Research Of Residue Network Alignment Algorithm

In general,functionally similar protein molecules have similar spatial structure,and local differences in structure may lead to differences in their properties,such as:protein thermostability,hydrophilicity,hydrophobicity,acid resistance,alkali resistance,and so on.The residue interaction network alignment is very important for studying the molecular basis and spatial structure of proteins.It is an effective method to explore the relationship between similarities&differences of protein structure and protein properties&functions.Therefore,encoding the three-dimensional structure of proteins as a residue interaction network and aligning the networks is an effective way to analyze the relationship between protein function,structure,and sequence from the system perspective.At present,there is no alignment algorithm for the residue interaction networks.The protein-protein interaction network alignment algorithm is generally used to align the residue interaction networks,which ignores the information of the amino acid residue.Therefore,based on the analysis of various algorithms for the protein-protein interaction network alignment,this paper uses the framework of the MAGNA topological network alignment algorithm,introduces the residue matching degree matrix based on the principle of the BLOSUM matrix,and uses the matrix as the sequence information of protein.And we introduce the sequence information of the protein into the optimization function of the algorithm,and propose the SI-MAGNA algorithm for the alignment of residue interaction networks.In order to research the interaction of the residue interaction network and factors affecting the thermostability of the protein,we first selected 7 groups of homologous protein pairs with different thermostability as the research objects.In order to verify the superiority of the SI-MAGNA algorithm in the residue interaction networks alignment,we chose Edge Correctness?EC?as the measure for evaluating the quality of network alignment.We compared and analyzed the SI-MAGNA algorithm with the original MAGNA algorithm from two aspects?iteration number and EC?and confirmed the stability&superiority of the SI-MAGNA algorithm in the residue interaction network alignment.Moreover,the SI-MAGNA algorithm is compared with other topological network alignment algorithms GRAAL,MI-GRAAL and GEDEVO that can be used for the residue interaction network alignment.It is proved that the SI-MAGNA algorithm has a good effect in the residue interaction network alignment.We used the SI-MAGNA algorithm to align antifreeze protein pairs?9AME and 1WVO?with different thermostability,and briefly analyzed the reasons for the difference in thermostability.We find that a unique 3₁₀-helix structure in 9AME and its important interaction with the surrounding structure may be the reason for the different temperature dependence of the stability and activity of 9AME and 1WVO.Studying the heat resistance mechanism of xylanase can improve industrial production efficiency and economic efficiency.In this paper,we use residue interaction network alignment algorithm SI-MAGNA for the network alignment of thermostable xylanase from Thermoascus aurantiacus and normal temperature-type xylanase from Streptomyces lividans,to explore the factors that affect the structural stability and thermal stability of the two proteins.By analyzing the results of the alignment,we confirmed the low sequence conservation of the????₈-barrel structure and the effect of the?-sheet on the structural stability.We found a unique 3₁₀-helix structure in the loop₁ region of 1E0W which affects the structural stability.We also found a?₁'short helix structure and a relatively short?₄?₄-loop region in 1TUX which enhance the structural stability and the thermostability of the enzyme.And we inferred the unique hydrogen bonding transition structure in the?₄?₄-loop region of1TUX and two?-bridge structure unique to the 1E0W loop₆ region may cause a slight difference in the spatial structure,which affecting the thermostability of the enzyme.