橡胶HMGR蛋白的生物信息学分析与同源模建

Bioinformatics Analysis and Homology Modeling of HMGR Protein from Hevea brasiliensis

利用生物信息学方法分析了橡胶HMGR蛋白的氨基酸组成、等电点、疏水/亲水区、二级结构等蛋白质性质,并同荔枝、拟南芥和水稻的蛋白进行了对比,并用生物信息学软件对其空间结构进行了模拟,同时对模建结果进行了结构质量的分析与检测。结果表明:该蛋白共有575个氨基酸,等电点为6.44,二级结构中α螺旋占45.91%,β折叠片占13.04%,无规卷曲占35.83%。三维结构检测表明,此模型的结构符合立体化学规则。此外,利用该模型预测了配体SIM和ADP在HMGR结构空间的近似位置,并定位了与SIM和ADP作用的相关残基。

The characters of HMGR protein such as the constitution of amino acids, theoretical pI, alienation/proximity water area, secondary structure in Hevea brasiliensis were analyzed by a series of bioinformatics software, and then compared with those of Litchi chinensis, Arabidopsis thaliana and Oryza sativa. The three-dimensional structure of this protein was constructed by homology modeling, analyzed and then validated. The results show that HMGR protein of H. brasiliensis had 575 amino acids with the pI being 6.44. In the secondary structure a-helix,/3-sheet and random coil made up 45.91%, 13.04% and 35.83%, respectively. The validation of modeling accords with the stereochemistry. Moreover, appropriate binding sites of SIM and ADP in the structural space of HMGR were predicted by using this modeling, and relative residues which can possibly form H-bonds or interact with SIM and ADP were positioned.