论文标题
同源打结蛋白的同源
Homology of homologous knotted proteins
论文作者
论文摘要
蛋白质结构（例如打结的蛋白质）的定量和分类通常需要无噪声和完整的数据。在这里，我们开发了一种系统地分析蛋白质结构的数学管道。我们展示了这种几何框架上的蛋白质形成开放式三叶结结，我们证明了数学工具持续的同源性忠实地代表了它们的结构同源性。该拓扑管道确定了蛋白质纠缠的重要几何特征，并根据其深度将Trefoil蛋白的空间簇。持久性景观量化了同一结构同源类中的打结和无结蛋白家族之间的拓扑差异。随着同源性发电机的系统计算的最新进步，这种差异是本地化的，并用几何解释。我们发现的拓扑和几何量化对嘈杂的输入数据是可靠的，这证明了这种方法在标准结理论工具失败的上下文中的潜力。
Quantification and classification of protein structures, such as knotted proteins, often requires noise-free and complete data. Here we develop a mathematical pipeline that systematically analyzes protein structures. We showcase this geometric framework on proteins forming open-ended trefoil knots, and we demonstrate that the mathematical tool, persistent homology, faithfully represents their structural homology. This topological pipeline identifies important geometric features of protein entanglement and clusters the space of trefoil proteins according to their depth. Persistence landscapes quantify the topological difference between a family of knotted and unknotted proteins in the same structural homology class. This difference is localized and interpreted geometrically with recent advancements in systematic computation of homology generators. The topological and geometric quantification we find is robust to noisy input data, which demonstrates the potential of this approach in contexts where standard knot theoretic tools fail.
