基于SwissPdbViewer和MATLAB对东北虎Sox蛋白三级结构建模及分析(英文)

Modeling Tertiary Structures of Sox Protein in Panthera tigris altaica Based on SwissPdbViewer and MATLAB

SOX蛋白具有一个与DNA特异结合的高保守HMG-box结构域。为研究东北虎SOX蛋白三级结构的分子机理,利用MATLAB的Bioinformatics工具从GenBank中下载东北虎SOX蛋白序列信息,以三级结构已知的SOX2为模板,联合SwissPdbViewer与MATLAB,采用同源建模方法对SOX蛋白HMG-box进行建模、预测;利用MATLAB的Visualization Tool分析预测结果的三维结构。结果显示PtSox蛋白的HMG-box由3个α-螺旋和2个loop区构成;热稳定性分析表明PtSox蛋白loop区的热力学结构不稳定;表面静电分布显示出PtSox蛋白C-端的中间有一个可能与其它小分子或蛋白质的相互作用位点的N/C腔,上述空间结构可能与其活性与功能的调控有关。

Sox proteins are characterized by a conserved high mobility group HMG-box domain, which is responsible for DNA binding and bending. In order to research the molecular mechanism of Sox protein in Panthera tigris altaica, the amino acid sequences of PtSox were downloaded from the GenBank database using bioinformatics tools of MATLAB. The tertiary structures of PtSox proteins were modeled using computer programs SwissPdbViewer and MATLAB, homology modeling method, and the known tertiary structure of Sox2 as templates. The three-dimensional structures of predicted PtSox proteins were visualized using Visualization Tool of MATLAB. The results showed that the tertiary structure of PtSox appeared to three a-helices and two loop regions. Thermostability analysis showed that the loop regions of PtSox structures were relatively unstable thermodynamically. Analysis of the electrostatic surfaces showed the C-terminal half of PtSox formed an N/C cavity where interacted with organic molecules or proteins could be possible. This observation suggested that the spatial structure of Sox was more likely to regulate the activity and function of this protein.