环糊精水解酶底物运输通道的动态结构分析

Dynamic Structural Study on Substrate Transport Channels of Cyclodextrin Hydrolase

【目的】环糊精水解酶是作用于特殊底物的水解酶,可以水解圆锥形结构的底物。分析这个酶的底物通道为水解特殊结构底物提供研究基础。【方法】利用分子动力学模拟环糊精水解酶存在的底物通道,比较环糊精水解酶BsCMD_1J0H和TspCMD_1SMA在底物运输通道上的差异。【结果】BsCMD_1J0H和TspCMD_1SMA都为糖基水解酶家族13的蛋白质,它们的碳骨架基本吻合,而在α?螺旋分布上,TspCMD_1SMA相比于BsCMD_1J0H来说,螺旋结构更趋向于在蛋白质中心聚集。BsCMD_1J0H有6条底物通道连通蛋白质表面和活性中心,TspCMD_1SMA有8条底物通道连通。BsCMD_1J0H的底物通道平均半径为1,TspCMD_1SMA的底物通道平均半径为1.2。【结论】本研究提供了BsCMD_1J0H和TspCMD_1SMA两个蛋白质在和底物接触中的相关底物通道信息。

[Objeetive]Cyclodextrin hydrolase contains a special function on substrate. It can hydrolyze cyclodextrin molecule with a conical structure. The analysis of the substrate channels of this enzyme would help the basic research on enzymatic hydrolysis of special substrate. [Method]The analyses of substrate tunnels from cyclodextrin hydrolases, named BsCMD_1J0H and TspCMD_1SMA,were performed with the method of molecular dynamics simulation. [Resuit]These two proteins belong to glycosyl hydrolase family 13. In the structural alignment, both BsCMD_1JOH and TspCMD 1SMA showed a basic consistent of the carbon skeleton. However, the distribution of the α-helix of TspCMD_ 1SMA was tend to gathering at the center compared with BsCMD_1JOH. The analysis of substrate channels shows that there are six channels connected protein surface and the active center in BsCMD 1JOH , while eight channels in TspCMD_ISMA. The average radius of substrate tunnels are 1A and 1. 2,A for BsCMD_ 1JOH and TspCMD_ 1SMA, respectively. [Conclusion]This study provided the substrate channels of BsCMD_IJOH and TspCMD_ISMA pro teins.