基于SwissPdbViewer和MATLAB对人类SOX蛋白三级结构建模及分析

SOX蛋白具有一个与DNA特异结合的高保守HMG-box结合域。利用MATLAB的Sequence Analysis工具从Genbank中下载人类SOX蛋白序列信息,二次筛选获得22个有效的序列数据。以三级结构已知的SOX2、SRY、SOX5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SOX蛋白HMG-box的三级结构极为相似,由3个α螺旋和2个热力学结构不稳定的loop区构成;表面静电分析显示SOX蛋白C端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。SOX蛋白的上述空间结构可能与其活性与功能的调控有关。

Modeling and Analysis Tertiary Structure of Human SOX Protein Based on SwissPdbViewer and MATLAB

SOX proteins are characterized by a conserved high mobility group HMG-box domain, which is responsible for DNA binding and bending. The amino acid sequences of human SOX were downloaded from the GenBank database using Sequence Analysis Tool of MATLAB, and 22 available sequences data were obtained by second screened. The tertiary structures of SOX proteins were modeled using computer programs SwissPdbViewer and MATLAB, homology modeling method, and the known tertiary structure of SOX2, SRY and SOX5 as templates. The three-dimensional structure of predicted SOX proteins were visualized using Visualization Tool of MATLAB. The results show that the tertiary structures of all SOX are similar, which appears to three α-helices and two loop regions, and the loop regions of SOX protein HMG-box are relatively unstable thermodynamically. Analysis of the Electrostatic Surfaces show the C-terminal half of SOX forms an N/C cavity where interactions with organic molecules or proteins could be possible. This observation suggests that the spatial structure of SOX is more likely to regulate the activity and function of this protein.