑战。此外，它对于理解蛋白质如何进化、突变如何与疾病相关以及如何对未知结构的序列进行功能注释具有许多意义。实验上如何我们将通过设计、工程和分析许多战略蛋白质开关来确定折叠转换的普遍性并定义其共同原理，我们提出的研究采用广泛用于实验和计算折叠研究的小蛋白质。 ，将我们未来的结果与大量知识联系起来：1）许多折叠可以转换成其他完全不同的拓扑；2）可以设计/进化这样的开关；3）可以理解开关的结构和能量学。 4）理解可以导致先前对天然折叠开关和工程折叠开关的预测表明，折叠开关通常需要三个条件：1）两个折叠的稳定性较低；2）折叠之间疏水核心的兼容性；3） 一个折叠中的长程相互作用可以覆盖另一个折叠中的局部相互作用，折叠转换的系统研究需要足够强大的设计和选择方法来创建多个转换示例，我们选择了一系列代表折叠的原始折叠。一系列常见的拓扑结构（正交束、3 螺旋束、¿- 抓握、SH3 桶）将被切换为不同的上下文驱动的目标折叠（¿/¿ 辫子、¿/¿ 三明治、这种方法使我们能够满足上述转换的三个一般条件，它还通过使用噬菌体展示方法来模拟子结构域的进化迁移，从而产生异形和双功能蛋白质。将用于结构和能量分析。 通过微量热法、环糊精和核磁共振等多种物理方法进行研究，详细的结构和热力学分析将为折叠转换的物理化学基础提供重要的见解，其能量和结构结果将揭示多个折叠如何通过短突变途径连接。折叠空间将创建可能的折叠迁移网络，我们的结果还将使计算生物学家能够在折叠模拟、折叠网络研究以及稳定性和结构预测算法的进一步开发和完善中使用这些数据。