The M Protein of SARS-CoV: Basic Structural and Immunological Properties

Hu, Yongwu; Wen, Jie; Tang, Lin; Zhang, Haijun; Zhang, Xiaowei; Li, Yan; Wang, Jing; Han, Yujun; Li, Guoqing; Shi, Jianping; Tian, Xiangjun; Jiang, Feng; Zhao, Xiaoqian; Wang, Jun; Liu, Siqi; Zeng, Changqing; Wang, Jian; Yang, Huanming

An important discrepancy between biological and bioinformatic data was encountered during our analysis with the TM prediction software (Figure 9). Results of molecular biological and medical experiments strongly suggest that the M protein in MHV has its N-terminus in the exterior (4). But. TMHMM, currently rated as the best software for TM prediction (7), yields a reverse orientation with the N-terminus in the interior. To rule out possible artifacts, we applied several currently available software packages to predict the TM orientation of the M protein. All other software closely replicated our results with TMHMM and predicted a similar structure of the corresponding regions in the M protein. The subregionally predicted orientation of the first and second inter-TM segments, as well as the predicted conformation of an α-helical structure and other features identified in all three TM domains, not only provide strong evidence for the existence of the TM structure, but also support the predicted orientation.