The Study Of ?-agarase's Themostability Based On The Structure And Molecular Dynamics Simulation

As a natural biological catalyst,enzyme has great potential for application in industrial production and good prospects of development based on the characteristics of substrate specificity and catalytic efficiency.However,it restricted the application for the thermal instability of natural enzymes.Therefore,insight into the mechanism of protein's thermostability has become the hotspots in protein engineering.Having a good comprehend of the protein thermostability can not only help us understand the relation of the protein structure and function,but also can expand the application scope of enzymes.In this paper,we studied the ?-agarase's thermostability based on the cognitive structure and molecular dynamics simulation.Firstly,we analyzed the sequence and structure features of ?-agarase to associate with their thermal stability by support vector machine(SVM)regression.According to the regression result of segmentation of amino acids and the enzymes' the optimum temperature,the amino acid composition of ?-agarase in M and N end had a greater influence on the thermal stability,and then,the model was built to predict the optimum temperature of ?-agarase.In addition,by combined the relative solution accessibility with their optimum temperature for regression analysis,the results showed that the charge amino acids locating in inner region of relative solution accessibility were closely tied to the optimum temperature.At the same time,we proposed a model to predict temperature of ?-agarase according to significant difference significant difference of T test.The predicted temperatures of our three?-agarases was very close to their experimental temperature,with the error of within the range of ± 5 ? based on the models of section of amino acids.The predicted temperatures based on the other prediction model built by relative solution accessibility,with the errors of 2.2 ?,2.6 ? and 0.1 ?,respectively.That is to say,the predicted temperature of these models for ?-agarases are reliable,especially the model based on relative solution accessibility.Secondly,we investigated the thermal stability mechanism of ?-agarase byusing molecular dynamics simulation.We chose the mesophilic and thermophilic?-agarase 1URX and 3WZ1 with crystal structures,then simulated their conformation under different simulative temperatures and analyzed the results of MD.The results illustrated that there are some sensitive areas or amino acids,such as the alpha helix and amino acids(Ala2,Gly83,Ser245,Ile277)in 3WZ1,amino acid Ser36 in 1URX;what's more,the quantity and category of salt bridge,and the number of hydrogen bond in ?-agarase also have a significant effect for thermal stability.At the same time,it could also provide guidance for the design of ?-agarase.