A topological measurement of protein compressibility
A topological measurement of protein compressibility
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DOI：
10.1007/s13160-014-0153-5
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发表时间：
2015-03-01
影响因子：
0.9
通讯作者：
Nanda, Vidit
中科院分区：
文献类型：
--
作者：
Gameiro, Marcio;Hiraoka, Yasuaki;Nanda, Vidit
本文部分阐明了蛋白质的可压缩性与其分子几何结构之间的关系。为了识别和理解给定蛋白质的相关拓扑特征，我们将其分子建模为α过滤，从而获得对其隧道和空腔结构的多尺度洞察。这种α过滤的持久性图以紧凑而有意义的方式捕捉了这种隧道和空洞的大小和坚固性。从这些持久性图中，我们提取了可压缩性的度量，这些可压缩性来源于物理和化学性质所暗示的拓扑特征。由于组合拓扑的最新进展，该度量可以从蛋白质数据库（PDB）中找到的信息有效且直接地计算出来。我们的主要结果在拓扑测量和实验确定的大多数蛋白质的可压缩性之间建立了明确的线性相关性，其中PDB信息和实验可压缩性数据都是可用的。最后，我们建立了拓扑测量和线性相关对于输入数据中的小扰动是稳定的，例如由可压缩性和x射线晶体学实验中的实验误差引起的扰动。
In this paper we partially clarify the relation between the compressibility of a protein and its molecular geometric structure. To identify and understand the relevant topological features within a given protein, we model its molecule as an alpha filtration and hence obtain multi-scale insight into the structure of its tunnels and cavities. The persistence diagrams of this alpha filtration capture the sizes and robustness of such tunnels and cavities in a compact and meaningful manner. From these persistence diagrams, we extract a measure of compressibility derived from those topological features whose relevance is suggested by physical and chemical properties. Due to recent advances in combinatorial topology, this measure is efficiently and directly computable from information found in the Protein Data Bank (PDB). Our main result establishes a clear linear correlation between the topological measure and the experimentally-determined compressibility of most proteins for which both PDB information and experimental compressibility data are available. Finally, we establish that both the topological measurement and the linear correlation are stable with respect to small perturbations in the input data, such as those arising from experimental errors in compressibility and X-ray crystallography experiments.