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Structure and stability of 3_alpha vs alpha_beta folds

3_alpha 与 alpha_beta 折叠的结构和稳定性

基本信息

批准号：
9036397
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
项目类别：
财政年份：
2002
资助国家：
美国
起止时间：
2002-03-01 至 2018-03-31
项目状态：
已结题

项目摘要

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）：大多数蛋白质符合经典观点，即多肽链占据单一、稳定的天然状态。然而，折叠转换现象，其中蛋白质序列可以存在于完全不同的折叠之间的界面，对我们理解氨基酸序列如何编码3D结构产生了严重的挑战。此外，它对理解蛋白质如何进化、突变如何与疾病相关以及功能如何被注释到未知结构的序列中具有许多意义。在这里，总体目标是通过实验确定氨基酸序列如何通过折叠空间迁移。我们将确定折叠开关的一般性，并通过设计，工程和分析一些战略蛋白质开关定义其共同的原则。我们提出的研究采用了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的知识联系起来。我们的目标是表明：1）许多折叠可以切换到其他完全不同的拓扑结构; 2）这样的开关可以被设计/进化; 3）开关的结构和能量可以被理解; 4）理解可以导致对其他开关的预测。先前对天然折叠开关和工程化折叠开关的研究已经表明，折叠开关通常需要三个条件：1）两个折叠的低稳定性; 2）折叠之间疏水核的相容性;以及3）折叠之间疏水核的相容性。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。折叠开关的方法研究需要足够强大的设计和选择方法来创建多个开关的例子。为了创建不同的开关，我们选择了一系列代表一系列常见拓扑结构（正交束，3螺旋束，<$- grasp，SH 3桶）的源折叠，这些拓扑结构将被切换到不同的上下文驱动的目的地折叠（<$/<$plait，<$/<$sandwich，Rossman like）。这种方法允许我们满足上面提到的三个一般切换条件。它也模仿子域通过褶皱空间的演化迁移。通过使用噬菌体展示方法的选择将产生异形和双功能蛋白质，其将用于结构和能量分析。这些蛋白质将通过各种物理方法，包括微量热法，CD和NMR进行研究。详细的结构和热力学分析将为折叠开关的物理化学基础提供重要的见解。能量和结构的结果将揭示多重折叠是如何通过短的突变途径连接起来的。褶皱空间中的这些突变连通性将产生可能的褶皱迁移网络。我们的研究结果还将使计算生物学家能够在折叠模拟，折叠网络研究中使用这些数据，并进一步开发和改进稳定性和结构预测算法。

项目成果

期刊论文数量（23）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Solution NMR structure of a sheddase inhibitor prodomain from the malarial parasite Plasmodium falciparum.

疟疾寄生虫恶性疟原虫脱落酶抑制剂前结构域的溶液核磁共振结构。

DOI：
10.1002/prot.24187
发表时间：
2012
期刊：
Proteins
影响因子：
2.9
作者：
He,Yanan;Chen,Yihong;Oganesyan,Natalia;Ruan,Biao;O'Brochta,David;Bryan,PhilipN;Orban,John
通讯作者：
Orban,John

Ady3p links spindle pole body function to spore wall synthesis in Saccharomyces cerevisiae.

Ady3p 将酿酒酵母中纺锤体极体功能与孢子壁合成联系起来。