基于残基-水作用网络的木聚糖酶耐热性研究

Research of Xylanase Thermostability Based on Residue-Water Interaction Network

DOI：10.3969/j.issn.1673-1689.2019.09.011

中文关键词: 残基-水相互作用网络 网络拓扑特征 网络聚类 木聚糖酶热稳定性

英文关键词: residue-water interaction network,network topological characteristics,network clustering,the thermal stability of xylanase

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中文摘要:

水在蛋白质折叠、相互作用、分子识别、动力学及耐热性方面发挥着重要作用。利用Voronoi算法识别出与耐热和常温木聚糖酶存在相互作用的水。以氨基酸残基和水为节点，残基-残基及残基-水相互作用为边，构建残基-水相互作用网络。计算网络中节点的度、聚类系数、接近中心性和节点中心性，发现水的这些参数均与木聚糖酶耐热性成正相关关系。耐热木聚糖酶中度为2的hub水数量要比常温酶多，可见水在耐热木聚糖酶中参与了更多的相互作用。以度为2的水为聚类中心，以氨基酸残基节点的度18为阈值进行聚类。子网表明hub水多与hub残基聚为一类，即网络存在“富人俱乐部”现象。这表明，水不仅参与了耐热木聚糖酶的残基-水相互作用，还加强了残基-残基相互作用，更有利于酶形成稳定的结构来抵御高温。

英文摘要:

Water plays an important role in protein folding，protein-protein interaction，molecular recognition，protein dynamics，thermal stability and so on. In this paper，Voronoi algorithm is used to identify waters interacting with residues of xylanase. Take waters and all residues as nodes，and take residue-residue interactions and residue-water interactions as edges，we constructed residue-water interaction networks. After calculating network topology parameters such as the network node degree，clustering coefficient，closeness centrality and node centrality，we found that these parameters were positively correlated with the thermal stability of xylanase. The number of hub water with degree 2 in thermophilic xylanase network is much higher than in mesophilic xylanase network，which means water is involved in more interaction in thermostable xylanase. Then take hub water with degree 2 as clustering center and set residue degree≥18 as threshold degree，we modularized the networks. Analyzing the sub-networks obtained from clustering the whole network，we found hub waters and hub residues are usually clustered into a group. That means residue-water interaction networks of xylanase exist "rich-club phenomenon". These results indicate that water is not only involved in the residue-water interaction，but also strengthen the residue-residue interaction，which is more helpful to the formation of a stable structure to resist high temperature.

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