从局部搜索的角度看蛋白质残基网络
Protein residue networks from a local search perspective
摘要：
我们从局部搜索的角度研究了蛋白质残基网络（PRNs），以了解为什么PRNs在短路径对蛋白质功能很重要时高度聚集。我们发现，通过采用局部搜索的角度来看，这种形式和功能之间的冲突得到解决，因为增加集群实际上有助于减少PRN中的路径长度。此外，通过我们的EDS本地搜索算法找到的路径更符合蛋白质内通信的特点。EDS识别被称为捷径的PRN边缘的子集，其是不同的，具有高使用率，影响EDS路径长度、多样性和拉伸，并且由短程接触主导。这些捷径形成了一个网络（SCN），随着蛋白质的折叠，它的大小和传递性都会增加。SCN的结构支持其功能和形成，SCN的功能影响其形成。成功和不成功的MD轨迹之间的SCN的结构，功能和形成的几个显着差异。通过将PRN的静态和动态方面联系起来，蛋白质折叠过程变成了一个图形形成问题，目的是在蛋白质内形成合适的途径。
英文摘要：
We examined protein residue networks (PRNs) from a local search perspective to understand why PRNs are highly clustered when having short paths is important for protein functionality. We found that by adopting a local search perspective, this conflict between form and function is resolved as increased clustering actually helps to reduce path length in PRNs. Further, the paths found via our EDS local search algorithm are more congruent with the characteristics of intra-protein communication. EDS identifies a subset of PRN edges called short-cuts that are distinct, have high usage, impacts EDS path length, diversity and stretch, and are dominated by short-range contacts. The short-cuts form a network (SCN) that increases in size and transitivity as a protein folds. The structure of a SCN supports its function and formation, and the function of a SCN influences its formation. Several significant differences in terms of SCN structure, function and formation is found between successful and unsuccessful MD trajectories. By connecting the static and the dynamic aspects of PRNs, the protein folding process becomes a problem of graph formation with the purpose of forming suitable pathways within proteins.
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