Research Of Xylanase Thermostability Based On Molecular Dynamics Simulation And Complex Network Theory

Xylanases are widely distributed in various organisms,which can catalyze the hydrolysis of xylan into five carbons sugar.Thermostable xylanase can be used in industrial production because of its high activity at high temperature.Therefore,the research on the thermal stability of thermostable xylanase will have significant social and economic benefits.In this paper,the amino acid interaction network and the amino acid and amino acid interaction network are constructed based on trajectory of molecular dynamics simulation.The complex network theory is used to analyze the two types of networks,and the mechanism of the difference in thermostability of thermostable xylanase and xylanase is analyzed.The main contents of this paper are as follows:In this paper,the Voronoi algorithm is used to identify waters interacting with residues of xylanase.We constructed residue-water interaction networks by taking waters and all residues as nodes,and take residue-residue interactions and residue-water interactions as edges.After calculating network topology parameters including the network node degree,clustering coefficient,closeness centrality and node centrality,we find that these parameters are 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.We modularized the networks by taking hub water with degree 2 as clustering center and setting residue degree?18 as threshold degree.Analyzing the sub-networks obtained from clustering the whole network,we find 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.The unweighted amino acid network is constructed,and the key residues in the amino acid network are identified by using the methods of identifying the important nodes in the complex network and multivariate statistical analysis.It is found that most of the critical residues in the amino acid network are uniformly distributed in the secondary structures,and a large number of key residues are hydrophobic residues.Compared with that in mesophilic xylanase,it is found that the key residues in the thermostable xylanase could maintain the dominant position in the amino acid network.S-FCM clustering method suitable for complex biological networks is proposed for FCM algorithm has some defects,such as the strong dependence of parameters and the sensitivity to initial clustering centers.Firstly,S-FCM introduces a data pretreatment method based on density so that it can obtain the initial clustering centers and the number of classification according to the density characteristics of the input amino acid network,which ensures the reliability of clustering results.Then S-FCM improves the clustering quality and accuracy by adding sequence information and considering the influence of sequence information between amino acids.In addition,the modularity of thermostable xylanase is higher than the mesophilic xylanase,which reveals that the interaction between the thermostable xylanase modules is weaker.And the change of a module has little effect on other modules,which can maintain the stability of amino acid interaction to some extent,and thus affect the thermal stability of xylanase.In order to analyze the evolution law of the community in xylanase amino acid network,an evolutionary clustering framework and S-FCM algorithm are used.The amino acid networks at different temperatures are analyzed and the network snapshots at each time step are clustered,and the rules of community evolution in amino acid networks are quantitatively analyzed by measuring the most basic characteristics of the community.When the similarity value is 0.3,there is a more reasonable node allocation accuracy and quantity identification value.In addition,it is found that there are more hydrophobic amino acids and regular secondary structure in the thermostable xylanase community.With the increase of temperature,the thermostable xylanase amino acid network has a more obvious community structure,and the community has a closer interaction.To sum up,we find that there is a positive correlation between the effect of water on the thermal stability of xylanase and the network parameters through the comparative analysis of thermostable xylanase and mesophilic xylanase.At the same time,the community structure of the thermostable xylanase amino acid network is more obvious,and the residue-residue interaction is more closely.