Elucidating Novel Topological Features in Protein Structures

描述(申请人提供)：天然蛋白质采用复杂的折叠构型。它们是如何达到折叠构型的，这是一个人们非常感兴趣的话题。此外，蛋白质必须保持其天然构型的稳定性，关于如何实现这一点还存在悬而未决的问题，特别是必须在恶劣条件下生存的蛋白质。采用特别复杂结构的蛋白质为这两个问题提供了独特的见解。这项建议侧重于发现和分析其结构揭示拓扑复杂性的蛋白质，如蛋白质链的打结和连接。这些蛋白质在蛋白质折叠和稳定性领域提供了有价值的测试案例和具有挑战性的问题。直到最近，自然打结的蛋白质链的可能性被认为是非常有问题的，几乎是被禁止的。但最近对不断增长的结构数据库进行的计算分析揭示了一些深度打结的蛋白质折叠，这些都吸引了实验者和理论家的兴趣。在这个建议中：(1)使用一种新的算法，我们在已知蛋白质结构的数据库中揭示了一种新型的拓扑复杂性：滑移结。在这些情况下，一个结是由蛋白质链的某一部分形成的，而整个链似乎是解开的。我们已经确认了其中的几个案例，这些案例都逃过了之前的结点分析。(2)通过确定特定生物体的新结构来增加已知拓扑复杂蛋白质的集合，其中我们有证据表明连接和打结相对常见；(3)我们开发了一种将打结蛋白质转换为非打结蛋白质的蛋白质设计策略，以便为研究蛋白质中复杂拓扑特征的稳定作用提供一个试验台。支持生物物理实验也包括在内。生物医学相关性：人类疾病与蛋白质不稳定和展开之间的联系正变得越来越清楚。目前，关于蛋白质折叠的规律和机制仍存在一些悬而未决的问题。这里要研究的蛋白质具有独特的特性，这使它们在努力实现对蛋白质结构和稳定性的基本了解方面具有重要价值。

DESCRIPTION (provided by applicant): Natural proteins adopt complex folded configurations. How they reach their folded configurations is a subject of intense interest. In addition, proteins must maintain stability in their native configurations, and there are open questions about how this is achieved, especially by proteins that must survive harsh conditions. Proteins that adopt particularly complex structures provide unique insights into both of these questions. This proposal focuses on the discovery and analysis of proteins whose structures reveal topological complexity, such as knotting, and linking of protein chains. Such proteins provide valuable test cases and challenging questions in the areas of protein folding and stabilization. Until recently, the possibility of naturally knotted protein chains was considered so problematic as to be nearly forbidden. But recent computational analysis of the growing structural database has revealed a few deeply knotted protein folds, and these have drawn the interest of experimentalists and theorists alike. In this proposal: (1) Using a new algorithm, we reveal a novel type of topologically complexity in the database of known protein structures: slip-knots. These are cases where a knot is created by some part of the protein chain, while the chain in its entirety appears to be unknotted. These cases, of which we have identified several, have escaped previous knot analysis. (2) We add to the set of known topologically complex proteins by determining new structures from a particular organism where we have evidence that linking and knotting are relatively common; (3) We develop a protein design strategy for converting knotted proteins into unknotted ones and vice-versa, in order to provide a test bed for studying the stabilizing effects of complex topological features in proteins. Supporting biophysical experiments are included. Biomedical relevance: The connections between human disease and protein destabilization and unfolding are becoming increasingly clear. At the present time, there are still open questions about the rules and mechanisms of protein folding. The proteins to be studied here possess unique features that make them valuable in efforts to achieve a fundamental understanding of protein structure and stability.