Persistent homology analysis of protein structure, flexibility, and folding.
Persistent homology analysis of protein structure, flexibility, and folding.
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DOI：
10.1002/cnm.2655
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发表时间：
2014-08
影响因子：
2.1
通讯作者：
Wei GW
中科院分区：
文献类型：
--
作者：
Xia K;Wei GW
蛋白质是生物体中最重要的生物分子。对蛋白质结构、功能、动力学和转运的理解是生物科学中最具挑战性的任务之一。在本工作中，持久同源性，首次引入提取分子拓扑指纹（MTF）的基础上的分子拓扑不变量的持久性。MTF用于蛋白质表征、鉴定和分类。提出了一种基于切片的蛋白质拓扑不变量几何起源跟踪方法。构造了MTF的全原子表示和粗粒度表示。提出了一种新的类截止滤波方法，用以解决弹性网络模型中的最优截止距离问题。基于蛋白质的紧密性、刚性和连接性之间的相关性，提出了一种基于持久拓扑不变量的蛋白质柔性定量建模方法。为此，开发了基于相关矩阵的过滤。这种方法可以准确预测蛋白质B因子分析中使用的最佳特征距离。最后，利用MTF表征蛋白质折叠过程中的拓扑演化，定量预测蛋白质的折叠稳定性。我们的持续同源性预测结果与分子动力学模拟结果具有很好的一致性，揭示了蛋白质的拓扑-功能关系。
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is, for the first time, introduced for extracting molecular topological fingerprints (MTFs) based on the persistence of molecular topological invariants. MTFs are utilized for protein characterization, identification and classification. The method of slicing is proposed to track the geometric origin of protein topological invariants. Both all-atom and coarse-grained representations of MTFs are constructed. A new cutoff-like filtration is proposed to shed light on the optimal cutoff distance in elastic network models. Based on the correlation between protein compactness, rigidity and connectivity, we propose an accumulated bar length generated from persistent topological invariants for the quantitative modeling of protein flexibility. To this end, a correlation matrix based filtration is developed. This approach gives rise to an accurate prediction of the optimal characteristic distance used in protein B-factor analysis. Finally, MTFs are employed to characterize protein topological evolution during protein folding and quantitatively predict the protein folding stability. An excellent consistence between our persistent homology prediction and molecular dynamics simulation is found. This work reveals the topology-function relationship of proteins.
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DOI：
10.1002/cnm.1458
发表时间：
2012-01
影响因子：
2.1
作者：
Chen D;Chen Z;Wei GW
通讯作者：
Wei GW
影响因子：
3.7
作者：
Chang HW;Bacallado S;Pande VS;Carlsson GE
通讯作者：
Carlsson GE
DOI：
10.1016/s1359-0278(97)00024-2
发表时间：
1997-01-01
期刊：
FOLDING & DESIGN
影响因子：
--
作者：
Bahar, I;Atilgan, AR;Erman, B
通讯作者：
Erman, B
影响因子：
6.2
作者：
Dey, Tamal K.;Li, Kuiyu;Cohen-Steiner, David
通讯作者：
Cohen-Steiner, David
影响因子：
4.4
作者：
Cui, Q
通讯作者：
Cui, Q